diff --git a/docs/doxygen/doxy_1.8.9/Doxyfile b/docs/doxygen/doxy_1.8.9/Doxyfile new file mode 100644 index 0000000000000000000000000000000000000000..37ab18ffe84c651f1352a6801cf66b6451f6c764 --- /dev/null +++ b/docs/doxygen/doxy_1.8.9/Doxyfile @@ -0,0 +1,2410 @@ +# Doxyfile 1.8.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "MOOSE - Multiscale Object Oriented Simulation Environment" + +# The PROJECT_NUMBER +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = moose_log.png + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./cpp + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = YES + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = YES + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = NO + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if <section_label> ... \endif and \cond <section_label> +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = cpp/doxygen-logfile + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = ../../moose-core/basecode \ + ../../moose-core/biophysics \ + ../../moose-core/builtins \ + ../../moose-core/device \ + ../../moose-core/diffusion \ + ../../moose-core/hsolve \ + ../../moose-core/intfire \ + ../../moose-core/kinetics \ + ../../moose-core/ksolve \ + ../../moose-core/mesh \ + ../../moose-core/mpi \ + ../../moose-core/msg \ + ../../moose-core/randnum \ + ../../moose-core/pymoose \ + ../../moose-core/scheduling \ + ../../moose-core/shell \ + ../../moose-core/signeur \ + ../../moose-core/synapse \ + ../../moose-core/utility + + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = *.cpp \ + *.hpp \ + *.c \ + *.h \ + *.cc \ + *.hh \ + *.cxx \ + *.hxx + + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# <filter> <input-file> +# +# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# compiled with the --with-libclang option. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = YES + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = -std=c++11 + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use <access key> + S +# (what the <access key> is depends on the OS and browser, but it is typically +# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down +# key> to jump into the search results window, the results can be navigated +# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel +# the search. The filter options can be selected when the cursor is inside the +# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys> +# to select a filter and <Enter> or <escape> to activate or cancel the filter +# option. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. There +# are two flavors of web server based searching depending on the EXTERNAL_SEARCH +# setting. When disabled, doxygen will generate a PHP script for searching and +# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing +# and searching needs to be provided by external tools. See the section +# "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain the +# search results. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). +# +# See the section "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will return the search results when EXTERNAL_SEARCH is enabled. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). See the section "External Indexing and +# Searching" for details. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. +# The default file is: searchdata.xml. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of +# to a relative location where the documentation can be found. The format is: +# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ... +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# Configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. +# The default value is: YES. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. +# +# Note that when enabling USE_PDFLATEX this option is only used for generating +# bitmaps for formulas in the HTML output, but not in the Makefile that is +# written to the output directory. +# The default file is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate +# index for LaTeX. +# The default file is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used by the +# printer. +# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x +# 14 inches) and executive (7.25 x 10.5 inches). +# The default value is: a4. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names +# that should be included in the LaTeX output. To get the times font for +# instance you can specify +# EXTRA_PACKAGES=times +# If left blank no extra packages will be included. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the +# generated LaTeX document. The header should contain everything until the first +# chapter. If it is left blank doxygen will generate a standard header. See +# section "Doxygen usage" for information on how to let doxygen write the +# default header to a separate file. +# +# Note: Only use a user-defined header if you know what you are doing! The +# following commands have a special meaning inside the header: $title, +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the +# generated LaTeX document. The footer should contain everything after the last +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. +# +# Note: Only use a user-defined footer if you know what you are doing! +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_FOOTER = + +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the LATEX_OUTPUT output +# directory. Note that the files will be copied as-is; there are no commands or +# markers available. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is +# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will +# contain links (just like the HTML output) instead of page references. This +# makes the output suitable for online browsing using a PDF viewer. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a +# higher quality PDF documentation. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode +# command to the generated LaTeX files. This will instruct LaTeX to keep running +# if errors occur, instead of asking the user for help. This option is also used +# when generating formulas in HTML. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BATCHMODE = NO + +# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the +# index chapters (such as File Index, Compound Index, etc.) in the output. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HIDE_INDICES = NO + +# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source +# code with syntax highlighting in the LaTeX output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. See +# http://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# The default value is: plain. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# Configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The +# RTF output is optimized for Word 97 and may not look too pretty with other RTF +# readers/editors. +# The default value is: NO. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: rtf. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will +# contain hyperlink fields. The RTF file will contain links (just like the HTML +# output) instead of page references. This makes the output suitable for online +# browsing using Word or some other Word compatible readers that support those +# fields. +# +# Note: WordPad (write) and others do not support links. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's config +# file, i.e. a series of assignments. You only have to provide replacements, +# missing definitions are set to their default value. +# +# See also section "Doxygen usage" for information on how to generate the +# default style sheet that doxygen normally uses. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an RTF document. Syntax is +# similar to doxygen's config file. A template extensions file can be generated +# using doxygen -e rtf extensionFile. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_EXTENSIONS_FILE = + +# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code +# with syntax highlighting in the RTF output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for +# classes and files. +# The default value is: NO. + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. A directory man3 will be created inside the directory specified by +# MAN_OUTPUT. +# The default directory is: man. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to the generated +# man pages. In case the manual section does not start with a number, the number +# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is +# optional. +# The default value is: .3. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_EXTENSION = .3 + +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + +# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it +# will generate one additional man file for each entity documented in the real +# man page(s). These additional files only source the real man page, but without +# them the man command would be unable to find the correct page. +# The default value is: NO. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that +# captures the structure of the code including all documentation. +# The default value is: NO. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: xml. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_OUTPUT = xml + +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program +# listings (including syntax highlighting and cross-referencing information) to +# the XML output. Note that enabling this will significantly increase the size +# of the XML output. +# The default value is: YES. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files +# that can be used to generate PDF. +# The default value is: NO. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. +# The default directory is: docbook. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_OUTPUT = docbook + +# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the +# program listings (including syntax highlighting and cross-referencing +# information) to the DOCBOOK output. Note that enabling this will significantly +# increase the size of the DOCBOOK output. +# The default value is: NO. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_PROGRAMLISTING = NO + +#--------------------------------------------------------------------------- +# Configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sf.net) file that captures the +# structure of the code including all documentation. Note that this feature is +# still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module +# file that captures the structure of the code including all documentation. +# +# Note that this feature is still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary +# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI +# output from the Perl module output. +# The default value is: NO. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely +# formatted so it can be parsed by a human reader. This is useful if you want to +# understand what is going on. On the other hand, if this tag is set to NO, the +# size of the Perl module output will be much smaller and Perl will parse it +# just the same. +# The default value is: YES. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file are +# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful +# so different doxyrules.make files included by the same Makefile don't +# overwrite each other's variables. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all +# C-preprocessor directives found in the sources and include files. +# The default value is: YES. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names +# in the source code. If set to NO, only conditional compilation will be +# performed. Macro expansion can be done in a controlled way by setting +# EXPAND_ONLY_PREDEF to YES. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then +# the macro expansion is limited to the macros specified with the PREDEFINED and +# EXPAND_AS_DEFINED tags. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES, the include files in the +# INCLUDE_PATH will be searched if a #include is found. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by the +# preprocessor. +# This tag requires that the tag SEARCH_INCLUDES is set to YES. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will be +# used. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that are +# defined before the preprocessor is started (similar to the -D option of e.g. +# gcc). The argument of the tag is a list of macros of the form: name or +# name=definition (no spaces). If the definition and the "=" are omitted, "=1" +# is assumed. To prevent a macro definition from being undefined via #undef or +# recursively expanded use the := operator instead of the = operator. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this +# tag can be used to specify a list of macro names that should be expanded. The +# macro definition that is found in the sources will be used. Use the PREDEFINED +# tag if you want to use a different macro definition that overrules the +# definition found in the source code. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will +# remove all references to function-like macros that are alone on a line, have +# an all uppercase name, and do not end with a semicolon. Such function macros +# are typically used for boiler-plate code, and will confuse the parser if not +# removed. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES tag can be used to specify one or more tag files. For each tag +# file the location of the external documentation should be added. The format of +# a tag file without this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where loc1 and loc2 can be relative or absolute paths or URLs. See the +# section "Linking to external documentation" for more information about the use +# of tag files. +# Note: Each tag file must have a unique name (where the name does NOT include +# the path). If a tag file is not located in the directory in which doxygen is +# run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create a +# tag file that is based on the input files it reads. See section "Linking to +# external documentation" for more information about the usage of tag files. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES, all external class will be listed in +# the class index. If set to NO, only the inherited external classes will be +# listed. +# The default value is: NO. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will be +# listed. +# The default value is: YES. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in +# the related pages index. If set to NO, only the current project's pages will +# be listed. +# The default value is: YES. + +EXTERNAL_PAGES = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of 'which perl'). +# The default file (with absolute path) is: /usr/bin/perl. + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram +# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to +# NO turns the diagrams off. Note that this option also works with HAVE_DOT +# disabled, but it is recommended to install and use dot, since it yields more +# powerful graphs. +# The default value is: YES. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see: +# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# You can include diagrams made with dia in doxygen documentation. Doxygen will +# then run dia to produce the diagram and insert it in the documentation. The +# DIA_PATH tag allows you to specify the directory where the dia binary resides. +# If left empty dia is assumed to be found in the default search path. + +DIA_PATH = + +# If set to YES the inheritance and collaboration graphs will hide inheritance +# and usage relations if the target is undocumented or is not a class. +# The default value is: YES. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz (see: +# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent +# Bell Labs. The other options in this section have no effect if this option is +# set to NO +# The default value is: YES. + +HAVE_DOT = NO + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed +# to run in parallel. When set to 0 doxygen will base this on the number of +# processors available in the system. You can set it explicitly to a value +# larger than 0 to get control over the balance between CPU load and processing +# speed. +# Minimum value: 0, maximum value: 32, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_NUM_THREADS = 0 + +# When you want a differently looking font in the dot files that doxygen +# generates you can specify the font name using DOT_FONTNAME. You need to make +# sure dot is able to find the font, which can be done by putting it in a +# standard location or by setting the DOTFONTPATH environment variable or by +# setting DOT_FONTPATH to the directory containing the font. +# The default value is: Helvetica. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTNAME = Ubuntu Mono + +# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of +# dot graphs. +# Minimum value: 4, maximum value: 24, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the default font as specified with +# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set +# the path where dot can find it using this tag. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTPATH = + +# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for +# each documented class showing the direct and indirect inheritance relations. +# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a +# graph for each documented class showing the direct and indirect implementation +# dependencies (inheritance, containment, and class references variables) of the +# class with other documented classes. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for +# groups, showing the direct groups dependencies. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LOOK = YES + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside the +# class node. If there are many fields or methods and many nodes the graph may +# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the +# number of items for each type to make the size more manageable. Set this to 0 +# for no limit. Note that the threshold may be exceeded by 50% before the limit +# is enforced. So when you set the threshold to 10, up to 15 fields may appear, +# but if the number exceeds 15, the total amount of fields shown is limited to +# 10. +# Minimum value: 0, maximum value: 100, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LIMIT_NUM_FIELDS = 10 + +# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and +# collaboration graphs will show the relations between templates and their +# instances. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +TEMPLATE_RELATIONS = YES + +# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to +# YES then doxygen will generate a graph for each documented file showing the +# direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDE_GRAPH = YES + +# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are +# set to YES then doxygen will generate a graph for each documented file showing +# the direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH tag is set to YES then doxygen will generate a call +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALL_GRAPH = YES + +# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALLER_GRAPH = YES + +# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical +# hierarchy of all classes instead of a textual one. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the +# dependencies a directory has on other directories in a graphical way. The +# dependency relations are determined by the #include relations between the +# files in the directories. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. +# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order +# to make the SVG files visible in IE 9+ (other browsers do not have this +# requirement). +# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd, +# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo, +# gif:cairo:gd, gif:gd, gif:gd:gd and svg. +# The default value is: png. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_IMAGE_FORMAT = svg + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# +# Note that this requires a modern browser other than Internet Explorer. Tested +# and working are Firefox, Chrome, Safari, and Opera. +# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make +# the SVG files visible. Older versions of IE do not have SVG support. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +INTERACTIVE_SVG = YES + +# The DOT_PATH tag can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the \dotfile +# command). +# This tag requires that the tag HAVE_DOT is set to YES. + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the \mscfile +# command). + +MSCFILE_DIRS = + +# The DIAFILE_DIRS tag can be used to specify one or more directories that +# contain dia files that are included in the documentation (see the \diafile +# command). + +DIAFILE_DIRS = + +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes +# that will be shown in the graph. If the number of nodes in a graph becomes +# larger than this value, doxygen will truncate the graph, which is visualized +# by representing a node as a red box. Note that doxygen if the number of direct +# children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that +# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. +# Minimum value: 0, maximum value: 10000, default value: 50. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs +# generated by dot. A depth value of 3 means that only nodes reachable from the +# root by following a path via at most 3 edges will be shown. Nodes that lay +# further from the root node will be omitted. Note that setting this option to 1 +# or 2 may greatly reduce the computation time needed for large code bases. Also +# note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. +# Minimum value: 0, maximum value: 1000, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not seem +# to support this out of the box. +# +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) support +# this, this feature is disabled by default. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_MULTI_TARGETS = YES + +# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page +# explaining the meaning of the various boxes and arrows in the dot generated +# graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot +# files that are used to generate the various graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_CLEANUP = YES diff --git a/docs/doxygen/doxy_1.8.9/Doxyfile.full b/docs/doxygen/doxy_1.8.9/Doxyfile.full new file mode 100644 index 0000000000000000000000000000000000000000..ab7cf523dedbb56db6740e3624f24d786a389298 --- /dev/null +++ b/docs/doxygen/doxy_1.8.9/Doxyfile.full @@ -0,0 +1,2410 @@ +# Doxyfile 1.8.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "MOOSE - Multiscale Object Oriented Simulation Environment" + +# The PROJECT_NUMBER +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = moose_log.png + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./cpp + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = YES + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = YES + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = NO + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if <section_label> ... \endif and \cond <section_label> +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = cpp/doxygen-logfile + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = ../../moose-core/basecode \ + ../../moose-core/biophysics \ + ../../moose-core/builtins \ + ../../moose-core/device \ + ../../moose-core/diffusion \ + ../../moose-core/hsolve \ + ../../moose-core/intfire \ + ../../moose-core/kinetics \ + ../../moose-core/ksolve \ + ../../moose-core/mesh \ + ../../moose-core/mpi \ + ../../moose-core/msg \ + ../../moose-core/randnum \ + ../../moose-core/pymoose \ + ../../moose-core/scheduling \ + ../../moose-core/shell \ + ../../moose-core/signeur \ + ../../moose-core/synapse \ + ../../moose-core/utility + + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = *.cpp \ + *.hpp \ + *.c \ + *.h \ + *.cc \ + *.hh \ + *.cxx \ + *.hxx + + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# <filter> <input-file> +# +# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# compiled with the --with-libclang option. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = YES + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = -std=c++11 + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use <access key> + S +# (what the <access key> is depends on the OS and browser, but it is typically +# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down +# key> to jump into the search results window, the results can be navigated +# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel +# the search. The filter options can be selected when the cursor is inside the +# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys> +# to select a filter and <Enter> or <escape> to activate or cancel the filter +# option. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. There +# are two flavors of web server based searching depending on the EXTERNAL_SEARCH +# setting. When disabled, doxygen will generate a PHP script for searching and +# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing +# and searching needs to be provided by external tools. See the section +# "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain the +# search results. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). +# +# See the section "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will return the search results when EXTERNAL_SEARCH is enabled. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). See the section "External Indexing and +# Searching" for details. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. +# The default file is: searchdata.xml. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of +# to a relative location where the documentation can be found. The format is: +# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ... +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# Configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. +# The default value is: YES. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. +# +# Note that when enabling USE_PDFLATEX this option is only used for generating +# bitmaps for formulas in the HTML output, but not in the Makefile that is +# written to the output directory. +# The default file is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate +# index for LaTeX. +# The default file is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used by the +# printer. +# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x +# 14 inches) and executive (7.25 x 10.5 inches). +# The default value is: a4. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names +# that should be included in the LaTeX output. To get the times font for +# instance you can specify +# EXTRA_PACKAGES=times +# If left blank no extra packages will be included. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the +# generated LaTeX document. The header should contain everything until the first +# chapter. If it is left blank doxygen will generate a standard header. See +# section "Doxygen usage" for information on how to let doxygen write the +# default header to a separate file. +# +# Note: Only use a user-defined header if you know what you are doing! The +# following commands have a special meaning inside the header: $title, +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the +# generated LaTeX document. The footer should contain everything after the last +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. +# +# Note: Only use a user-defined footer if you know what you are doing! +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_FOOTER = + +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the LATEX_OUTPUT output +# directory. Note that the files will be copied as-is; there are no commands or +# markers available. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is +# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will +# contain links (just like the HTML output) instead of page references. This +# makes the output suitable for online browsing using a PDF viewer. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a +# higher quality PDF documentation. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode +# command to the generated LaTeX files. This will instruct LaTeX to keep running +# if errors occur, instead of asking the user for help. This option is also used +# when generating formulas in HTML. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BATCHMODE = NO + +# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the +# index chapters (such as File Index, Compound Index, etc.) in the output. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HIDE_INDICES = NO + +# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source +# code with syntax highlighting in the LaTeX output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. See +# http://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# The default value is: plain. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# Configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The +# RTF output is optimized for Word 97 and may not look too pretty with other RTF +# readers/editors. +# The default value is: NO. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: rtf. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will +# contain hyperlink fields. The RTF file will contain links (just like the HTML +# output) instead of page references. This makes the output suitable for online +# browsing using Word or some other Word compatible readers that support those +# fields. +# +# Note: WordPad (write) and others do not support links. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's config +# file, i.e. a series of assignments. You only have to provide replacements, +# missing definitions are set to their default value. +# +# See also section "Doxygen usage" for information on how to generate the +# default style sheet that doxygen normally uses. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an RTF document. Syntax is +# similar to doxygen's config file. A template extensions file can be generated +# using doxygen -e rtf extensionFile. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_EXTENSIONS_FILE = + +# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code +# with syntax highlighting in the RTF output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for +# classes and files. +# The default value is: NO. + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. A directory man3 will be created inside the directory specified by +# MAN_OUTPUT. +# The default directory is: man. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to the generated +# man pages. In case the manual section does not start with a number, the number +# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is +# optional. +# The default value is: .3. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_EXTENSION = .3 + +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + +# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it +# will generate one additional man file for each entity documented in the real +# man page(s). These additional files only source the real man page, but without +# them the man command would be unable to find the correct page. +# The default value is: NO. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that +# captures the structure of the code including all documentation. +# The default value is: NO. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: xml. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_OUTPUT = xml + +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program +# listings (including syntax highlighting and cross-referencing information) to +# the XML output. Note that enabling this will significantly increase the size +# of the XML output. +# The default value is: YES. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files +# that can be used to generate PDF. +# The default value is: NO. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. +# The default directory is: docbook. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_OUTPUT = docbook + +# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the +# program listings (including syntax highlighting and cross-referencing +# information) to the DOCBOOK output. Note that enabling this will significantly +# increase the size of the DOCBOOK output. +# The default value is: NO. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_PROGRAMLISTING = NO + +#--------------------------------------------------------------------------- +# Configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sf.net) file that captures the +# structure of the code including all documentation. Note that this feature is +# still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module +# file that captures the structure of the code including all documentation. +# +# Note that this feature is still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary +# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI +# output from the Perl module output. +# The default value is: NO. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely +# formatted so it can be parsed by a human reader. This is useful if you want to +# understand what is going on. On the other hand, if this tag is set to NO, the +# size of the Perl module output will be much smaller and Perl will parse it +# just the same. +# The default value is: YES. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file are +# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful +# so different doxyrules.make files included by the same Makefile don't +# overwrite each other's variables. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all +# C-preprocessor directives found in the sources and include files. +# The default value is: YES. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names +# in the source code. If set to NO, only conditional compilation will be +# performed. Macro expansion can be done in a controlled way by setting +# EXPAND_ONLY_PREDEF to YES. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then +# the macro expansion is limited to the macros specified with the PREDEFINED and +# EXPAND_AS_DEFINED tags. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES, the include files in the +# INCLUDE_PATH will be searched if a #include is found. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by the +# preprocessor. +# This tag requires that the tag SEARCH_INCLUDES is set to YES. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will be +# used. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that are +# defined before the preprocessor is started (similar to the -D option of e.g. +# gcc). The argument of the tag is a list of macros of the form: name or +# name=definition (no spaces). If the definition and the "=" are omitted, "=1" +# is assumed. To prevent a macro definition from being undefined via #undef or +# recursively expanded use the := operator instead of the = operator. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this +# tag can be used to specify a list of macro names that should be expanded. The +# macro definition that is found in the sources will be used. Use the PREDEFINED +# tag if you want to use a different macro definition that overrules the +# definition found in the source code. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will +# remove all references to function-like macros that are alone on a line, have +# an all uppercase name, and do not end with a semicolon. Such function macros +# are typically used for boiler-plate code, and will confuse the parser if not +# removed. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES tag can be used to specify one or more tag files. For each tag +# file the location of the external documentation should be added. The format of +# a tag file without this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where loc1 and loc2 can be relative or absolute paths or URLs. See the +# section "Linking to external documentation" for more information about the use +# of tag files. +# Note: Each tag file must have a unique name (where the name does NOT include +# the path). If a tag file is not located in the directory in which doxygen is +# run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create a +# tag file that is based on the input files it reads. See section "Linking to +# external documentation" for more information about the usage of tag files. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES, all external class will be listed in +# the class index. If set to NO, only the inherited external classes will be +# listed. +# The default value is: NO. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will be +# listed. +# The default value is: YES. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in +# the related pages index. If set to NO, only the current project's pages will +# be listed. +# The default value is: YES. + +EXTERNAL_PAGES = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of 'which perl'). +# The default file (with absolute path) is: /usr/bin/perl. + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram +# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to +# NO turns the diagrams off. Note that this option also works with HAVE_DOT +# disabled, but it is recommended to install and use dot, since it yields more +# powerful graphs. +# The default value is: YES. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see: +# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# You can include diagrams made with dia in doxygen documentation. Doxygen will +# then run dia to produce the diagram and insert it in the documentation. The +# DIA_PATH tag allows you to specify the directory where the dia binary resides. +# If left empty dia is assumed to be found in the default search path. + +DIA_PATH = + +# If set to YES the inheritance and collaboration graphs will hide inheritance +# and usage relations if the target is undocumented or is not a class. +# The default value is: YES. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz (see: +# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent +# Bell Labs. The other options in this section have no effect if this option is +# set to NO +# The default value is: YES. + +HAVE_DOT = YES + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed +# to run in parallel. When set to 0 doxygen will base this on the number of +# processors available in the system. You can set it explicitly to a value +# larger than 0 to get control over the balance between CPU load and processing +# speed. +# Minimum value: 0, maximum value: 32, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_NUM_THREADS = 0 + +# When you want a differently looking font in the dot files that doxygen +# generates you can specify the font name using DOT_FONTNAME. You need to make +# sure dot is able to find the font, which can be done by putting it in a +# standard location or by setting the DOTFONTPATH environment variable or by +# setting DOT_FONTPATH to the directory containing the font. +# The default value is: Helvetica. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTNAME = Ubuntu Mono + +# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of +# dot graphs. +# Minimum value: 4, maximum value: 24, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the default font as specified with +# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set +# the path where dot can find it using this tag. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTPATH = + +# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for +# each documented class showing the direct and indirect inheritance relations. +# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a +# graph for each documented class showing the direct and indirect implementation +# dependencies (inheritance, containment, and class references variables) of the +# class with other documented classes. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for +# groups, showing the direct groups dependencies. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LOOK = YES + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside the +# class node. If there are many fields or methods and many nodes the graph may +# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the +# number of items for each type to make the size more manageable. Set this to 0 +# for no limit. Note that the threshold may be exceeded by 50% before the limit +# is enforced. So when you set the threshold to 10, up to 15 fields may appear, +# but if the number exceeds 15, the total amount of fields shown is limited to +# 10. +# Minimum value: 0, maximum value: 100, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LIMIT_NUM_FIELDS = 10 + +# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and +# collaboration graphs will show the relations between templates and their +# instances. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +TEMPLATE_RELATIONS = YES + +# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to +# YES then doxygen will generate a graph for each documented file showing the +# direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDE_GRAPH = YES + +# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are +# set to YES then doxygen will generate a graph for each documented file showing +# the direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH tag is set to YES then doxygen will generate a call +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALL_GRAPH = YES + +# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALLER_GRAPH = YES + +# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical +# hierarchy of all classes instead of a textual one. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the +# dependencies a directory has on other directories in a graphical way. The +# dependency relations are determined by the #include relations between the +# files in the directories. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. +# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order +# to make the SVG files visible in IE 9+ (other browsers do not have this +# requirement). +# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd, +# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo, +# gif:cairo:gd, gif:gd, gif:gd:gd and svg. +# The default value is: png. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_IMAGE_FORMAT = svg + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# +# Note that this requires a modern browser other than Internet Explorer. Tested +# and working are Firefox, Chrome, Safari, and Opera. +# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make +# the SVG files visible. Older versions of IE do not have SVG support. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +INTERACTIVE_SVG = YES + +# The DOT_PATH tag can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the \dotfile +# command). +# This tag requires that the tag HAVE_DOT is set to YES. + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the \mscfile +# command). + +MSCFILE_DIRS = + +# The DIAFILE_DIRS tag can be used to specify one or more directories that +# contain dia files that are included in the documentation (see the \diafile +# command). + +DIAFILE_DIRS = + +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes +# that will be shown in the graph. If the number of nodes in a graph becomes +# larger than this value, doxygen will truncate the graph, which is visualized +# by representing a node as a red box. Note that doxygen if the number of direct +# children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that +# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. +# Minimum value: 0, maximum value: 10000, default value: 50. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs +# generated by dot. A depth value of 3 means that only nodes reachable from the +# root by following a path via at most 3 edges will be shown. Nodes that lay +# further from the root node will be omitted. Note that setting this option to 1 +# or 2 may greatly reduce the computation time needed for large code bases. Also +# note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. +# Minimum value: 0, maximum value: 1000, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not seem +# to support this out of the box. +# +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) support +# this, this feature is disabled by default. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_MULTI_TARGETS = YES + +# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page +# explaining the meaning of the various boxes and arrows in the dot generated +# graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot +# files that are used to generate the various graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_CLEANUP = YES diff --git a/docs/doxygen/doxy_1.8.9/Doxyfile.intermediate b/docs/doxygen/doxy_1.8.9/Doxyfile.intermediate new file mode 100644 index 0000000000000000000000000000000000000000..5e2634d0c45e6f10ac79a63ed24a38063ef3daea --- /dev/null +++ b/docs/doxygen/doxy_1.8.9/Doxyfile.intermediate @@ -0,0 +1,2410 @@ +# Doxyfile 1.8.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "MOOSE - Multiscale Object Oriented Simulation Environment" + +# The PROJECT_NUMBER +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = moose_log.png + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./cpp + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = YES + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = YES + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = NO + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if <section_label> ... \endif and \cond <section_label> +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = cpp/doxygen-logfile + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = ../../moose-core/basecode \ + ../../moose-core/biophysics \ + ../../moose-core/builtins \ + ../../moose-core/device \ + ../../moose-core/diffusion \ + ../../moose-core/hsolve \ + ../../moose-core/intfire \ + ../../moose-core/kinetics \ + ../../moose-core/ksolve \ + ../../moose-core/mesh \ + ../../moose-core/mpi \ + ../../moose-core/msg \ + ../../moose-core/randnum \ + ../../moose-core/pymoose \ + ../../moose-core/scheduling \ + ../../moose-core/shell \ + ../../moose-core/signeur \ + ../../moose-core/synapse \ + ../../moose-core/utility + + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = *.cpp \ + *.hpp \ + *.c \ + *.h \ + *.cc \ + *.hh \ + *.cxx \ + *.hxx + + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# <filter> <input-file> +# +# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# compiled with the --with-libclang option. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = YES + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = -std=c++11 + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use <access key> + S +# (what the <access key> is depends on the OS and browser, but it is typically +# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down +# key> to jump into the search results window, the results can be navigated +# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel +# the search. The filter options can be selected when the cursor is inside the +# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys> +# to select a filter and <Enter> or <escape> to activate or cancel the filter +# option. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. There +# are two flavors of web server based searching depending on the EXTERNAL_SEARCH +# setting. When disabled, doxygen will generate a PHP script for searching and +# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing +# and searching needs to be provided by external tools. See the section +# "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain the +# search results. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). +# +# See the section "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will return the search results when EXTERNAL_SEARCH is enabled. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). See the section "External Indexing and +# Searching" for details. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. +# The default file is: searchdata.xml. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of +# to a relative location where the documentation can be found. The format is: +# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ... +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# Configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. +# The default value is: YES. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. +# +# Note that when enabling USE_PDFLATEX this option is only used for generating +# bitmaps for formulas in the HTML output, but not in the Makefile that is +# written to the output directory. +# The default file is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate +# index for LaTeX. +# The default file is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used by the +# printer. +# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x +# 14 inches) and executive (7.25 x 10.5 inches). +# The default value is: a4. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names +# that should be included in the LaTeX output. To get the times font for +# instance you can specify +# EXTRA_PACKAGES=times +# If left blank no extra packages will be included. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the +# generated LaTeX document. The header should contain everything until the first +# chapter. If it is left blank doxygen will generate a standard header. See +# section "Doxygen usage" for information on how to let doxygen write the +# default header to a separate file. +# +# Note: Only use a user-defined header if you know what you are doing! The +# following commands have a special meaning inside the header: $title, +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the +# generated LaTeX document. The footer should contain everything after the last +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. +# +# Note: Only use a user-defined footer if you know what you are doing! +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_FOOTER = + +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the LATEX_OUTPUT output +# directory. Note that the files will be copied as-is; there are no commands or +# markers available. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is +# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will +# contain links (just like the HTML output) instead of page references. This +# makes the output suitable for online browsing using a PDF viewer. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a +# higher quality PDF documentation. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode +# command to the generated LaTeX files. This will instruct LaTeX to keep running +# if errors occur, instead of asking the user for help. This option is also used +# when generating formulas in HTML. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BATCHMODE = NO + +# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the +# index chapters (such as File Index, Compound Index, etc.) in the output. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HIDE_INDICES = NO + +# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source +# code with syntax highlighting in the LaTeX output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. See +# http://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# The default value is: plain. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# Configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The +# RTF output is optimized for Word 97 and may not look too pretty with other RTF +# readers/editors. +# The default value is: NO. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: rtf. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will +# contain hyperlink fields. The RTF file will contain links (just like the HTML +# output) instead of page references. This makes the output suitable for online +# browsing using Word or some other Word compatible readers that support those +# fields. +# +# Note: WordPad (write) and others do not support links. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's config +# file, i.e. a series of assignments. You only have to provide replacements, +# missing definitions are set to their default value. +# +# See also section "Doxygen usage" for information on how to generate the +# default style sheet that doxygen normally uses. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an RTF document. Syntax is +# similar to doxygen's config file. A template extensions file can be generated +# using doxygen -e rtf extensionFile. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_EXTENSIONS_FILE = + +# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code +# with syntax highlighting in the RTF output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for +# classes and files. +# The default value is: NO. + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. A directory man3 will be created inside the directory specified by +# MAN_OUTPUT. +# The default directory is: man. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to the generated +# man pages. In case the manual section does not start with a number, the number +# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is +# optional. +# The default value is: .3. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_EXTENSION = .3 + +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + +# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it +# will generate one additional man file for each entity documented in the real +# man page(s). These additional files only source the real man page, but without +# them the man command would be unable to find the correct page. +# The default value is: NO. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that +# captures the structure of the code including all documentation. +# The default value is: NO. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: xml. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_OUTPUT = xml + +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program +# listings (including syntax highlighting and cross-referencing information) to +# the XML output. Note that enabling this will significantly increase the size +# of the XML output. +# The default value is: YES. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files +# that can be used to generate PDF. +# The default value is: NO. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. +# The default directory is: docbook. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_OUTPUT = docbook + +# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the +# program listings (including syntax highlighting and cross-referencing +# information) to the DOCBOOK output. Note that enabling this will significantly +# increase the size of the DOCBOOK output. +# The default value is: NO. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_PROGRAMLISTING = NO + +#--------------------------------------------------------------------------- +# Configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sf.net) file that captures the +# structure of the code including all documentation. Note that this feature is +# still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module +# file that captures the structure of the code including all documentation. +# +# Note that this feature is still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary +# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI +# output from the Perl module output. +# The default value is: NO. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely +# formatted so it can be parsed by a human reader. This is useful if you want to +# understand what is going on. On the other hand, if this tag is set to NO, the +# size of the Perl module output will be much smaller and Perl will parse it +# just the same. +# The default value is: YES. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file are +# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful +# so different doxyrules.make files included by the same Makefile don't +# overwrite each other's variables. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all +# C-preprocessor directives found in the sources and include files. +# The default value is: YES. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names +# in the source code. If set to NO, only conditional compilation will be +# performed. Macro expansion can be done in a controlled way by setting +# EXPAND_ONLY_PREDEF to YES. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then +# the macro expansion is limited to the macros specified with the PREDEFINED and +# EXPAND_AS_DEFINED tags. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES, the include files in the +# INCLUDE_PATH will be searched if a #include is found. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by the +# preprocessor. +# This tag requires that the tag SEARCH_INCLUDES is set to YES. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will be +# used. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that are +# defined before the preprocessor is started (similar to the -D option of e.g. +# gcc). The argument of the tag is a list of macros of the form: name or +# name=definition (no spaces). If the definition and the "=" are omitted, "=1" +# is assumed. To prevent a macro definition from being undefined via #undef or +# recursively expanded use the := operator instead of the = operator. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this +# tag can be used to specify a list of macro names that should be expanded. The +# macro definition that is found in the sources will be used. Use the PREDEFINED +# tag if you want to use a different macro definition that overrules the +# definition found in the source code. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will +# remove all references to function-like macros that are alone on a line, have +# an all uppercase name, and do not end with a semicolon. Such function macros +# are typically used for boiler-plate code, and will confuse the parser if not +# removed. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES tag can be used to specify one or more tag files. For each tag +# file the location of the external documentation should be added. The format of +# a tag file without this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where loc1 and loc2 can be relative or absolute paths or URLs. See the +# section "Linking to external documentation" for more information about the use +# of tag files. +# Note: Each tag file must have a unique name (where the name does NOT include +# the path). If a tag file is not located in the directory in which doxygen is +# run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create a +# tag file that is based on the input files it reads. See section "Linking to +# external documentation" for more information about the usage of tag files. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES, all external class will be listed in +# the class index. If set to NO, only the inherited external classes will be +# listed. +# The default value is: NO. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will be +# listed. +# The default value is: YES. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in +# the related pages index. If set to NO, only the current project's pages will +# be listed. +# The default value is: YES. + +EXTERNAL_PAGES = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of 'which perl'). +# The default file (with absolute path) is: /usr/bin/perl. + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram +# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to +# NO turns the diagrams off. Note that this option also works with HAVE_DOT +# disabled, but it is recommended to install and use dot, since it yields more +# powerful graphs. +# The default value is: YES. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see: +# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# You can include diagrams made with dia in doxygen documentation. Doxygen will +# then run dia to produce the diagram and insert it in the documentation. The +# DIA_PATH tag allows you to specify the directory where the dia binary resides. +# If left empty dia is assumed to be found in the default search path. + +DIA_PATH = + +# If set to YES the inheritance and collaboration graphs will hide inheritance +# and usage relations if the target is undocumented or is not a class. +# The default value is: YES. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz (see: +# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent +# Bell Labs. The other options in this section have no effect if this option is +# set to NO +# The default value is: YES. + +HAVE_DOT = YES + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed +# to run in parallel. When set to 0 doxygen will base this on the number of +# processors available in the system. You can set it explicitly to a value +# larger than 0 to get control over the balance between CPU load and processing +# speed. +# Minimum value: 0, maximum value: 32, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_NUM_THREADS = 0 + +# When you want a differently looking font in the dot files that doxygen +# generates you can specify the font name using DOT_FONTNAME. You need to make +# sure dot is able to find the font, which can be done by putting it in a +# standard location or by setting the DOTFONTPATH environment variable or by +# setting DOT_FONTPATH to the directory containing the font. +# The default value is: Helvetica. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTNAME = Ubuntu Mono + +# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of +# dot graphs. +# Minimum value: 4, maximum value: 24, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the default font as specified with +# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set +# the path where dot can find it using this tag. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTPATH = + +# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for +# each documented class showing the direct and indirect inheritance relations. +# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +CLASS_GRAPH = NO + +# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a +# graph for each documented class showing the direct and indirect implementation +# dependencies (inheritance, containment, and class references variables) of the +# class with other documented classes. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for +# groups, showing the direct groups dependencies. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LOOK = YES + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside the +# class node. If there are many fields or methods and many nodes the graph may +# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the +# number of items for each type to make the size more manageable. Set this to 0 +# for no limit. Note that the threshold may be exceeded by 50% before the limit +# is enforced. So when you set the threshold to 10, up to 15 fields may appear, +# but if the number exceeds 15, the total amount of fields shown is limited to +# 10. +# Minimum value: 0, maximum value: 100, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LIMIT_NUM_FIELDS = 10 + +# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and +# collaboration graphs will show the relations between templates and their +# instances. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +TEMPLATE_RELATIONS = YES + +# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to +# YES then doxygen will generate a graph for each documented file showing the +# direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDE_GRAPH = YES + +# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are +# set to YES then doxygen will generate a graph for each documented file showing +# the direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH tag is set to YES then doxygen will generate a call +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALL_GRAPH = YES + +# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALLER_GRAPH = YES + +# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical +# hierarchy of all classes instead of a textual one. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the +# dependencies a directory has on other directories in a graphical way. The +# dependency relations are determined by the #include relations between the +# files in the directories. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. +# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order +# to make the SVG files visible in IE 9+ (other browsers do not have this +# requirement). +# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd, +# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo, +# gif:cairo:gd, gif:gd, gif:gd:gd and svg. +# The default value is: png. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_IMAGE_FORMAT = svg + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# +# Note that this requires a modern browser other than Internet Explorer. Tested +# and working are Firefox, Chrome, Safari, and Opera. +# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make +# the SVG files visible. Older versions of IE do not have SVG support. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +INTERACTIVE_SVG = YES + +# The DOT_PATH tag can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the \dotfile +# command). +# This tag requires that the tag HAVE_DOT is set to YES. + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the \mscfile +# command). + +MSCFILE_DIRS = + +# The DIAFILE_DIRS tag can be used to specify one or more directories that +# contain dia files that are included in the documentation (see the \diafile +# command). + +DIAFILE_DIRS = + +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes +# that will be shown in the graph. If the number of nodes in a graph becomes +# larger than this value, doxygen will truncate the graph, which is visualized +# by representing a node as a red box. Note that doxygen if the number of direct +# children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that +# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. +# Minimum value: 0, maximum value: 10000, default value: 50. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs +# generated by dot. A depth value of 3 means that only nodes reachable from the +# root by following a path via at most 3 edges will be shown. Nodes that lay +# further from the root node will be omitted. Note that setting this option to 1 +# or 2 may greatly reduce the computation time needed for large code bases. Also +# note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. +# Minimum value: 0, maximum value: 1000, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not seem +# to support this out of the box. +# +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) support +# this, this feature is disabled by default. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_MULTI_TARGETS = YES + +# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page +# explaining the meaning of the various boxes and arrows in the dot generated +# graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot +# files that are used to generate the various graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_CLEANUP = YES diff --git a/docs/doxygen/doxy_1.8.9/Doxyfile.minimal b/docs/doxygen/doxy_1.8.9/Doxyfile.minimal new file mode 100644 index 0000000000000000000000000000000000000000..37ab18ffe84c651f1352a6801cf66b6451f6c764 --- /dev/null +++ b/docs/doxygen/doxy_1.8.9/Doxyfile.minimal @@ -0,0 +1,2410 @@ +# Doxyfile 1.8.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "MOOSE - Multiscale Object Oriented Simulation Environment" + +# The PROJECT_NUMBER +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = moose_log.png + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./cpp + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = YES + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = YES + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = NO + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if <section_label> ... \endif and \cond <section_label> +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = cpp/doxygen-logfile + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = ../../moose-core/basecode \ + ../../moose-core/biophysics \ + ../../moose-core/builtins \ + ../../moose-core/device \ + ../../moose-core/diffusion \ + ../../moose-core/hsolve \ + ../../moose-core/intfire \ + ../../moose-core/kinetics \ + ../../moose-core/ksolve \ + ../../moose-core/mesh \ + ../../moose-core/mpi \ + ../../moose-core/msg \ + ../../moose-core/randnum \ + ../../moose-core/pymoose \ + ../../moose-core/scheduling \ + ../../moose-core/shell \ + ../../moose-core/signeur \ + ../../moose-core/synapse \ + ../../moose-core/utility + + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = *.cpp \ + *.hpp \ + *.c \ + *.h \ + *.cc \ + *.hh \ + *.cxx \ + *.hxx + + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# <filter> <input-file> +# +# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# compiled with the --with-libclang option. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = YES + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = -std=c++11 + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use <access key> + S +# (what the <access key> is depends on the OS and browser, but it is typically +# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down +# key> to jump into the search results window, the results can be navigated +# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel +# the search. The filter options can be selected when the cursor is inside the +# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys> +# to select a filter and <Enter> or <escape> to activate or cancel the filter +# option. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. There +# are two flavors of web server based searching depending on the EXTERNAL_SEARCH +# setting. When disabled, doxygen will generate a PHP script for searching and +# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing +# and searching needs to be provided by external tools. See the section +# "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain the +# search results. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). +# +# See the section "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will return the search results when EXTERNAL_SEARCH is enabled. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: http://xapian.org/). See the section "External Indexing and +# Searching" for details. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. +# The default file is: searchdata.xml. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of +# to a relative location where the documentation can be found. The format is: +# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ... +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# Configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. +# The default value is: YES. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. +# +# Note that when enabling USE_PDFLATEX this option is only used for generating +# bitmaps for formulas in the HTML output, but not in the Makefile that is +# written to the output directory. +# The default file is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate +# index for LaTeX. +# The default file is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used by the +# printer. +# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x +# 14 inches) and executive (7.25 x 10.5 inches). +# The default value is: a4. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names +# that should be included in the LaTeX output. To get the times font for +# instance you can specify +# EXTRA_PACKAGES=times +# If left blank no extra packages will be included. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the +# generated LaTeX document. The header should contain everything until the first +# chapter. If it is left blank doxygen will generate a standard header. See +# section "Doxygen usage" for information on how to let doxygen write the +# default header to a separate file. +# +# Note: Only use a user-defined header if you know what you are doing! The +# following commands have a special meaning inside the header: $title, +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the +# generated LaTeX document. The footer should contain everything after the last +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. +# +# Note: Only use a user-defined footer if you know what you are doing! +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_FOOTER = + +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the LATEX_OUTPUT output +# directory. Note that the files will be copied as-is; there are no commands or +# markers available. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is +# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will +# contain links (just like the HTML output) instead of page references. This +# makes the output suitable for online browsing using a PDF viewer. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a +# higher quality PDF documentation. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode +# command to the generated LaTeX files. This will instruct LaTeX to keep running +# if errors occur, instead of asking the user for help. This option is also used +# when generating formulas in HTML. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BATCHMODE = NO + +# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the +# index chapters (such as File Index, Compound Index, etc.) in the output. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HIDE_INDICES = NO + +# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source +# code with syntax highlighting in the LaTeX output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. See +# http://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# The default value is: plain. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# Configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The +# RTF output is optimized for Word 97 and may not look too pretty with other RTF +# readers/editors. +# The default value is: NO. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: rtf. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will +# contain hyperlink fields. The RTF file will contain links (just like the HTML +# output) instead of page references. This makes the output suitable for online +# browsing using Word or some other Word compatible readers that support those +# fields. +# +# Note: WordPad (write) and others do not support links. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's config +# file, i.e. a series of assignments. You only have to provide replacements, +# missing definitions are set to their default value. +# +# See also section "Doxygen usage" for information on how to generate the +# default style sheet that doxygen normally uses. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an RTF document. Syntax is +# similar to doxygen's config file. A template extensions file can be generated +# using doxygen -e rtf extensionFile. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_EXTENSIONS_FILE = + +# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code +# with syntax highlighting in the RTF output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for +# classes and files. +# The default value is: NO. + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. A directory man3 will be created inside the directory specified by +# MAN_OUTPUT. +# The default directory is: man. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to the generated +# man pages. In case the manual section does not start with a number, the number +# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is +# optional. +# The default value is: .3. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_EXTENSION = .3 + +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + +# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it +# will generate one additional man file for each entity documented in the real +# man page(s). These additional files only source the real man page, but without +# them the man command would be unable to find the correct page. +# The default value is: NO. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that +# captures the structure of the code including all documentation. +# The default value is: NO. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: xml. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_OUTPUT = xml + +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program +# listings (including syntax highlighting and cross-referencing information) to +# the XML output. Note that enabling this will significantly increase the size +# of the XML output. +# The default value is: YES. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files +# that can be used to generate PDF. +# The default value is: NO. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. +# The default directory is: docbook. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_OUTPUT = docbook + +# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the +# program listings (including syntax highlighting and cross-referencing +# information) to the DOCBOOK output. Note that enabling this will significantly +# increase the size of the DOCBOOK output. +# The default value is: NO. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_PROGRAMLISTING = NO + +#--------------------------------------------------------------------------- +# Configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sf.net) file that captures the +# structure of the code including all documentation. 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This +# makes dot run faster, but since only newer versions of dot (>1.8.10) support +# this, this feature is disabled by default. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_MULTI_TARGETS = YES + +# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page +# explaining the meaning of the various boxes and arrows in the dot generated +# graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot +# files that are used to generate the various graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_CLEANUP = YES diff --git a/docs/user/Rdesigneur/index.rst b/docs/user/Rdesigneur/index.rst index 09de598b62bccf166d52bfb2c67c8870820fc2a9..9e352b4596f13ed290638789797619066167b26e 100644 --- a/docs/user/Rdesigneur/index.rst +++ b/docs/user/Rdesigneur/index.rst @@ -3,11 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Gui documentation for MOOSE -============================ +Reaction Diffusion and Electrical SIGnaling in NEURons +======================================================= +Rdesigneur (Reaction Diffusion and Electrical SIGnaling in NEURons) is an interface to the multiscale modeling capabilities in MOOSE. -MOOSE is the Multiscale Object-Oriented Simulation Environment. It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling. -This document describes the salient features of the Rdesigneur, a interface to the multiscale modeling capabilities in MOOSE Contents: .. toctree:: diff --git a/docs/user/html/Kkit12Documentation.html b/docs/user/html/Kkit12Documentation.html deleted file mode 100644 index 95abd860d0b0947c8b02bc6cdb5eb2a261e87d2b..0000000000000000000000000000000000000000 --- a/docs/user/html/Kkit12Documentation.html +++ /dev/null @@ -1,311 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <title></title> - <style type="text/css">code{white-space: pre;}</style> - <link rel="stylesheet" href="css/moosedocs.css" type="text/css" /> -</head> -<body> -<div id="TOC"> -<ul> -<li><a href="#kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a><ul> -<li><a href="#upi-bhalla">Upi Bhalla</a></li> -<li><a href="#harsha-rani">Harsha Rani</a><ul> -<li><a href="#dec-27-2014">Dec 27, 2014</a></li> -</ul></li> -</ul></li> -<li><a href="#introduction"><a href="#TOC">Introduction</a></a><ul> -<li><a href="#todo-what-are-chemical-kinetic-models"><a href="#TOC"><strong>TODO</strong> What are chemical kinetic models?</a></a></li> -<li><a href="#levels-of-model"><a href="#TOC">Levels of model</a></a></li> -<li><a href="#numerical-methods"><a href="#TOC">Numerical methods</a></a></li> -</ul></li> -<li><a href="#using-kinetikit-12"><a href="#TOC">Using Kinetikit 12</a></a><ul> -<li><a href="#overview"><a href="#TOC">Overview</a></a></li> -<li><a href="#model-layout-and-icons"><a href="#TOC">Model layout and icons</a></a><ul> -<li><a href="#compartment"><a href="#TOC">Compartment</a></a></li> -<li><a href="#pool"><a href="#TOC">Pool</a></a></li> -<li><a href="#buffered-pools"><a href="#TOC">Buffered pools</a></a></li> -<li><a href="#reaction"><a href="#TOC">Reaction</a></a></li> -<li><a href="#mass-action-enzymes"><a href="#TOC">Mass-action enzymes</a></a></li> -<li><a href="#michaelis-menten-enzymes"><a href="#TOC">Michaelis-Menten Enzymes</a></a></li> -<li><a href="#function"><a href="#TOC">Function</a></a></li> -</ul></li> -<li><a href="#model-operations"><a href="#TOC">Model operations</a></a></li> -<li><a href="#model-building"><a href="#TOC">Model building</a></a></li> -</ul></li> -</ul> -</div> -<h1 id="kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui"><a href="#kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a></h1> -<h2 id="upi-bhalla"><a href="#upi-bhalla">Upi Bhalla</a></h2> -<h2 id="harsha-rani"><a href="#harsha-rani">Harsha Rani</a></h2> -<h3 id="dec-27-2014"><a href="#dec-27-2014">Dec 27, 2014</a></h3> -<ul> -<li><p><a href="#introduction">Introduction</a></p></li> -<li><a href="#todo-what-are-chemical-kinetic-models"><strong>TODO</strong> What are chemical kinetic models?</a> -<ul> -<li><a href="#levels-of-model">Levels of model</a></li> -<li><a href="#numerical-methods">Numerical methods</a></li> -</ul></li> -<li><p><a href="#using-kinetikit-12">Using Kinetikit 12</a></p> -<pre><code>* [Overview](#overview)</code></pre> -<ul> -<li><p><a href="#model-layout-and-icons">Model layout and icons</a></p> -<pre><code> * [Compartment](#compartment)</code></pre> -<ul> -<li><a href="#pool">Pool</a></li> -<li><a href="#buffered-pools">Buffered pools</a></li> -<li><a href="#reaction">Reaction</a></li> -<li><a href="#mass-action-enzymes">Mass-action enzymes</a></li> -<li><a href="#michaelis-menten-enzymes">Michaelis-Menten Enzymes</a></li> -<li><a href="#function">Function</a></li> -</ul></li> -<li><a href="#model-operations">Model operations</a></li> -<li><p><a href="#model-building">Model Building</a></p></li> -</ul></li> -</ul> -<h1 id="introduction"><a href="#introduction"><a href="#TOC">Introduction</a></a></h1> -<p>Kinetikit 12 is a graphical interface for doing chemical kinetic modeling in MOOSE. It is derived in part from Kinetikit, which was the graphical interface used in GENESIS for similar models. Kinetikit, also known as kkit, was at version 11 with GENESIS. Here we start with Kinetikit 12.</p> -<h2 id="todo-what-are-chemical-kinetic-models"><a href="#todo-what-are-chemical-kinetic-models"><a href="#TOC"><strong>TODO</strong> What are chemical kinetic models?</a></a></h2> -<p>Much of neuronal computation occurs through chemical signaling. For example, many forms of synaptic plasticity begin with calcium influx into the synapse, followed by calcium binding to calmodulin, and then calmodulin activation of numerous enzymes. These events can be represented in chemical terms:</p> -<blockquote> -<p>4 Ca<sup>2+</sup> + CaM <===> Ca<sub>4</sub>.CaM</p> -</blockquote> -<p>Such chemical equations can be modeled through standard Ordinary Differential Equations, if we ignore space:</p> -<blockquote> -<p>d[Ca]/dt = −4K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + 4K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM] d[CaM]/dt = −K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM] d[Ca4.CaM]/dt = K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] − K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM]</p> -</blockquote> -<p>MOOSE models these chemical systems. This help document describes how to do such modelling using the graphical interface, Kinetikit 12.</p> -<h2 id="levels-of-model"><a href="#levels-of-model"><a href="#TOC">Levels of model</a></a></h2> -<p>Chemical kinetic models can be simple well-stirred (or point) models, or they could have multiple interacting compartments, or they could include space explicitly using reaction-diffusion. In addition such models could be solved either deterministically, or using a stochastic formulation. At present Kinetikit handles compartmental models but does not compute diffusion within the compartments, though MOOSE itself can do this at the script level. Kkit12 will do deterministic as well as stochastic chemical calculations.</p> -<h2 id="numerical-methods"><a href="#numerical-methods"><a href="#TOC">Numerical methods</a></a></h2> -<ul> -<li><strong>Deterministic</strong>: Adaptive timestep 5th order Runge-Kutta-Fehlberg from the GSL (GNU Scientific Library).</li> -<li><strong>Stochastic</strong>: Optimized Gillespie Stochastic Systems Algorithm, custom implementation.</li> -</ul> -<h1 id="using-kinetikit-12"><a href="#using-kinetikit-12"><a href="#TOC">Using Kinetikit 12</a></a></h1> -<h2 id="overview"><a href="#overview"><a href="#TOC">Overview</a></a></h2> -<ul> -<li>Load models using <strong><code>File -> Load model</code></strong>. A reaction schematic for the chemical system appears in the <strong><code>Editor view</code></strong> tab.</li> -<li>View parameters in <strong><code>Editor view</code></strong> tab by clicking on icons, and looking at entries in <strong><code>Properties</code></strong> table to the right.</li> -<li>Edit parameters by changing their values in the <strong><code>Properties</code></strong> table.</li> -<li>From Run View, Pools can be plotted by clicking on their icons and dragging the icons onto the plot Window. Presently only concentration is plottable.</li> -<li>Run models using <strong><code>Run</code></strong> button.</li> -<li>Select numerical method using options under <strong><code>Preferences</code></strong> button in simulation control.</li> -</ul> -<p><!--* Save plots using the icons at the bottom of the <strong><code>Plot Window</code></strong>.</p> -<p>Most of these operations are detailed in other sections, and are shared with other aspects of the MOOSE simulation interface. Here we focus on the Kinetikit-specific items.</p> -<h2 id="model-layout-and-icons"><a href="#model-layout-and-icons"><a href="#TOC">Model layout and icons</a></a></h2> -<p>When you are in the <strong><code>Model View</code></strong> tab you will see a collection of icons, arrows, and grey boxes surrounding these. This is a schematic of the reaction scheme being modeled. You can view and change parameters, and change the layout of the model.</p> -<div class="figure"> -<img src="../../images/Moose1.png" /> -</div> -<p>Resizing the model layout and icons:</p> -<ul> -<li><strong>Zoom</strong>: Comma and period keys. Alternatively, the mouse scroll wheel or vertical scroll line on the track pad will cause the display to zoom in and out.</li> -<li><strong>Pan</strong>: The arrow keys move the display left, right, up, and down.</li> -<li><strong>Entire Model View</strong>: Pressing the <strong><code>a</code></strong> key will fit the entire model into the entire field of view.</li> -<li><strong>Resize Icons</strong>: Angle bracket keys, that is, <strong><code><</code></strong> and <strong><code>></code></strong> or <strong><code>+</code></strong> and <strong><code>-</code></strong>. This resizes the icons while leaving their positions on the screen layout more or less the same.</li> -<li><strong>Original Model View</strong>: Presing the <strong><code>A</code></strong> key (capital <code>A</code>) will revert to the original model view including the original icon scaling.</li> -</ul> -<h3 id="compartment"><a href="#compartment"><a href="#TOC">Compartment</a></a></h3> -<p>The <em>compartment</em> in moose is usually a contiguous domain in which a certain set of chemical reactions and molecular species occur. The definition is very closely related to that of a cell-biological compartment. Examples include the extracellular space, the cell membrane, the cytosol, and the nucleus. Compartments can be nested, but of course you cannot put a bigger compartment into a smaller one.</p> -<ul> -<li><strong>Icon</strong>: Grey boundary around a set of reactions.</li> -<li><strong>Moving Compartments</strong>: Click and drag on the boundary.</li> -<li><strong>Resizing Compartment boundary</strong>: Happens automatically when contents are repositioned, so that the boundary just contains contents.</li> -<li><p><strong>Compartment editable parameters</strong>:</p> -<ul> -<li><strong><code>name</code></strong>: The name of the compartment.</li> -<li><strong><code>size</code></strong>: This is the volume, surface area or length of the compartment, depending on its type.</li> -</ul></li> -<li><p><strong>Compartment fixed parameters</strong>:</p> -<ul> -<li><strong><code>numDimensions</code></strong>: This specifies whether the compartment is a volume, a 2-D surface, or if it is just being represented as a length.</li> -</ul></li> -</ul> -<h3 id="pool"><a href="#pool"><a href="#TOC">Pool</a></a></h3> -<p>This is the set of molecules of a given species within a compartment. Different chemical states of the same molecule are in different pools.</p> -<ul> -<li><strong>Icon</strong>: <img src="../../images/Pool.png" /> Colored rectangle with pool name in it.</li> -<li><strong>Moving pools</strong>: Click and drag.</li> -<li><p><strong>Pool editable parameters</strong>:</p> -<ul> -<li><strong><code>name</code></strong>: Name of the pool</li> -<li><strong><code>n</code></strong>: Number of molecules in the pool</li> -<li><strong><code>nInit</code></strong>: Initial number of molecules in the pool. <code>n</code> gets set to this value when the <code>reinit</code> operation is done.</li> -<li><p><strong><code>conc</code></strong>: Concentration of the molecules in the pool.</p> -<blockquote> -<p>conc = n * unit_scale_factor / (N<sub>A</sub> * vol)</p> -</blockquote></li> -<li><p><strong><code>concInit</code></strong>: Initial concentration of the molecules in the pool.</p> -<blockquote> -<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value when the <code>reinit</code> operation is done.</p> -</blockquote></li> -</ul></li> -<li><p><strong>Pool fixed parameters</strong></p> -<ul> -<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.</li> -</ul></li> -</ul> -<h3 id="buffered-pools"><a href="#buffered-pools"><a href="#TOC">Buffered pools</a></a></h3> -<p>Some pools are set to a fixed <code>n</code>, that is number of molecules, and therefore a fixed concentration, throughout a simulation. These are buffered pools.</p> -<ul> -<li><strong>Icon</strong>: <img src="../../images/BufPool.png" /> Colored rectangle with pool name in it.</li> -<li><strong>Moving Buffered pools</strong>: Click and drag.</li> -<li><p><strong>Buffered Pool editable parameters</strong></p> -<ul> -<li><strong><code>name</code></strong>: Name of the pool</li> -<li><strong><code>nInit</code></strong>: Fixed number of molecules in the pool. <code>n</code> gets set to this value throughout the run.</li> -<li><p><strong><code>concInit</code></strong>: Fixed concentration of the molecules in the pool.</p> -<blockquote> -<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value throughout the run.</p> -</blockquote></li> -</ul></li> -<li><p><strong>Pool fixed parameters</strong>:</p> -<ul> -<li><strong><code>n</code></strong>: Number of molecules in the pool. Derived from <code>nInit</code>.</li> -<li><strong><code>conc</code></strong>: Concentration of molecules in the pool. Derived from <code>concInit</code>.</li> -<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.</li> -</ul></li> -</ul> -<h3 id="reaction"><a href="#reaction"><a href="#TOC">Reaction</a></a></h3> -<p>These are conversion reactions between sets of pools. They are reversible, but you can set either of the rates to zero to get irreversibility. In the illustration below, <strong><code>D</code></strong> and <strong><code>A</code></strong> are substrates, and <strong><code>B</code></strong> is the product of the reaction. This is indicated by the direction of the green arrow.</p> -<div class="figure"> -<img src="../../images/KkitReaction.png" /> -</div> -<ul> -<li><strong>Icon</strong>: <img src="../../images/KkitReacIcon.png" /> Reversible reaction arrow.</li> -<li><strong>Moving Reactions</strong>: Click and drag.</li> -<li><p><strong>Reaction editable parameters</strong>:</p> -<ul> -<li><strong><code>name</code></strong>: Name of reaction</li> -<li><strong><code>K</code><sub><code>f</code></sub></strong>: Forward rate of reaction, in <code>concentration/time</code> units. This is the normal way to express and manipulate the reaction rate.</li> -<li><strong><code>k</code><sub><code>f</code></sub></strong>: Forward rate of reaction, in <code>number/time</code> units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.</li> -<li><strong><code>K</code><sub><code>b</code></sub></strong>: Backward rate of reaction, in <code>concentration/time</code> units. This is the normal way to express and manipulate the reaction rate.</li> -<li><strong><code>k</code><sub><code>b</code></sub></strong>: Backward rate of reaction, in <code>number/time</code> units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.</li> -</ul></li> -<li><p><strong>Reaction fixed parameters</strong>:</p> -<ul> -<li><strong><code>numProducts</code></strong>: Number of product molecules.</li> -<li><strong><code>numSubstrates</code></strong>: Number of substrates molecules.</li> -</ul></li> -</ul> -<h3 id="mass-action-enzymes"><a href="#mass-action-enzymes"><a href="#TOC">Mass-action enzymes</a></a></h3> -<p>These are enzymes that model the chemical equations</p> -<blockquote> -<p>E + S <===> E.S —> E + P</p> -</blockquote> -<p>Note that the second reaction is irreversible. Note also that mass-action enzymes include a pool to represent the <strong><code>E.S</code></strong> (enzyme-substrate) complex. In the example below, the enzyme pool is named <strong><code>MassActionEnz</code></strong>, the substrate is <strong><code>C</code></strong>, and the product is <strong><code>E</code></strong>. The direction of the enzyme reaction is indicated by the red arrows.</p> -<div class="figure"> -<img src="../../images/MassActionEnzReac.png" /> -</div> -<ul> -<li><p><strong>Icon</strong>: <img src="../../images/MassActionEnzIcon.png" /> Colored ellipse atop a small square. The ellipse represents the enzyme. The small square represents <strong><code>E.S</code></strong>, the enzyme-substrate complex. The ellipse icon has the same color as the enzyme pool <strong><code>E</code></strong>. It is connected to the enzyme pool <strong><code>E</code></strong> with a straight line of the same color.</p> -<p>The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product.</p> -<p>A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.</p></li> -<li><strong>Moving Enzymes</strong>: Click and drag on the ellipse.</li> -<li><p><strong>Enzyme editable parameters</strong></p> -<ul> -<li><strong><code>name</code></strong>: Name of enzyme.</li> -<li><strong><code>K</code><sub><code>m</code></sub></strong>: Michaelis-Menten value for enzyme, in <code>concentration</code> units.</li> -<li><strong><code>k</code><sub><code>cat</code></sub></strong>: Production rate of enzyme, in <code>1/time</code> units. Equal to <code>k</code><sub><code>3</code></sub>, the rate of the second, irreversible reaction.</li> -<li><strong><code>k</code><sub><code>1</code></sub></strong>: Forward rate of the <strong><code>E+S</code></strong> reaction, in number and <code>1/time</code> units. This is what is used in the internal calculations.</li> -<li><strong><code>k</code><sub><code>2</code></sub></strong>: Backward rate of the <strong><code>E+S</code></strong> reaction, in <code>1/time</code> units. Used in internal calculations.</li> -<li><strong><code>k</code><sub><code>3</code></sub></strong>: Forward rate of the <strong><code>E.S —> E + P</code></strong> reaction, in <code>1/time</code> units. Equivalent to <code>k</code><sub><code>cat</code></sub>. Used in internal calculations.</li> -<li><strong><code>ratio</code></strong>: This is equal to <code>k</code><sub><code>2</code></sub><code>/k</code><sub><code>3</code></sub>. Needed to define the internal rates in terms of <code>K</code><sub><code>m</code></sub> and <code>k</code><sub><code>cat</code></sub>. I usually use a value of 4.</li> -</ul></li> -<li><p><strong>Enzyme-substrate-complex editable parameters</strong>: These are identical to those of any other pool.</p> -<ul> -<li><strong><code>name</code></strong>: Name of the <strong><code>E.S</code></strong> complex. Defaults to <strong><code><enzymeName>_cplx</code></strong>.</li> -<li><strong><code>n</code></strong>: Number of molecules in the pool</li> -<li><strong><code>nInit</code></strong>: Initial number of molecules in the complex. <code>n</code> gets set to this value when the <code>reinit</code> operation is done.</li> -<li><p><strong><code>conc</code></strong>: Concentration of the molecules in the pool.</p> -<blockquote> -<p>conc = n * unit_scale_factor / (N<sub>A</sub> * vol)</p> -</blockquote></li> -<li><p><strong><code>concInit</code></strong>: Initial concentration of the molecules in the pool.</p> -<blockquote> -<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value when the <code>reinit</code> operation is done.</p> -</blockquote></li> -</ul></li> -<li><p><strong>Enzyme-substrate-complex fixed parameters</strong>:</p> -<ul> -<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment. Note that the Enzyme-substrate-complex is assumed to be in the same compartment as the enzyme molecule.</li> -</ul></li> -</ul> -<h3 id="michaelis-menten-enzymes"><a href="#michaelis-menten-enzymes"><a href="#TOC">Michaelis-Menten Enzymes</a></a></h3> -<p>These are enzymes that obey the Michaelis-Menten equation</p> -<blockquote> -<p>V = V<sub>max</sub> * [S] / ( K<sub>m</sub> + [S] ) = k<sub>cat</sub> * [Etot] * [S] / ( K<sub>m</sub> + [S] )</p> -</blockquote> -<p>where</p> -<ul> -<li><code>V</code><sub><code>max</code></sub> is the maximum rate of the enzyme</li> -<li><code>[Etot]</code> is the total amount of the enzyme</li> -<li><code>K</code><sub><code>m</code></sub> is the Michaelis-Menten constant</li> -<li><code>S</code> is the substrate.</li> -</ul> -<p>Nominally these enzymes model the same chemical equation as the mass-action enzyme:</p> -<blockquote> -<p>E + S <===> E.S —> E + P</p> -</blockquote> -<p>but they make the assumption that the <strong><code>E.S</code></strong> is in a quasi-steady-state with <strong><code>E</code></strong> and <strong><code>S</code></strong>, and they also ignore sequestration of the enzyme into the complex. So there is no representation of the <strong><code>E.S</code></strong> complex. In the example below, the enzyme pool is named <strong><code>MM_Enz</code></strong>, the substrate is <strong><code>E</code></strong>, and the product is <strong><code>F</code></strong>. The direction of the enzyme reaction is indicated by the red arrows.</p> -<div class="figure"> -<img src="../../images/MM_EnzReac.png" /> -</div> -<ul> -<li><strong>Icon</strong>: <img src="../../images/MM_EnzIcon.png" /> Colored ellipse. The ellipse represents the enzyme The ellipse icon has the same color as the enzyme <strong><code>MM_Enz</code></strong>. It is connected to the enzyme pool <strong><code>MM_Enz</code></strong> with a straight line of the same color. The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product. A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.</li> -<li><strong>Moving Enzymes</strong>: Click and drag.</li> -<li><p><strong>Enzyme editable parameters</strong>:</p> -<ul> -<li><strong><code>name</code></strong>: Name of enzyme.</li> -<li><strong><code>K</code><sub><code>m</code></sub></strong>: Michaelis-Menten value for enzyme, in <code>concentration</code> units.</li> -<li><strong><code>k</code><sub><code>cat</code></sub></strong>: Production rate of enzyme, in <code>1/time</code> units. Equal to <code>k</code><sub><code>3</code></sub>, the rate of the second, irreversible reaction.</li> -</ul></li> -</ul> -<h3 id="function"><a href="#function"><a href="#TOC">Function</a></a></h3> -<p>Function objects can be used to evaluate expressions with arbitrary number of variables and constants. We can assign expression of the form:</p> -<p>f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )</p> -<p>where ci‘s are constants and xi‘s and yi‘s are variables.</p> -<p>It can parse mathematical expression defining a function and evaluate it and/or its derivative for specified variable values. The variables can be input from other moose objects. In case of arbitrary variable names, the source message must have the variable name as the first argument.</p> -<ul> -<li><strong>Icon</strong>: Colored rectangle with pool name. This is <strong><code>ƒ</code></strong> in the example image below. The input pools <strong><code>A</code></strong> and <strong><code>B</code></strong> connect to the <strong>ƒ</strong> with blue arrows. The function ouput's to BuffPool</li> -</ul> -<h2 id="model-operations"><a href="#model-operations"><a href="#TOC">Model operations</a></a></h2> -<ul> -<li><strong>Loading models</strong>: <strong><code>File -> Load Model -> select from dialog</code></strong>. This operation makes the previously loaded model disable and loads newly selected models in <strong><code>Model View</code></strong></li> -<li><strong>New</strong>: <strong><code>File -> New -> Model name</code></strong>. This opens a empty widget for model building</li> -<li><strong>Saving models</strong>: <strong><code>File -> Save Model -> select from dialog</code></strong>.</li> -<li><p><strong>Changing numerical methods</strong>: <strong><code>Preference->Chemical tab</code></strong> item from Simulation Control. Currently supports:</p> -<ul> -<li>Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.</li> -<li>Gillespie: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.</li> -<li>Exponential Euler:This methods computes the solution of partial and ordinary differential equations.</li> -</ul></li> -</ul> -<h2 id="model-building"><a href="#model-building"><a href="#TOC">Model building</a></a></h2> -<div class="figure"> -<img src="../../images/chemical_CS.png" /> -</div> -<ul> -<li><p>The Edit Widget includes various menu options and model icons on the top.* Use the mouse buttton to click and drag icons from toolbar to Edit Widget, two things will happen, icon will appear in the editor widget and a object editor will pop up with lots of parameters with respect to moose object. Rules:</p> -<pre><code>* Compartment has to be created firstly (At present only single compartment model is allowed)</code></pre> -<ul> -<li>Enzyme should be dropped on a pool as parent and function should be dropped on buffPool for output -<li> -Drag in pool's and reaction on to the editor widget, now one can set up a reaction.Click on mooseObject one can find a little arrow on the top right corner of the object, drag from this little arrow to any object for connection.E.g pool to reaction and reaction to pool. Specific connection type gets specific colored arrow. E.g. Green color arrow for specifying connection between reactant and product for reaction. Clicking on the object one can rearrange object for clean layout. Second order reaction can also be done by repeating the connection over again</li> -</ul></li> -<li><p>Each connection can be deleted and using rubberband selection each moose object can be deleted</p></li> -</ul> -<div class="figure"> -<img src="../../images/Chemical_run.png" /> -</div> -<ul> -<li>From run widget, pools are draggable to plot window for plotting. (Currently <strong><code>conc</code></strong> is plotted as default field) Plots are color-coded as per in model.</li> -<li>Model can be run by clicking start button. One can stop button in mid-stream and start up again without affectiong the calculations. The reset button clears the simulation.</li> -</ul> -</body> -</html> diff --git a/docs/user/html/MooseGuiDocs.html b/docs/user/html/MooseGuiDocs.html deleted file mode 100644 index f1cb9434744d7409f496184451c48ef7b1f04617..0000000000000000000000000000000000000000 --- a/docs/user/html/MooseGuiDocs.html +++ /dev/null @@ -1,167 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <title></title> - <style type="text/css">code{white-space: pre;}</style> - <link rel="stylesheet" href="css/moosedocs.css" type="text/css" /> -</head> -<body> -<div id="TOC"> -<ul> -<li><a href="#moose-gui"><strong>MOOSE GUI</strong></a><ul> -<li><a href="#contents">Contents</a></li> -<li><a href="#introduction">Introduction</a></li> -<li><a href="#interface">Interface</a><ul> -<li><a href="#menu-bar">Menu Bar</a></li> -<li><a href="#editor-view">Editor View</a></li> -<li><a href="#run-view">Run View</a></li> -</ul></li> -</ul></li> -</ul> -</div> -<h1 id="moose-gui"><a href="#moose-gui"><strong>MOOSE GUI</strong></a></h1> -<p><strong>Graphical interface for MOOSE</strong></p> -<p><em>Harsha Rani, Aviral Goel, Upinder S. Bhalla</em></p> -<hr /> -<h2 id="contents"><a href="#contents">Contents</a></h2> -<ul> -<li><a href="#introduction">Introduction</a></li> -<li><a href="#interface">Interface</a> -<ul> -<li><a href="#menu-bar">Menu Bar</a> -<ul> -<li><a href="#menu-file">File</a> -<ul> -<li><a href="#file-new">New</a></li> -<li><a href="#file-load-model">Load Model</a></li> -<li><a href="#file-connect-biomodels">Connect BioModels</a></li> -<li><a href="#file-quit">Quit</a></li> -</ul></li> -<li><a href="#menu-view">View</a> -<ul> -<li><a href="#editor-view">Editor View</a></li> -<li><a href="#run-view">Run View</a></li> -<li><a href="#dock-widgets">Dock Widgets</a></li> -<li><a href="#subwindows">SubWindows</a></li> -</ul></li> -<li><a href="#menu-help">Help</a> -<ul> -<li><a href="#about-moose">About MOOSE</a></li> -<li><a href="#built-in-documentation">Built-in Documentation</a></li> -<li><a href="#report-a-bug">Report a bug</a></li> -</ul></li> -</ul></li> -<li><a href="#editor-view">Editor View</a> -<ul> -<li><a href="#model-editor">Model Editor</a></li> -<li><a href="#property-editor">Property Editor</a></li> -</ul></li> -<li><a href="#run-view">Run View</a> -<ul> -<li><a href="#simulation-controls">Simulation Controls</a></li> -<li><a href="#plot-widget">Plot Widget</a> -<ul> -<li><a href="#plot-widget-toolbar">Toolbar</a></li> -<li><a href="#plot-widget-context-menu">Context Menu</a></li> -</ul></li> -</ul></li> -</ul></li> -</ul> -<h2 id="introduction"><a href="#introduction">Introduction</a></h2> -<p>The Moose GUI lets you work on both <a href="Kkit12Documentation.html">chemical</a> and <a href="Nkit2Documentation.html">compartmental/electrical</a> neuronal models using a common interface. This document describes the salient features of the GUI</p> -<h2 id="interface"><a href="#interface">Interface</a></h2> -<p>The common interface layout consists of a a <a href="#menu-bar">menu bar</a> and two views, <a href="#editor-view">editor view</a> and <a href="#run-view">run view</a>.</p> -<h3 id="menu-bar"><a href="#menu-bar">Menu Bar</a></h3> -<div class="figure"> -<img src="../../images/MooseGuiMenuImage.png" /> -</div> -<p>The menu bar appears at the top of the top of the main window. In Ubuntu 12.04, the menu bar appears only when the mouse is in the top menu strip of the screen. It consists of the following options -</p> -<h4 id="file"><a href="#file">File</a></h4> -<p>The File menu option provides the following sub options -</p> -<ul> -<li><a href="#file-new">New</a> - Create a new chemical signalling model.</li> -<li><a href="#file-load-model">Load Model</a> - Load a chemical signalling or compartmental neuronal model from a file.</li> -<li><a href="#recently-loaded-models">Recently Loaded Models</a> - List of models loaded in MOOSE.</li> -<li><a href="#file-connect-biomodels">Connect BioModels</a> - Load chemical signaling models from the BioModels database.</li> -<li><a href="#file-quit">Quit</a> - Quit the interface.</li> -</ul> -<h4 id="view"><a href="#view">View</a></h4> -<p>View menu option provides the following sub options -</p> -<ul> -<li><a href="#editor-view">Editor View</a> - Switch to the editor view for editing models.</li> -<li><a href="#run-view">Run View</a> - Switch to run view for running models.</li> -<li><a href="#dock-widgets">Dock Widgets</a> - Following dock widgets are provided - -<ul> -<li><a href="#dock-widget-python">Python</a> - Brings up a full fledged python interpreter integrated with MOOSE GUI. You can interact with loaded models and load new models through the PyMoose API. The entire power of python language is accessible, as well as MOOSE-specific functions and classes.</li> -<li><a href="#dock-widget-edit">Edit</a> - A property editor for viewing and editing the fields of a selected object such as a pool, enzyme, function or compartment. Editable field values can be changed by clicking on them and overwriting the new values. Please be sure to press enter once the editing is complete, in order to save your changes.</li> -</ul></li> -<li><a href="#subwindows">SubWindows</a> - This allows you to tile or tabify the run and editor views.</li> -</ul> -<h4 id="help"><a href="#help">Help</a></h4> -<ul> -<li><a href="#about-moose">About Moose</a> - Version and general information about MOOSE.</li> -<li><a href="#butilt-in-documentation">Built-in documentation</a> - Documentation of MOOSE GUI.</li> -<li><a href="#report-a-bug">Report a bug</a> - Directs to the SourceForge bug tracker for reporting bugs.</li> -</ul> -<h3 id="editor-view"><a href="#editor-view">Editor View</a></h3> -<p>The editor view provides two windows -</p> -<ul> -<li><a href="#model-editor">Model Editor</a> - The model editor is a workspace to edit and create models. Using click-and-drag from the icons in the menu bar, you can create model entities such as chemical pools, reactions, and so on. A click on any object brings its property editor on screen (see below). In objects that can be interconnected, a click also brings up a special arrow icon that is used to connect objects together with messages. You can move objects around within the edit window using click-and-drag. Finally, you can delete objects by selecting one or more, and then choosing the delete option from the pop-up menu. When displaying a neuronal model, most of the editing options are disabled. However, you can still click on a dendrite in order to bring up the property editor.</li> -</ul> -<p>The Model Editor is different for chemical signalling and compartmental neuronal models. The links below the screenshots point to the details for the respective editors.</p> -<div class="figure"> -<img src="../../images/ChemicalSignallingEditor.png" alt="Chemical Signalling Model Editor" /><p class="caption">Chemical Signalling Model Editor</p> -</div> -<div class="figure"> -<img src="../../images/CompartmentalEditor.png" alt="Compartmental Model Editor" /><p class="caption">Compartmental Model Editor</p> -</div> -<ul> -<li><a href="#property-editor">Property Editor</a> - The property editor provides a way of viewing and editing the properties of objects selected in the model editor.</li> -</ul> -<div class="figure"> -<img src="../../images/PropertyEditor.png" alt="Property Editor" /><p class="caption">Property Editor</p> -</div> -<h3 id="run-view"><a href="#run-view">Run View</a></h3> -<p>The Run view, as the name suggests, puts the GUI into a mode where the model can be simulated. As a first step in this, you can click-and-drag an object to the graph window in order to create a time-series plot for that object. For example, in a chemical reaction, you could drag a pool into the graph window and subsequent simulations will display a graph of the concentration of the pool as a function of time. Within the Run View window, the time-evolution of the simulation is displayed as an animation. For chemical kinetic models, the size of the icons for reactant pools scale to indicate concentration. For neuronal models, the colour of dendritic segments changes to indicate membrane potential. Above the Run View window, there is a special tool bar with a set of simulation controls to run the simulation.</p> -<h4 id="simulation-controls"><a href="#simulation-controls">Simulation Controls</a></h4> -<div class="figure"> -<img src="../../images/SimulationControl.png" alt="Simulation Control" /><p class="caption">Simulation Control</p> -</div> -<p>This panel allows you to control the various aspects of the simulation.</p> -<ul> -<li><a href="#run-time">Run Time</a> - Determines duration for which simulation is to run. A simulation which has already run, runs further for the specified additional period.</li> -<li><a href="#reset">Reset</a> - Restores simulation to its initial state; re-initializes all variables to t = 0.</li> -<li><a href="#stop">Stop</a> - This button halts an ongoing simulation.</li> -<li><a href="#current-time">Current time</a> - This reports the current simulation time.</li> -<li><a href="#preferences">Preferences</a> - Allows you to set simulation and visualization related preferences.</li> -</ul> -<h4 id="plot-widget"><a href="#plot-widget">Plot Widget</a></h4> -<h5 id="toolbar"><a href="#toolbar">Toolbar</a></h5> -<p>On top of plot window there is a little row of icons:</p> -<div class="figure"> -<img src="../../images/PlotWindowIcons.png" /> -</div> -<p>These are the plot controls. If you hover the mouse over them for a few seconds, a tooltip pops up. The icons represent the following functions:</p> -<ul> -<li><p><img src="../../images/Addgraph.png" /> - Add a new plot window</p></li> -<li><p><img src="../../images/delgraph.png" /> - Deletes current plot window</p></li> -<li><p><img src="../../images/grid.png" /> - Toggle X-Y axis grid</p></li> -<li><p><img src="../../images/MatPlotLibHomeIcon.png" /> - Returns the plot display to its default position</p></li> -<li><p><img src="../../images/MatPlotLibDoUndo.png" /> - Undoes or re-does manipulations you have done to the display.</p></li> -<li><p><img src="../../images/MatPlotLibPan.png" /> - The plots will pan around with the mouse when you hold the left button down. The plots will zoom with the mouse when you hold the right button down.</p></li> -<li><p><img src="../../images/MatPlotLibZoom.png" /> - With the <strong><code>left mouse button</code></strong>, this will zoom in to the specified rectangle so that the plots become bigger. With the <strong><code>right mouse button</code></strong>, the entire plot display will be shrunk to fit into the specified rectangle.</p></li> -<li><p><img src="../../images/MatPlotLibConfigureSubplots.png" /> - You don't want to mess with these .</p></li> -<li><p><img src="../../images/MatPlotLibSave.png" /> - Save the plot.</p></li> -</ul> -<h5 id="context-menu"><a href="#context-menu">Context Menu</a></h5> -<p>The context menu is enabled by right clicking on the plot window. It has the following options -</p> -<ul> -<li><strong>Export to CSV</strong> - Exports the plotted data to CSV format</li> -<li><strong>Toggle Legend</strong> - Toggles the plot legend</li> -<li><strong>Remove</strong> - Provides a list of plotted entities. The selected entity will not be plotted.</li> -</ul> -</body> -</html> diff --git a/docs/user/html/Nkit2Documentation.html b/docs/user/html/Nkit2Documentation.html deleted file mode 100644 index 0338697ccf34ec8e34a39495acd9b5e331d2e891..0000000000000000000000000000000000000000 --- a/docs/user/html/Nkit2Documentation.html +++ /dev/null @@ -1,119 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <title></title> - <style type="text/css">code{white-space: pre;}</style> - <link rel="stylesheet" href="css/moosedocs.css" type="text/css" /> -</head> -<body> -<div id="TOC"> -<ul> -<li><a href="#introduction">Introduction</a></li> -<li><a href="#neuronal-models">Neuronal models</a></li> -<li><a href="#neuronal-simulations-in-moosegui">Neuronal simulations in MOOSEGUI</a><ul> -<li><a href="#quick-start">Quick start</a><ul> -<li><a href="#editor-view">Editor View</a></li> -<li><a href="#run-view">Run View</a></li> -</ul></li> -<li><a href="#modeling-details">Modeling details</a></li> -<li><a href="#demos">Demos</a></li> -</ul></li> -</ul> -</div> -<h1 id="introduction"><a href="#introduction">Introduction</a></h1> -<p>Neuronal models in NeuroML 1.8 format can be loaded and simulated in the <strong>MOOSE Graphical User Interface</strong>. The GUI displays the neurons in 3D, and allows visual selection and editing of neuronal properties. Plotting and visualization of activity proceeds concurrently with the simulation. Support for creating and editing channels, morphology and networks is planned for the future.</p> -<h1 id="neuronal-models"><a href="#neuronal-models">Neuronal models</a></h1> -<p>Neurons are modeled as equivalent electrical circuits. The morphology of a neuron can be broken into isopotential compartments connected by axial resistances <code>R</code><sub><code>a</code></sub> denoting the cytoplasmic resistance. In each compartment, the neuronal membrane is represented as a capacitance <code>C</code><sub><code>m</code></sub> with a shunt leak resistance <code>R</code><sub><code>m</code></sub>. Electrochemical gradient (due to ion pumps) across the leaky membrane causes a voltage drive <code>E</code><sub><code>m</code></sub>, that hyperpolarizes the inside of the cell membrane compared to the outside.</p> -<p>Each voltage dependent ion channel, present on the membrane, is modeled as a voltage dependent conductance <code>G</code><sub><code>k</code></sub> with gating kinetics, in series with an electrochemical voltage drive (battery) <code>E</code><sub><code>k</code></sub>, across the membrane capacitance <code>C</code><sub><code>m</code></sub>, as in the figure below.</p> -<hr /> -<div class="figure"> -<img src="../../images/neuroncompartment.png" alt="Equivalent circuit of neuronal compartments" /><p class="caption"><strong>Equivalent circuit of neuronal compartments</strong></p> -</div> -<hr /> -<p>Neurons fire action potentials / spikes (sharp rise and fall of membrane potential <code>V</code><sub><code>m</code></sub>) due to voltage dependent channels. These result in opening of excitatory / inhibitory synaptic channels (conductances with batteries, similar to voltage gated channels) on other connected neurons in the network.</p> -<p>MOOSE can handle large networks of detailed neurons, each with complicated channel dynamics. Further, MOOSE can integrate chemical signaling with electrical activity. Presently, creating and simulating these requires PyMOOSE scripting, but these will be incorporated into the GUI in the future.</p> -<p>To understand channel kinetics and neuronal action potentials, run the Squid Axon demo installed along with MOOSEGUI and consult its help/tutorial.</p> -<p>Read more about compartmental modeling in the first few chapters of the <a href="http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html">Book of Genesis</a>.</p> -<p>Models can be defined in <a href="http://www.neuroml.org">NeuroML</a>, an XML format which is well supported across simulators. Channels, neuronal morphology (compartments), and networks can be specified using various levels of NeuroML, namely ChannelML, MorphML and NetworkML. Importing of cell models in the <a href="http://www.genesis-sim.org/GENESIS">GENESIS</a> <code>.p</code> format is supported for backwards compatibitility.</p> -<h1 id="neuronal-simulations-in-moosegui"><a href="#neuronal-simulations-in-moosegui">Neuronal simulations in MOOSEGUI</a></h1> -<h2 id="quick-start"><a href="#quick-start">Quick start</a></h2> -<ul> -<li>MOOSEGUI provides a few neuronal models in moose/Demos directory in user's home folder. For example, <em>File->Load</em> <code>~/moose/Demos/neuroml/PurkinjeCellPassive/PurkinjePassive.net.xml</code>, which is a model of the purkinje cell. A 3D rendering of the neuron appears in <strong><code>Editor</code></strong> tab.</li> -<li>Click and drag to rotate, scroll wheel to zoom, and arrow keys to pan the 3D rendering.</li> -<li>Click to select a compartment on the 3D model. The selected compartment is colored green.</li> -<li>An editor will appear on the right hand side where the properties of the compartment can be edited.</li> -<li>The 3D view of the model provided by the editor allows only editing of the compartment parameters.</li> -<li>In the <strong><code>Run</code></strong> tab you can see two subwindows. The one on the left provides a dynamic visualization of the compartment Vm as the simulation progresses. The one on the right is the plot window where you can plot the Vm of the various compartments.</li> -<li>Press <code>Ctrl</code> and click and drag a compartment from the visualizer to the plot window.</li> -<li>Run the model using <strong><code>Run</code></strong> button. You can see the colors of the compartments changing as the simulation progresses. The graphs gets updated simultaneously with the visualizer.</li> -</ul> -<h3 id="editor-view"><a href="#editor-view">Editor View</a></h3> -<div class="figure"> -<img src="../../images/NeurokitEditor.png" alt="Editor View" /><p class="caption"><strong>Editor View</strong></p> -</div> -<h3 id="run-view"><a href="#run-view">Run View</a></h3> -<div class="figure"> -<img src="../../images/NeurokitRunner.png" alt="Run View" /><p class="caption"><strong>Run View</strong></p> -</div> -<h2 id="modeling-details"><a href="#modeling-details">Modeling details</a></h2> -<p>MOOSE uses SI units throughout.</p> -<p>Some salient properties of neuronal building blocks in MOOSE are described below. Variables that are updated at every simulation time step are are listed <strong>dynamical</strong>. Rest are parameters.</p> -<ul> -<li><p><strong>Compartment</strong><br /> When you select a compartment, you can view and edit its properties in the right pane. <code>V</code><sub><code>m</code></sub> and <code>I</code><sub><code>m</code></sub> are plot-able.</p> -<ul> -<li><strong><code>V</code><sub><code>m</code></sub></strong> : <strong>dynamical</strong> membrane potential (across <code>C</code><sub><code>m</code></sub>) in Volts.</li> -<li><strong><code>C</code><sub><code>m</code></sub></strong> : membrane capacitance in Farads.</li> -<li><strong><code>E</code><sub><code>m</code></sub></strong> : membrane leak potential in Volts due to the electrochemical gradient setup by ion pumps.</li> -<li><strong><code>I</code><sub><code>m</code></sub></strong> : <strong>dynamical</strong> current in Amperes across the membrane via leak resistance <code>R</code><sub><code>m</code></sub>.</li> -<li><strong><code>inject</code></strong> : current in Amperes injected externally into the compartment.</li> -<li><strong><code>initVm</code></strong> : initial <code>V</code><sub><code>m</code></sub> in Volts.</li> -<li><strong><code>R</code><sub><code>m</code></sub></strong> : membrane leak resistance in Ohms due to leaky channels.</li> -<li><strong><code>diameter</code></strong> : diameter of the compartment in metres.</li> -<li><strong><code>length</code></strong> : length of the compartment in metres.</li> -</ul> -<p>After selecting a compartment, you can click <strong><code>See children</code></strong> on the right pane to list its membrane channels, Ca pool, etc.</p></li> -<li><p><strong>HHChannel</strong><br /> Hodgkin-Huxley channel with voltage dependent dynamical gates.</p> -<ul> -<li><strong><code>Gbar</code></strong> : peak channel conductance in Siemens.</li> -<li><strong><code>E</code><sub><code>k</code></sub></strong> : reversal potential of the channel, due to electrochemical gradient of the ion(s) it allows.</li> -<li><p><strong><code>G</code><sub><code>k</code></sub></strong> : <strong>dynamical</strong> conductance of the channel in Siemens.</p> -<blockquote> -<p>G<sub>k</sub>(t) = Gbar × X(t)<sup>Xpower</sup> × Y(t)<sup>Ypower</sup> × Z(t)<sup>Zpower</sup></p> -</blockquote></li> -<li><p><strong><code>I</code><sub><code>k</code></sub></strong> : <strong>dynamical</strong> current through the channel into the neuron in Amperes.</p> -<blockquote> -<p>I<sub>k</sub>(t) = G<sub>k</sub>(t) × (E<sub>k</sub>-V<sub>m</sub>(t))</p> -</blockquote></li> -<li><p><strong><code>X</code></strong>, <strong><code>Y</code></strong>, <strong><code>Z</code></strong> : <strong>dynamical</strong> gating variables (range <code>0.0</code> to <code>1.0</code>) that may turn on or off as voltage increases with different time constants.</p> -<blockquote> -<p>dX(t)/dt = X<sub>inf</sub>/τ - X(t)/τ</p> -</blockquote> -Here, <code>X</code><sub><code>inf</code></sub> and <code>τ</code> are typically sigmoidal/linear/linear-sigmoidal functions of membrane potential <code>V</code><sub><code>m</code></sub>, which are described in a ChannelML file and presently not editable from MOOSEGUI. Thus, a gate may open <code>(X</code><sub><code>inf</code></sub><code>(V</code><sub><code>m</code></sub><code>) → 1)</code> or close <code>(X</code><sub><code>inf</code></sub><code>(V</code><sub><code>m</code></sub><code>) → 0)</code> on increasing <code>V</code><sub><code>m</code></sub>, with time constant <code>τ(V</code><sub><code>m</code></sub><code>)</code>.</li> -<li><p><strong><code>Xpower</code></strong>, <strong><code>Ypower</code></strong>, <strong><code>Zpower</code></strong> : powers to which gates are raised in the <code>G</code><sub><code>k</code></sub><code>(t)</code> formula above.</p></li> -</ul></li> -<li><p><strong>HHChannel2D</strong><br /> The Hodgkin-Huxley channel2D can have the usual voltage dependent dynamical gates, and also gates that dependent on voltage and an ionic concentration, as for say Ca-dependent K conductance. It has the properties of HHChannel above, and a few more like <code>Xindex</code> as in the <a href="http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#ss26.61">GENESIS tab2Dchannel reference</a>.</p></li> -<li><strong>CaConc</strong><br /> This is a pool of Ca ions in each compartment, in a shell volume under the cell membrane. The dynamical Ca concentration increases when Ca channels open, and decays back to resting with a specified time constant τ. Its concentration controls Ca-dependent K channels, etc. -<ul> -<li><p><code>Ca</code> : <strong>dynamical</strong> Ca concentration in the pool in units <code>mM</code> ( i.e., <code>mol/m</code><sup><code>3</code></sup>).</p> -<blockquote> -<p>d[Ca<sup>2+</sup>]/dt = B × I<sub>Ca</sub> - [Ca<sup>2+</sup>]/τ</p> -</blockquote></li> -<li><code>CaBasal</code>/<code>Ca_base</code> : Base Ca concentration to which the Ca decays</li> -<li><code>tau</code> : time constant with which the Ca concentration decays to the base Ca level.</li> -<li><code>B</code> : constant in the <code>[Ca</code><sup><code>2+</code></sup><code>]</code> equation above.</li> -<li><p><code>thick</code> : thickness of the Ca shell within the cell membrane which is used to calculate <code>B</code> (see Chapter 19 of <a href="http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html">Book of GENESIS</a>.)</p></li> -</ul></li> -</ul> -<h2 id="demos"><a href="#demos">Demos</a></h2> -<ul> -<li><p><strong>Cerebellar granule cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/GranuleCell/GranuleCell.net.xml</code><br /> This is a single compartment Cerebellar granule cell with a variety of channels <a href="http://www.tnb.ua.ac.be/models/network.shtml">Maex, R. and De Schutter, E., 1997</a> (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). Click on its soma, and <strong>See children</strong> for its list of channels. Vary the <code>Gbar</code> of these channels to obtain regular firing, adapting and bursty behaviour (may need to increase tau of the Ca pool).</p></li> -<li><p><strong>Purkinje cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/PurkinjeCell/Purkinje.net.xml</code><br /> This is a purely passive cell, but with extensive morphology [De Schutter, E. and Bower, J. M., 1994] (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). The channel specifications are in an obsolete ChannelML format which MOOSE does not support.</p></li> -<li><p><strong>Olfactory bulb subnetwork</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml</code><br /> This is a pruned and decimated version of a detailed network model of the Olfactory bulb [Gilra A. and Bhalla U., in preparation] without channels and synaptic connections. We hope to post the ChannelML specifications of the channels and synapses soon.</p></li> -<li><p><strong>All channels cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/allChannelsCell/allChannelsCell.net.xml</code><br /> This is the Cerebellar granule cell as above, but with loads of channels from various cell types (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). Play around with the channel properties to see what they do. You can also edit the ChannelML files in <code>~/moose/Demos/neuroml/allChannelsCell/cells_channels/</code> to experiment further.</p></li> -<li><p><strong>NeuroML python scripts</strong><br /> In directory <code>~/moose/Demos/neuroml/GranuleCell</code>, you can run <code>python FvsI_Granule98.py</code> which plots firing rate vs injected current for the granule cell. Consult this python script to see how to read in a NeuroML model and to set up simulations. There are ample snippets in <code>~/moose/Demos/snippets</code> too.</p></li> -</ul> -</body> -</html> diff --git a/docs/user/html/css/moosebuiltindocs.css b/docs/user/html/css/moosebuiltindocs.css deleted file mode 100644 index 211c84f34d188b8c3acf7b8819413f3b46337ecc..0000000000000000000000000000000000000000 --- a/docs/user/html/css/moosebuiltindocs.css +++ /dev/null @@ -1,16 +0,0 @@ -#index-for-moose-classes > table, #index-for-moose-functions > table { - table-layout: fixed; -} - -th:nth-child( 1 ) { - width: 15%; -} - -th:nth-child( 2 ) { - width: 30%; -} - -/* - * Shows table-of-contents only 2 levels deep, and hides beyond that. - */ -div#TOC > ul > li > ul > li ul { display: none; } diff --git a/docs/user/html/css/moosedocs.css b/docs/user/html/css/moosedocs.css deleted file mode 100644 index 8b5cd22792dbce02d06d2936969329a246e84b46..0000000000000000000000000000000000000000 --- a/docs/user/html/css/moosedocs.css +++ /dev/null @@ -1,163 +0,0 @@ -body { - /* - max-width: 70em; - 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and functions</title> - <style type="text/css">code{white-space: pre;}</style> - <link rel="stylesheet" href="css/moosedocs.css" type="text/css" /> - <link rel="stylesheet" href="css/moosebuiltindocs.css" type="text/css" /> -</head> -<body> -<div id="header"> -<h1 class="title">Documentation for all MOOSE classes and functions</h1> -<h2 class="author">As visible in the Python module</h2> -<h3 class="date">Auto-generated on January 07, 2013</h3> -</div> -<h1 id="index-for-moose-classes">Index for MOOSE Classes</h1> -<table> -<tbody> -<tr class="odd"> -<td align="left"><strong>A</strong></td> -<td align="left"><a href="#enz"><code>Enz</code></a></td> -<td align="left"><a href="#interpol2d"><code>Interpol2D</code></a></td> -<td align="left"><a href="#nmdachan"><code>NMDAChan</code></a></td> -<td align="left"><a href="#species"><code>Species</code></a></td> -<td align="left"><a href="#vectortable"><code>VectorTable</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#adaptor"><code>Adaptor</code></a></td> -<td align="left"><a href="#enzbase"><code>EnzBase</code></a></td> -<td align="left"><a href="#intfire"><code>IntFire</code></a></td> -<td align="left"><strong>O</strong></td> -<td align="left"><a href="#spherepanel"><code>SpherePanel</code></a></td> -<td align="left"><strong>Z</strong></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#annotator"><code>Annotator</code></a></td> -<td align="left"><strong>F</strong></td> -<td align="left"><a href="#izhikevichnrn"><code>IzhikevichNrn</code></a></td> -<td align="left"><a href="#onetoallmsg"><code>OneToAllMsg</code></a></td> -<td align="left"><a href="#spikegen"><code>SpikeGen</code></a></td> -<td align="left"><a href="#zbufpool"><code>ZBufPool</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#arith"><code>Arith</code></a></td> -<td align="left"><a href="#finfo"><code>Finfo</code></a></td> -<td align="left"><strong>L</strong></td> -<td align="left"><a href="#onetoonemsg"><code>OneToOneMsg</code></a></td> -<td align="left"><a href="#stats"><code>Stats</code></a></td> -<td align="left"><a href="#zenz"><code>ZEnz</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><strong>B</strong></td> -<td align="left"><a href="#funcbase"><code>FuncBase</code></a></td> -<td align="left"><a href="#leakyiaf"><code>LeakyIaF</code></a></td> -<td align="left"><strong>P</strong></td> -<td align="left"><a href="#stimulustable"><code>StimulusTable</code></a></td> -<td align="left"><a href="#zfuncpool"><code>ZFuncPool</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#boundary"><code>Boundary</code></a></td> -<td align="left"><a href="#funcpool"><code>FuncPool</code></a></td> -<td align="left"><strong>M</strong></td> -<td align="left"><a href="#panel"><code>Panel</code></a></td> -<td align="left"><a href="#stoich"><code>Stoich</code></a></td> -<td align="left"><a href="#zmmenz"><code>ZMMenz</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#bufpool"><code>BufPool</code></a></td> -<td align="left"><strong>G</strong></td> -<td align="left"><a href="#markovchannel"><code>MarkovChannel</code></a></td> -<td align="left"><a href="#pidcontroller"><code>PIDController</code></a></td> -<td align="left"><a href="#stoichcore"><code>StoichCore</code></a></td> -<td align="left"><a href="#zombiebufpool"><code>ZombieBufPool</code></a></td> -</tr> -<tr class="even"> -<td align="left"><strong>C</strong></td> -<td align="left"><a href="#geometry"><code>Geometry</code></a></td> -<td align="left"><a href="#markovgslsolver"><code>MarkovGslSolver</code></a></td> -<td align="left"><a href="#pool"><code>Pool</code></a></td> -<td align="left"><a href="#stoichpools"><code>StoichPools</code></a></td> -<td align="left"><a href="#zombiecaconc"><code>ZombieCaConc</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#caconc"><code>CaConc</code></a></td> -<td align="left"><a href="#ghk"><code>GHK</code></a></td> -<td align="left"><a href="#markovratetable"><code>MarkovRateTable</code></a></td> -<td align="left"><a href="#poolbase"><code>PoolBase</code></a></td> -<td align="left"><a href="#sumfunc"><code>SumFunc</code></a></td> -<td align="left"><a href="#zombiecompartment"><code>ZombieCompartment</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#chanbase"><code>ChanBase</code></a></td> -<td align="left"><a href="#group"><code>Group</code></a></td> -<td align="left"><a href="#markovsolver"><code>MarkovSolver</code></a></td> -<td align="left"><a href="#port"><code>Port</code></a></td> -<td align="left"><a href="#surface"><code>Surface</code></a></td> -<td align="left"><a href="#zombieenz"><code>ZombieEnz</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#chemmesh"><code>ChemMesh</code></a></td> -<td align="left"><a href="#gslintegrator"><code>GslIntegrator</code></a></td> -<td align="left"><a href="#markovsolverbase"><code>MarkovSolverBase</code></a></td> -<td align="left"><a href="#pulsegen"><code>PulseGen</code></a></td> -<td align="left"><a href="#symcompartment"><code>SymCompartment</code></a></td> -<td align="left"><a href="#zombiefuncpool"><code>ZombieFuncPool</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#cinfo"><code>Cinfo</code></a></td> -<td align="left"><a href="#gslstoich"><code>GslStoich</code></a></td> -<td align="left"><a href="#mathfunc"><code>MathFunc</code></a></td> -<td align="left"><strong>R</strong></td> -<td align="left"><a href="#synapse"><code>Synapse</code></a></td> -<td align="left"><a href="#zombiehhchannel"><code>ZombieHHChannel</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#clock"><code>Clock</code></a></td> -<td align="left"><a href="#gssastoich"><code>GssaStoich</code></a></td> -<td align="left"><a href="#mdouble"><code>Mdouble</code></a></td> -<td align="left"><a href="#rc"><code>RC</code></a></td> -<td align="left"><a href="#synbase"><code>SynBase</code></a></td> -<td align="left"><a href="#zombiemmenz"><code>ZombieMMenz</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#compartment"><code>Compartment</code></a></td> -<td align="left"><strong>H</strong></td> -<td align="left"><a href="#meshentry"><code>MeshEntry</code></a></td> -<td align="left"><a href="#reac"><code>Reac</code></a></td> -<td align="left"><a href="#synchan"><code>SynChan</code></a></td> -<td align="left"><a href="#zombiepool"><code>ZombiePool</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#cplxenzbase"><code>CplxEnzBase</code></a></td> -<td align="left"><a href="#hdf5datawriter"><code>HDF5DataWriter</code></a></td> -<td align="left"><a href="#mgblock"><code>MgBlock</code></a></td> -<td align="left"><a href="#reacbase"><code>ReacBase</code></a></td> -<td align="left"><a href="#synchanbase"><code>SynChanBase</code></a></td> -<td align="left"><a href="#zombiereac"><code>ZombieReac</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#cubemesh"><code>CubeMesh</code></a></td> -<td align="left"><a href="#hdf5writerbase"><code>HDF5WriterBase</code></a></td> -<td align="left"><a href="#mmenz"><code>MMenz</code></a></td> -<td align="left"><a href="#rectpanel"><code>RectPanel</code></a></td> -<td align="left"><strong>T</strong></td> -<td align="left"><a href="#zombiesumfunc"><code>ZombieSumFunc</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#cylmesh"><code>CylMesh</code></a></td> -<td align="left"><a href="#hemispherepanel"><code>HemispherePanel</code></a></td> -<td align="left"><a href="#msg"><code>Msg</code></a></td> -<td align="left"><a href="#reducemsg"><code>ReduceMsg</code></a></td> -<td align="left"><a href="#table"><code>Table</code></a></td> -<td align="left"><a href="#zpool"><code>ZPool</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#cylpanel"><code>CylPanel</code></a></td> -<td align="left"><a href="#hhchannel"><code>HHChannel</code></a></td> -<td align="left"><a href="#mstring"><code>Mstring</code></a></td> -<td align="left"><strong>S</strong></td> -<td align="left"><a href="#tablebase"><code>TableBase</code></a></td> -<td align="left"><a href="#zreac"><code>ZReac</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><strong>D</strong></td> -<td align="left"><a href="#hhchannel2d"><code>HHChannel2D</code></a></td> -<td align="left"><strong>N</strong></td> -<td align="left"><a href="#shell"><code>Shell</code></a></td> -<td align="left"><a href="#tableentry"><code>TableEntry</code></a></td> -<td align="left"></td> -</tr> -<tr class="even"> -<td align="left"><a href="#diagonalmsg"><code>DiagonalMsg</code></a></td> -<td align="left"><a href="#hhgate"><code>HHGate</code></a></td> -<td align="left"><a href="#nernst"><code>Nernst</code></a></td> -<td align="left"><a href="#simmanager"><code>SimManager</code></a></td> -<td align="left"><a href="#testsched"><code>testSched</code></a></td> -<td align="left"></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#diffamp"><code>DiffAmp</code></a></td> -<td align="left"><a href="#hhgate2d"><code>HHGate2D</code></a></td> -<td align="left"><a href="#neuromesh"><code>NeuroMesh</code></a></td> -<td align="left"><a href="#singlemsg"><code>SingleMsg</code></a></td> -<td align="left"><a href="#tick"><code>Tick</code></a></td> -<td align="left"></td> -</tr> -<tr class="even"> -<td align="left"><a href="#diskpanel"><code>DiskPanel</code></a></td> -<td align="left"><a href="#hsolve"><code>HSolve</code></a></td> -<td align="left"><a href="#neuron"><code>Neuron</code></a></td> -<td align="left"><a href="#solverjunction"><code>SolverJunction</code></a></td> -<td align="left"><a href="#tripanel"><code>TriPanel</code></a></td> -<td align="left"></td> -</tr> -<tr class="odd"> -<td align="left"><strong>E</strong></td> -<td align="left"><strong>I</strong></td> -<td align="left"><a href="#neutral"><code>Neutral</code></a></td> -<td align="left"><a href="#sparsemsg"><code>SparseMsg</code></a></td> -<td align="left"><strong>V</strong></td> -<td align="left"></td> -</tr> -</tbody> -</table> -<h1 id="index-for-moose-functions">Index for MOOSE Functions</h1> -<table> -<tbody> -<tr class="odd"> -<td align="left"><strong>C</strong></td> -<td align="left"><a href="#element"><code>element</code></a></td> -<td align="left"><a href="#getmoosedoc"><code>getmoosedoc</code></a></td> -<td align="left"><a href="#move"><code>move</code></a></td> -<td align="left"><a href="#savemodel"><code>saveModel</code></a></td> -<td align="left"><a href="#stop"><code>stop</code></a></td> -</tr> -<tr class="even"> -<td align="left"><a href="#ce"><code>ce</code></a></td> -<td align="left"><a href="#exists"><code>exists</code></a></td> -<td align="left"><strong>I</strong></td> -<td align="left"><strong>P</strong></td> -<td align="left"><a href="#seed"><code>seed</code></a></td> -<td align="left"><a href="#syncdatahandler"><code>syncDataHandler</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#connect"><code>connect</code></a></td> -<td align="left"><strong>G</strong></td> -<td align="left"><a href="#isrunning"><code>isRunning</code></a></td> -<td align="left"><a href="#pwe"><code>pwe</code></a></td> -<td align="left"><a href="#setclock"><code>setClock</code></a></td> -<td align="left"><strong>U</strong></td> -</tr> -<tr class="even"> -<td align="left"><a href="#copy"><code>copy</code></a></td> -<td align="left"><a href="#getcwe"><code>getCwe</code></a></td> -<td align="left"><strong>L</strong></td> -<td align="left"><strong>Q</strong></td> -<td align="left"><a href="#setcwe"><code>setCwe</code></a></td> -<td align="left"><a href="#useclock"><code>useClock</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><strong>D</strong></td> -<td align="left"><a href="#getfield"><code>getField</code></a></td> -<td align="left"><a href="#le"><code>le</code></a></td> -<td align="left"><a href="#quit"><code>quit</code></a></td> -<td align="left"><a href="#showfield"><code>showfield</code></a></td> -<td align="left"><strong>W</strong></td> -</tr> -<tr class="even"> -<td align="left"><a href="#delete"><code>delete</code></a></td> -<td align="left"><a href="#getfielddict"><code>getFieldDict</code></a></td> -<td align="left"><a href="#listmsg"><code>listmsg</code></a></td> -<td align="left"><strong>R</strong></td> -<td align="left"><a href="#showfields"><code>showfields</code></a></td> -<td align="left"><a href="#wildcardfind"><code>wildcardFind</code></a></td> -</tr> -<tr class="odd"> -<td align="left"><a href="#doc"><code>doc</code></a></td> -<td align="left"><a href="#getfielddoc"><code>getfielddoc</code></a></td> -<td align="left"><a href="#loadmodel"><code>loadModel</code></a></td> -<td align="left"><a href="#reinit"><code>reinit</code></a></td> -<td align="left"><a href="#showmsg"><code>showmsg</code></a></td> -<td align="left"><a href="#writesbml"><code>writeSBML</code></a></td> -</tr> -<tr class="even"> -<td align="left"><strong>E</strong></td> -<td align="left"><a href="#getfieldnames"><code>getFieldNames</code></a></td> -<td align="left"><strong>M</strong></td> -<td align="left"><strong>S</strong></td> -<td align="left"><a href="#start"><code>start</code></a></td> -<td align="left"></td> -</tr> -</tbody> -</table> -<h1 id="moose-classes">MOOSE Classes</h1> -<h2 id="adaptor">Adaptor</h2> -<p><strong>Author</strong>: Upinder S. Bhalla, 2008, NCBS</p> -<p><strong>Description</strong>: Averages and rescales values to couple different kinds of simulation</p> -<h4 id="value-fields">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inputOffset</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Offset to apply to input message, before scaling</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputOffset</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Offset to apply at output, after scaling</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>scale</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Scaling factor to apply to input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">This is the linearly transformed output.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputSrc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends the output value every timestep.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestInput</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out the request. Issued from the process call.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Input message to the adaptor. If multiple inputs are received, the system averages the inputs.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'process' call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleInput</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle the returned value.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from the scheduler.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>inputRequest</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to request and handle value messages from fields.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="annotator">Annotator</h2> -<h4 id="value-fields-1">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x field. Typically display coordinate x</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y field. Typically display coordinate y</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z field. Typically display coordinate z</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>notes</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">A string to hold some text notes about parent object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>color</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>textColor</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>icon</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">A string to specify icon to use for display</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-1">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-1">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-1">Shared message fields</h4> -<h4 id="lookup-fields-1">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="arith">Arith</h2> -<h4 id="value-fields-2">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>function</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Arithmetic function to perform on inputs.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputValue</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Value of output as computed last timestep.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>arg1Value</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Value of arg1 as computed last timestep.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-2">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out the computed value</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-2">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>arg1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles argument 1. This just assigns it</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>arg2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles argument 2. This just assigns it</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>arg3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles argument 3. This sums in each input, and clears each clock tick.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>arg1x2</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Store the product of the two arguments in output_</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-2">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-2">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>anyValue</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.</td> -</tr> -</tbody> -</table> -<h2 id="boundary">Boundary</h2> -<h4 id="value-fields-3">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reflectivity</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">What happens to a molecule hitting it: bounces, absorbed, diffused?</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-3">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toAdjacent</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy message going to adjacent compartment.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toInside</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy message going to surrounded compartment.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-3">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>adjacent</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy message coming from adjacent compartment to current oneImplies that compts are peers: do not surround each other</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>outside</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy message coming from surrounding compartment to this one.Implies that the originating compartment surrounds this one</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-3">Shared message fields</h4> -<h4 id="lookup-fields-3">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="bufpool">BufPool</h2> -<h4 id="value-fields-4">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-4">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-4">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>increment</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>decrement</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-4">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-4">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="caconc">CaConc</h2> -<h4 id="value-fields-5">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ca</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Calcium concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>CaBasal</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Basal Calcium concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ca_base</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Basal Calcium concentration, synonym for CaBasal</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tau</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Settling time for Ca concentration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>B</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Volume scaling factor</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>thick</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Thickness of Ca shell.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ceiling</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>floor</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Floor value for Ca concentration. If Ca < floor, Ca = floor</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-5">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>concOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of Ca in pool</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-5">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>current</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Calcium Ion current, due to be converted to conc.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>currentFraction</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Fraction of total Ion current, that is carried by Ca2+.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>increase</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Any input current that increases the concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>decrease</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Any input current that decreases the concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>basal</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Synonym for assignment of basal conc.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-5">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-5">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="chanbase">ChanBase</h2> -<h4 id="value-fields-6">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-6">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-6">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-6">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-6">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="chemmesh">ChemMesh</h2> -<h4 id="value-fields-7">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numDimensions</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-7">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshStats</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-7">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>buildDefaultMesh</code></strong></td> -<td align="left"><code>double,unsigned int</code></td> -<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRequestMeshStats</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request from SimManager for mesh stats</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleNodeInfo</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-7">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>nodeMeshing</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-7">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="cinfo">Cinfo</h2> -<p><strong>Author</strong>: Upi Bhalla</p> -<p><strong>Description</strong>: Class information object.</p> -<h4 id="value-fields-8">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>docs</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Documentation</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>baseClass</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of base class</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-8">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-8">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-8">Shared message fields</h4> -<h4 id="lookup-fields-8">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="clock">Clock</h2> -<h4 id="value-fields-9">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>runTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Duration to run the simulation</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>currentTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current simulation time</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nsteps</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numTicks</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of clock ticks</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>currentStep</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Current simulation step</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dts</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Utility function returning the dt (timestep) of all ticks.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>isRunning</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Utility function to report if simulation is in progress.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-9">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>childTick</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Parent of Tick element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>finished</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Signal for completion of run</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ack</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Acknowledgement signal for receipt/completion of function.Goes back to Shell on master node</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-9">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>start</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sets off the simulation for the specified duration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>step</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Sets off the simulation for the specified # of steps</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stop</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Halts the simulation, with option to restart seamlessly</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setupTick</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Sets up a specific clock tick: args tick#, dt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Zeroes out all ticks, starts at t = 0</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-9">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>clockControl</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Controls all scheduling aspects of Clock, usually from Shell</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-9">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="compartment">Compartment</h2> -<p><strong>Author</strong>: Upi Bhalla</p> -<p><strong>Description</strong>: Compartment object, for branching neuron models.</p> -<h4 id="value-fields-10">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Cm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane capacitance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Em</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Resting membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Im</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current going through membrane</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inject</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current injection to deliver into compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value for membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Rm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane resistance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ra</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Axial resistance of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diameter</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diameter of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>length</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Length of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y coordinate of start of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x coordinate of end of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y coordinate of end of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z coordinate of end of compartment</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-10">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>axialOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxialOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-10">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>randInject</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cable</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'process' call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initProc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initReinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleChannel</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles conductance and Reversal potential arguments from Channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRaxial</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles Raxial info: arguments are Ra and Vm.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleAxial</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Axial information. Argument is just Vm.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-10">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>axial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>raxial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-10">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="cplxenzbase">CplxEnzBase</h2> -<p><strong>Author</strong>: Upi Bhalla</p> -<p><strong>Description</strong>:: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S ----> E + P</p> -<h4 id="value-fields-11">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward reaction from enz + sub to complex</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>k2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse reaction from complex to enz + sub</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant from complex to product + enz</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ratio</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ratio of k2/k3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concK1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-11">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toEnz</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toCplx</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-11">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplxDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of enz-sub complex</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-11">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enz</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enzyme pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplx</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enz-sub complex pool</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-11">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="cubemesh">CubeMesh</h2> -<h4 id="value-fields-12">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numDimensions</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>isToroid</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>preserveNumEntries</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X coord of one end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y coord of one end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z coord of one end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X coord of other end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y coord of other end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z coord of other end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dx</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X size for mesh</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y size for mesh</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dz</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z size for mesh</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nx</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of subdivisions in mesh in X</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ny</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of subdivisions in mesh in Y</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nz</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of subdivisions in mesh in Z</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dz</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshToSpace</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array in which each mesh entry stores spatial (cubic) index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>spaceToMesh</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>surface</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-12">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshStats</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-12">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>buildDefaultMesh</code></strong></td> -<td align="left"><code>double,unsigned int</code></td> -<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRequestMeshStats</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request from SimManager for mesh stats</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleNodeInfo</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-12">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>nodeMeshing</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-12">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="cylmesh">CylMesh</h2> -<h4 id="value-fields-13">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numDimensions</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x coord of one end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y coord of one end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z coord of one end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>r0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Radius of one end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x coord of other end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y coord of other end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z coord of other end</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>r1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Radius of other end</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>lambda</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength lambda on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute lambda as totLength/numEntries</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 lambda</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>totLength</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Total length of cylinder</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-13">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshStats</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-13">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>buildDefaultMesh</code></strong></td> -<td align="left"><code>double,unsigned int</code></td> -<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRequestMeshStats</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request from SimManager for mesh stats</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleNodeInfo</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-13">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>nodeMeshing</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-13">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="cylpanel">CylPanel</h2> -<h4 id="value-fields-14">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-14">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-14">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-14">Shared message fields</h4> -<h4 id="lookup-fields-14">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="diagonalmsg">DiagonalMsg</h2> -<h4 id="value-fields-15">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>stride</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-15">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-15">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-15">Shared message fields</h4> -<h4 id="lookup-fields-15">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="diffamp">DiffAmp</h2> -<h4 id="value-fields-16">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>gain</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>saturation</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output of the amplifier, i.e. gain * (plus - minus).</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-16">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current output level.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-16">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>gainIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message to control gain dynamically.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>plusIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>minusIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call, updates internal time stamp.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-16">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-16">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="diskpanel">DiskPanel</h2> -<h4 id="value-fields-17">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-17">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-17">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-17">Shared message fields</h4> -<h4 id="lookup-fields-17">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="enz">Enz</h2> -<h4 id="value-fields-18">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward reaction from enz + sub to complex</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>k2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse reaction from complex to enz + sub</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant from complex to product + enz</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ratio</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ratio of k2/k3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concK1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-18">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toEnz</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toCplx</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-18">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplxDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of enz-sub complex</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-18">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enz</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enzyme pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplx</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enz-sub complex pool</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-18">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="enzbase">EnzBase</h2> -<h4 id="value-fields-19">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-19">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-19">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-19">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-19">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="finfo">Finfo</h2> -<h4 id="value-fields-20">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of Finfo</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>docs</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Documentation for Finfo</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>type</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">RTTI type info for this Finfo</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>src</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Subsidiary SrcFinfos. Useful for SharedFinfos</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dest</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Subsidiary DestFinfos. Useful for SharedFinfos</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-20">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-20">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-20">Shared message fields</h4> -<h4 id="lookup-fields-20">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="funcbase">FuncBase</h2> -<h4 id="value-fields-21">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>result</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Outcome of function computation</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-21">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out sum on each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-21">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-21">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-21">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="funcpool">FuncPool</h2> -<h4 id="value-fields-22">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-22">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-22">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>increment</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>decrement</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input to control value of n_</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-22">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-22">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="ghk">GHK</h2> -<h4 id="value-fields-23">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane current</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal Potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>T</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Temperature of system</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>p</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Permeability of channel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Cin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Internal concentration</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Cout</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">External ion concentration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>valency</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Valence of ion</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-23">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Relay of membrane potential Vm.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">MembraneCurrent.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-23">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>addPermeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles permeability message coming in from channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>CinDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Alias for set_Cin</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>CoutDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Alias for set_Cout</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>addPermeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles permeability message coming in from channel</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-23">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message from channel to current Goldman-Hodgkin-Katz objectThis shared message connects to an HHChannel. The first entry is a MsgSrc which relays the Vm received from a compartment. The second entry is a MsgDest which receives channel conductance, and interprets it as permeability.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-23">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="geometry">Geometry</h2> -<h4 id="value-fields-24">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>epsilon</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">epsilon is the max deviation of surface-point from surface.I think it refers to when the molecule is stuck to the surface. Need to check with Steven.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighdist</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">neighdist is capture distance from one panel to another.When a molecule diffuses off one panel and is within neighdist of the other, it is captured by the second.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-24">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>returnSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Return size of compartment</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-24">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleSizeRequest</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles a request for size. Part of SharedMsg to ChemCompt.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-24">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>compt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to compartment(s) to specify geometry.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-24">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="group">Group</h2> -<h4 id="value-fields-25">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-25">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-25">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-25">Shared message fields</h4> -<h4 id="lookup-fields-25">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="gslintegrator">GslIntegrator</h2> -<h4 id="value-fields-26">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>isInitialized</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if the Stoich message has come in to set parms</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>method</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Numerical method to use.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>relativeAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Accuracy criterion</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>absoluteAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Another accuracy criterion</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-26">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-26">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stoich</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Handle data from Stoich</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-26">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-26">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="gslstoich">GslStoich</h2> -<h4 id="value-fields-27">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>isInitialized</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if the Stoich message has come in to set parms</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>method</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Numerical method to use.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>relativeAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Accuracy criterion</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>absoluteAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Another accuracy criterion</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>compartment</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">This is the Id of the compartment, which must be derived fromthe ChemMesh baseclass. The GslStoich needsthe ChemMesh Id only for diffusion, and one can pass in Id() instead if there is no diffusion, or just leave it unset.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-27">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-27">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>addJunction</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Add a junction between the current solver and the one whose Id is passed in.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dropJunction</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stoich</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Assign the StoichCore and ChemMesh Ids. The GslStoich needsthe StoichCore pointer in all cases, in order to perform allcalculations.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initProc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles init call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initReinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles initReinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-27">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for init and initReinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-27">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="gssastoich">GssaStoich</h2> -<p><strong>Author</strong>: Upinder S. Bhalla, 2008, 2011, NCBS</p> -<p><strong>Description</strong>: GssaStoich: Gillespie Stochastic Simulation Algorithm object.Closely based on the Stoich object and inherits its handling functions for constructing the matrix. Sets up stoichiometry matrix based calculations from a</p> -<p>wildcard path for the reaction system.Knows how to compute derivatives for most common things, also knows how to handle special cases where the object will have to do its own computation.Generates a stoichiometry matrix, which is useful for lots of other operations as well.</p> -<h4 id="value-fields-28">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>useOneWayReacs</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nVarPools</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of variable molecule pools in the reac system</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numMeshEntries</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of meshEntries in reac-diff system</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>estimatedDt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Path of reaction system to take over</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Path of reaction system to take over and solve</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>method</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Numerical method to use for the GssaStoich. The defaultand currently the only method is Gillespie1.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-28">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>plugin</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Sends out Stoich Id so that plugins can directly access fields and functions</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nodeDiffBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>poolsReactingAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacRollbacksAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reacRatesAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations <em>V</em> is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-28">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleReacRatesAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handlePoolsReactingAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleReacRollbacksAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinint call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-28">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>boundaryReacOut</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>boundaryReacIn</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-28">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hdf5datawriter">HDF5DataWriter</h2> -<p><strong>Author</strong>: Subhasis Ray</p> -<p><strong>Description</strong>: HDF5 file writer for saving data tables. It saves the tables connected to it via <code>requestData</code> field into an HDF5 file. The path of the table is maintained in the HDF5 file, with a HDF5 group for each element above the table.</p> -<p>Thus, if you have a table <code>/data/VmTable</code> in MOOSE, then it will be written as an HDF5 table called <code>VmTable</code> inside an HDF5 Group called <code>data</code>.</p> -<p>However Table inside Table is considered a pathological case and is not handled.</p> -<p>At every process call it writes the contents of the tables to the file and clears the table vectors. You can explicitly force writing of the data via the <code>flush</code> function.</p> -<h4 id="value-fields-29">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>filename</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of the file associated with this HDF5 writer object.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>isOpen</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if this object has an open file handle.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>mode</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-29">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestData</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Sends request for a field to target object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clear</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Send request to clear a Table vector.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-29">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>flush</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Write all buffer contents to file and clear the buffers.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>recvData</code></strong></td> -<td align="left"><code>bad</code></td> -<td align="left">Handles data sent back following request</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle process calls. Write data to file and clear all Table objects associated with this. Hence you want to keep it on a slow clock 1000 times or more slower than that for the tables.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Reinitialize the object. If the current file handle is valid, it tries to close that and open the file specified in current filename field.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-29">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-29">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hdf5writerbase">HDF5WriterBase</h2> -<p><strong>Author</strong>: Subhasis Ray</p> -<p><strong>Description</strong>: HDF5 file writer base class. This is not to be used directly. Instead, it should be subclassed to provide specific data writing functions. This class provides most basic properties like filename, file opening mode, file open status.</p> -<h4 id="value-fields-30">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>filename</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of the file associated with this HDF5 writer object.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>isOpen</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if this object has an open file handle.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>mode</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-30">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-30">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>flush</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Write all buffer contents to file and clear the buffers.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-30">Shared message fields</h4> -<h4 id="lookup-fields-30">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hhchannel">HHChannel</h2> -<h4 id="value-fields-31">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Xpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for X gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ypower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Y gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Zpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Z gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>instant</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>X</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for X gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>useConcentration</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Flag: when true, use concentration message rather than Vm tocontrol Z gate</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-31">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-31">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>concen</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Incoming message from Concen object to specific conc to usein the Z gate calculations</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>createGate</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Function to create specified gate.Argument: Gate type [X Y Z]</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-31">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td> -</tr> -<tr class="even"> -<td align="left"></td> -<td align="left"></td> -<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-31">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hhchannel2d">HHChannel2D</h2> -<h4 id="value-fields-32">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Xindex</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">String for setting X index.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Yindex</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">String for setting Y index.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Zindex</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">String for setting Z index.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Xpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for X gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ypower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Y gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Zpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Z gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>instant</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>X</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for X gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-32">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-32">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>concen</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Incoming message from Concen object to specific conc to useas the first concen variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concen2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Incoming message from Concen object to specific conc to useas the second concen variable</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-32">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td> -</tr> -<tr class="even"> -<td align="left"></td> -<td align="left"></td> -<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-32">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hhgate">HHGate</h2> -<h4 id="value-fields-33">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>alpha</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>beta</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tau</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mInfinity</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>min</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum range for lookup</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>max</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum range for lookup</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>divs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Divisions for lookup. Zero means to use linear interpolation</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tableA</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Table of A entries</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tableB</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Table of alpha + beta entries</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>useInterpolation</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: use linear interpolation if true, else direct lookup</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-33">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-33">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>setupAlpha</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setupTau</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tweakAlpha</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tweakTau</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>setupGate</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-33">Shared message fields</h4> -<h4 id="lookup-fields-33">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>A</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>B</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.</td> -</tr> -</tbody> -</table> -<h2 id="hhgate2d">HHGate2D</h2> -<h4 id="value-fields-34">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-34">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-34">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-34">Shared message fields</h4> -<h4 id="lookup-fields-34">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>A</code></strong></td> -<td align="left"><code>vector<double>,double</code></td> -<td align="left">lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>B</code></strong></td> -<td align="left"><code>vector<double>,double</code></td> -<td align="left">lookupB: Look up B gate value from two doubles in a vector.</td> -</tr> -</tbody> -</table> -<h2 id="hsolve">HSolve</h2> -<h4 id="value-fields-35">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>seed</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Use this field to specify path to a 'seed' compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>target</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The time-step for this solver.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>caAdvance</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vDiv</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Specifies number of divisions for lookup tables of voltage-sensitive channels.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>vMin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vMax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>caDiv</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Specifies number of divisions for lookup tables of calcium-sensitive channels.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>caMin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>caMax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-35">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-35">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'process' call: Solver advances by one time-step.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' call: Solver reads in model.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-35">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' and 'process' calls from a clock.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-35">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="hemispherepanel">HemispherePanel</h2> -<h4 id="value-fields-36">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-36">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-36">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-36">Shared message fields</h4> -<h4 id="lookup-fields-36">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="intfire">IntFire</h2> -<h4 id="value-fields-37">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSynapses</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of synapses on SynBase</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tau</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">charging time-course</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>thresh</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">firing threshold</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>refractoryPeriod</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum time between successive spikes</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-37">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>spike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out spike events</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-37">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-37">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-37">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="interpol2d">Interpol2D</h2> -<h4 id="value-fields-38">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xmin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xmax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xdivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dx</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increment on x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ymin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for y axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ymax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ydivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on y axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increment on y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tableVector2D</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Get the entire table.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-38">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>trig</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">respond to a request for a value lookup</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-38">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lookup</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Looks up table value based on indices v1 and v2, and sendsvalue back using the 'trig' message</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-38">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>lookupReturn2D</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-38">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>table</code></strong></td> -<td align="left"><code>vector<unsigned int>,double</code></td> -<td align="left">Lookup an entry on the table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>vector<double>,double</code></td> -<td align="left">Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.</td> -</tr> -</tbody> -</table> -<h2 id="izhikevichnrn">IzhikevichNrn</h2> -<h4 id="value-fields-39">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vmax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>c</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reset potential. Membrane potential is reset to c whenever it reaches Vmax.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>d</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Parameter d in Izhikevich model. Unit is V/s.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>a</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Parameter a in Izhikevich model. Unit is s^{-1}</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>b</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Parameter b in Izhikevich model. Unit is s^{-1}</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>u</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Parameter u in Izhikevich equation. Unit is V/s</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane potential, equivalent to v in Izhikevich equation.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Im</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Total current going through the membrane. Unit is A.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Rm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Hidden cefficient of input current term (I) in Izhikevich model. Defaults to 1e6 Ohm.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial membrane potential. Unit is V.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initU</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of u.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>alpha</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>beta</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>gamma</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-39">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>spike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out spike events</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-39">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Injection current into the neuron.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message to modify parameter c at runtime.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message to modify parameter d at runtime.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>bDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message to modify parameter b at runtime</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>aDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message modify parameter a at runtime.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-39">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-39">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="leakyiaf">LeakyIaF</h2> -<h4 id="value-fields-40">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Cm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane capacitance.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Rm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane resistance, inverse of leak-conductance.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Em</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Leak reversal potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Inital value of membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vreset</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reset potnetial after firing.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vthreshold</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">firing threshold</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>refractoryPeriod</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum time between successive spikes</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inject</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Injection current.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tSpike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Time of the last spike</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-40">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>spike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out spike events</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-40">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination for current input.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-40">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-40">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="mmenz">MMenz</h2> -<h4 id="value-fields-41">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-41">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-41">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-41">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-41">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="markovchannel">MarkovChannel</h2> -<h4 id="value-fields-42">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ligandconc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ligand concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane voltage.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numstates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">The number of states that the channel can occupy.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numopenstates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">The number of states which are open/conducting.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>state</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">This is a row vector that contains the probabilities of finding the channel in each state.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initialstate</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>labels</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Labels for each state.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>gbar</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">A row vector containing the conductance associated with each of the open/conducting states.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-42">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-42">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleligandconc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Deals with incoming messages containing information of ligand concentration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handlestate</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Deals with incoming message from MarkovSolver object containing state information of the channel.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-42">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-42">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="markovgslsolver">MarkovGslSolver</h2> -<h4 id="value-fields-43">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>isInitialized</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if the message has come in to set solver parameters.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>method</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Numerical method to use.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>relativeAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Accuracy criterion</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>absoluteAccuracy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Another accuracy criterion</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>internalDt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">internal timestep to use.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-43">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stateOut</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends updated state to the MarkovChannel class.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-43">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Initialize solver parameters.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleQ</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-43">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-43">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="markovratetable">MarkovRateTable</h2> -<h4 id="value-fields-44">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane voltage.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ligandconc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ligand concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Q</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Instantaneous rate matrix.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Dimension of the families of lookup tables. Is always equal to the number of states in the model.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-44">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>instratesOut</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Sends out instantaneous rate information of varying transition rates at each time step.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-44">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing voltage information.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Initialization of the class. Allocates memory for all the tables.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleLigandConc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing ligand concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>set1d</code></strong></td> -<td align="left"><code>unsigned int,unsigned int,Id,unsigned int</code></td> -<td align="left">Setting up of 1D lookup table for the (i,j)'th rate.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>set2d</code></strong></td> -<td align="left"><code>unsigned int,unsigned int,Id</code></td> -<td align="left">Setting up of 2D lookup table for the (i,j)'th rate.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setconst</code></strong></td> -<td align="left"><code>unsigned int,unsigned int,double</code></td> -<td align="left">Setting a constant value for the (i,j)'th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-44">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-44">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="markovsolver">MarkovSolver</h2> -<h4 id="value-fields-45">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Q</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Instantaneous rate matrix.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>state</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Current state of the channel.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initialstate</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Initial state of the channel.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xmin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xmax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xdivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>invdx</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reciprocal of increment on x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ymin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ymax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for y axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ydivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>invdy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reciprocal of increment on y axis of lookup table</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-45">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stateOut</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends updated state to the MarkovChannel class.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-45">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing voltage information.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ligandconc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing ligand concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>Id,double</code></td> -<td align="left">Setups the table of matrix exponentials associated with the solver object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-45">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-45">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="markovsolverbase">MarkovSolverBase</h2> -<h4 id="value-fields-46">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Q</code></strong></td> -<td align="left"><code>vector< vector<double> ></code></td> -<td align="left">Instantaneous rate matrix.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>state</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Current state of the channel.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initialstate</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Initial state of the channel.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xmin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xmax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xdivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on x axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>invdx</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reciprocal of increment on x axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ymin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value for y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ymax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value for y axis of lookup table</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ydivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of divisions on y axis of lookup table</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>invdy</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reciprocal of increment on y axis of lookup table</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-46">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stateOut</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends updated state to the MarkovChannel class.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-46">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing voltage information.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ligandconc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles incoming message containing ligand concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>Id,double</code></td> -<td align="left">Setups the table of matrix exponentials associated with the solver object.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-46">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-46">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="mathfunc">MathFunc</h2> -<h4 id="value-fields-47">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>mathML</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">MathML version of expression to compute</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>function</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">function is for functions of form f(x, y) = x + y</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>result</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">result value</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-47">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out result of computation</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-47">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>arg1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle arg1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>arg2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle arg2</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>arg3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle arg3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>arg4</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle arg4</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-47">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-47">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="mdouble">Mdouble</h2> -<h4 id="value-fields-48">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Access function for entire Mdouble object.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>value</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Access function for value field of Mdouble object,which happens also to be the entire contents of the object.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-48">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-48">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-48">Shared message fields</h4> -<h4 id="lookup-fields-48">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="meshentry">MeshEntry</h2> -<h4 id="value-fields-49">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Volume of this MeshEntry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>dimensions</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">number of dimensions of this MeshEntry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshType</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Coordinates</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Coordinates that define current MeshEntry. Depend on MeshType.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>neighbors</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Indices of other MeshEntries that this one connects to</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>DiffusionArea</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Diffusion area for geometry of interface</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>DiffusionScaling</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Diffusion scaling for geometry of interface</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-49">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remeshReacs</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-49">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-49">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for updating mesh volumes and subdivisions,typically controls pool sizes</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-49">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="mgblock">MgBlock</h2> -<h4 id="value-fields-50">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>KMg_A</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">1/eta</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>KMg_B</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">1/gamma</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>CMg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">[Mg] in mM</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current through MgBlock</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Zk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Charge on ion</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-50">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-50">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>origChannel</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left"></td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-50">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-50">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="msg">Msg</h2> -<h4 id="value-fields-51">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-51">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-51">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-51">Shared message fields</h4> -<h4 id="lookup-fields-51">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="mstring">Mstring</h2> -<h4 id="value-fields-52">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Access function for entire Mstring object.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>value</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Access function for value field of Mstring object,which happens also to be the entire contents of the object.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-52">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-52">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-52">Shared message fields</h4> -<h4 id="lookup-fields-52">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="nmdachan">NMDAChan</h2> -<p><strong>Author</strong>: Subhasis Ray, 2010, NCBS</p> -<p><strong>Description</strong>: NMDAChan: Extracellular [Mg2+] dependent NMDA channel.This channel has four states as described by Jahr and Stevens (J. Neurosci. 1990, 10(9)) This implementation is based on equation 4(a) in that article. The channel conductance is defined as : k * g(V, [Mg2+]o) * S(t) where k is a scaling constant. S(t) is the legand gated component of the conductance. It rises linearly for t = tau2. Then decays exponentially with time constant t = tau1. g is a function of voltage and the extracellular [Mg2+] defined as: 1 / { 1 + (a1 + a2) * (a1 * B1 + a2 * B2)/ [A * a1 * (b1 + B1) + A * a2 * (b2 + B2)]}</p> -<p>a1 = 1e3 * exp( - c0 * V - c1) s^{-1}, c0 = 16.0 / V, c1 = 2.91</p> -<p>a2 = 1e-3 * [Mg2+] * exp( -c2 * V - c3) mM^{-1} s, c2 = 45.0 / V, c3 = 6.97</p> -<p>b1 = 1e3 * exp(c4 * V + c5) s^{-1}, c4 = 9.0 / V, c5 = 1.22</p> -<p>b2 = 1e3 * exp(c6 * V + c7) s^{-1}, c6 = 17.0 / V, c7 = 0.96</p> -<p>A = 1e3 * exp(-c8) s^{-1}, c8 = 2.847</p> -<p>B1 = 1e3 * exp(-c9) s^{-1}, c9 = 0.693 s^{-1}</p> -<p>B2 = 1e3 * exp(-c10) s^{-1}, c10 = 3.101.</p> -<p>The behaviour of S(t) is as follows:</p> -<p>If a spike arrives, then the slope of the linear rise of S(t) is incremented by weight / tau2.</p> -<p>After tau2 time, this component is removed from the slope (reduced by weight/tau) and added over to the rate of decay of S(t).</p> -<h4 id="value-fields-53">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSynapses</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of synapses on SynBase</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tau1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Decay time constant for the synaptic conductance, tau1 >= tau2.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tau2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Rise time constant for the synaptic conductance, tau1 >= tau2.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>normalizeWeights</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>unblocked</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>MgConc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">External Mg2+ concentration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>unblocked</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>saturation</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Upper limit on the NMDA conductance.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-53">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-53">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>activation</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sometimes we want to continuously activate the channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>modulator</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Modulate channel response</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>MgConcDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Update [Mg2+] from other sources at every time step.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-53">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-53">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>c</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Transition parameters c0 to c10 in the Mg2+ dependentstate transitions.</td> -</tr> -</tbody> -</table> -<h2 id="nernst">Nernst</h2> -<h4 id="value-fields-54">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>E</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Computed reversal potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Temperature</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Temperature of cell</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>valence</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Valence of ion in Nernst calculation</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Cin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Internal conc of ion</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Cout</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">External conc of ion</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>scale</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Voltage scale factor</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-54">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Eout</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Computed reversal potential</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-54">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ci</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Set internal conc of ion, and immediately send out the updated E</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>co</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Set external conc of ion, and immediately send out the updated E</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-54">Shared message fields</h4> -<h4 id="lookup-fields-54">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="neuromesh">NeuroMesh</h2> -<h4 id="value-fields-55">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numDimensions</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cell</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>subTree</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>skipSpines</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: when skipSpines is true, the traversal does not includeany compartment with the string 'spine' or 'neck' in its name,and also then skips compartments below this skipped one.Allows to set up separate mesh for spines, based on the same cell model.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSegments</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of cylindrical/spherical segments in model</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numDiffCompts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of diffusive compartments in model</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>diffLength</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>geometryPolicy</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don't worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-55">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshStats</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-55">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>buildDefaultMesh</code></strong></td> -<td align="left"><code>double,unsigned int</code></td> -<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRequestMeshStats</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request from SimManager for mesh stats</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleNodeInfo</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setCellPortion</code></strong></td> -<td align="left"><code>Id,vector<Id></code></td> -<td align="left">Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the vectorof Ids to consider in meshing up the subpart.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-55">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>nodeMeshing</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-55">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="neuron">Neuron</h2> -<p><strong>Author</strong>: C H Chaitanya</p> -<p><strong>Description</strong>: Neuron - A compartment container</p> -<h4 id="value-fields-56">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-56">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-56">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-56">Shared message fields</h4> -<h4 id="lookup-fields-56">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="neutral">Neutral</h2> -<p><strong>Author</strong>: Upinder S. Bhalla, 2007, NCBS</p> -<p><strong>Description</strong>: Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.</p> -<h4 id="value-fields-57">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-57">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-57">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-57">Shared message fields</h4> -<h4 id="lookup-fields-57">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="onetoallmsg">OneToAllMsg</h2> -<h4 id="value-fields-58">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>i1</code></strong></td> -<td align="left"><code>DataId</code></td> -<td align="left">DataId of source Element.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-58">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-58">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-58">Shared message fields</h4> -<h4 id="lookup-fields-58">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="onetoonemsg">OneToOneMsg</h2> -<h4 id="value-fields-59">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-59">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-59">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-59">Shared message fields</h4> -<h4 id="lookup-fields-59">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="pidcontroller">PIDController</h2> -<h4 id="value-fields-60">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>gain</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>saturation</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Bound on the permissible range of output. Defaults to maximum double value.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>command</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sensed</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sensed (measured) value. This is commonly known as process variable(PV) in control theory.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tauI</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tauD</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )</td> -</tr> -<tr class="even"> -<td align="left"></td> -<td align="left"></td> -<td align="left">Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>error</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The error term, which is the difference between command and sensed value.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>integral</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>derivative</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The derivative term. This is (error - e_previous)/dt.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e_previous</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The error term for previous step.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-60">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-60">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>commandIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Command (desired value) input. This is known as setpoint (SP) in control theory.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>sensedIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>gainDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Destination message to control the PIDController gain dynamically.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle process calls.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Reinitialize the object.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-60">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-60">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="panel">Panel</h2> -<h4 id="value-fields-61">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-61">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-61">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-61">Shared message fields</h4> -<h4 id="lookup-fields-61">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="pool">Pool</h2> -<h4 id="value-fields-62">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-62">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-62">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>increment</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>decrement</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-62">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-62">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="poolbase">PoolBase</h2> -<h4 id="value-fields-63">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-63">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-63">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-63">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-63">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="port">Port</h2> -<h4 id="value-fields-64">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>scaleOutRate</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Scaling factor for outgoing rates. Applies to the RateTermscontrolled by this port. Represents a diffusion related term,or the permeability of the port</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>inStart</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Start index to S_ vector into which incoming molecules should add.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inEnd</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">End index to S_ vector into which incoming molecules should add.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outStart</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Start index to S_ vector from where outgoing molecules come.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>outEnd</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">End index to S_ vector from where outgoing molecules come.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-64">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>availableMolsAtPort</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">Sends out the full set of molecule Ids that are available for data transfer</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>efflux</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Molecule #s going out</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>matchedMolsAtPort</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">Sends out the set of molecule Ids that match between both ports</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>efflux</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Molecule #s going out</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-64">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMatchedMolsAtPort</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Handles list of matched molecules worked out by the other port</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>influx</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Molecule #s coming back in</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleAvailableMolsAtPort</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Handles list of all species that the other port cares about</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>influx</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Molecule #s coming back in</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-64">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>port1</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for port. This one initiates the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>port2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for port. This one responds to the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-64">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="pulsegen">PulseGen</h2> -<h4 id="value-fields-65">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output amplitude</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>baseLevel</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Basal level of the stimulus</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>firstLevel</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Amplitude of the first pulse in a sequence</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>firstWidth</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Width of the first pulse in a sequence</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>firstDelay</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Delay to start of the first pulse in a sequence</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>secondLevel</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Amplitude of the second pulse in a sequence</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>secondWidth</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Width of the second pulse in a sequence</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>secondDelay</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Delay to start of of the second pulse in a sequence</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>count</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of pulses in a sequence</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>trigMode</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Trigger mode for pulses in the sequence.</td> -</tr> -<tr class="odd"> -<td align="left"></td> -<td align="left"></td> -<td align="left">0 : free-running mode where it keeps looping its output</td> -</tr> -<tr class="even"> -<td align="left"></td> -<td align="left"></td> -<td align="left">1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses)</td> -</tr> -<tr class="odd"> -<td align="left"></td> -<td align="left"></td> -<td align="left">2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-65">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current output level.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-65">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handle incoming input that determines gating/triggering onset.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>levelIn</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Handle level value coming from other objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>widthIn</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Handle width value coming from other objects</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>delayIn</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Handle delay value coming from other objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call, updates internal time stamp.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-65">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-65">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>level</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Level of the pulse at specified index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>width</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Width of the pulse at specified index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>delay</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Delay of the pulse at specified index</td> -</tr> -</tbody> -</table> -<h2 id="rc">RC</h2> -<h4 id="value-fields-66">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>V0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of 'state'</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>R</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Series resistance of the RC circuit.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>C</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Parallel capacitance of the RC circuit.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>state</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output value of the RC circuit. This is the voltage across the capacitor.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inject</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Input value to the RC circuit.This is handled as an input current to the circuit.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-66">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current output level.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-66">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectIn</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Receives input to the RC circuit. All incoming messages are summed up to give the total input current.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle reinitialization</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-66">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-66">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="reac">Reac</h2> -<h4 id="value-fields-67">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in # units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in # units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in concentration units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in concentration units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates of reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numProducts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of products of reaction</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-67">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-67">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-67">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-67">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="reacbase">ReacBase</h2> -<h4 id="value-fields-68">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in # units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in # units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in concentration units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in concentration units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates of reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numProducts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of products of reaction</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-68">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-68">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-68">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-68">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="rectpanel">RectPanel</h2> -<h4 id="value-fields-69">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-69">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-69">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-69">Shared message fields</h4> -<h4 id="lookup-fields-69">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="reducemsg">ReduceMsg</h2> -<h4 id="value-fields-70">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>i1</code></strong></td> -<td align="left"><code>DataId</code></td> -<td align="left">DataId of source Element.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-70">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-70">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-70">Shared message fields</h4> -<h4 id="lookup-fields-70">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="shell">Shell</h2> -<h4 id="value-fields-71">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-71">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reduceArraySize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Look up maximum value of an index, here ragged array size,across many nodes, and assign uniformly to all nodes. Normallyfollowed by an operation to assign the size to the object thatwas resized.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestCreate</code></strong></td> -<td align="left"><code>string,Id,Id,string,vector<int></code></td> -<td align="left">requestCreate( class, parent, newElm, name, dimensions ): creates a new Element on all nodes with the specified Id. Initiates a callback to indicate completion of operation. Goes to all nodes including self.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestDelete</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">requestDelete( doomedElement ):Deletes specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestAddMsg</code></strong></td> -<td align="left"><code>string,unsigned int,ObjId,string,ObjId,string</code></td> -<td align="left">requestAddMsg( type, src, srcField, dest, destField );Creates specified Msg between specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestQuit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">requestQuit():Emerges from the inner loop, and wraps up. No return value.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>move</code></strong></td> -<td align="left"><code>Id,Id</code></td> -<td align="left">move( origId, newParent);Moves origId to become a child of newParent</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>copy</code></strong></td> -<td align="left"><code>vector<Id>,string,unsigned int,bool,bool</code></td> -<td align="left">copy( origId, newParent, numRepeats, toGlobal, copyExtMsg );Copies origId to become a child of newParent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>useClock</code></strong></td> -<td align="left"><code>string,string,unsigned int</code></td> -<td align="left">useClock( path, field, tick# );Specifies which clock tick to use for all elements in Path.The 'field' is typically process, but some cases need to sendupdates to the 'init' field.Tick # specifies which tick to be attached to the objects.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sync</code></strong></td> -<td align="left"><code>Id,unsigned int</code></td> -<td align="left">sync( ElementId, FuncId );Synchronizes Element data indexing across all nodes.Used when distributed ops like message setup might set updifferent #s of data entries on Elements on different nodes.The ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestReMesh</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">requestReMesh( meshId );Chops up specified mesh.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSetParserIdleFlag</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">SetParserIdleFlag( bool isParserIdle );When True, the main ProcessLoop waits a little each cycleso as to avoid pounding on the CPU.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ack</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">ack( unsigned int node#, unsigned int status ):Acknowledges receipt and completion of a command on a worker node.Goes back only to master node.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestStart</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">requestStart( runtime ):Starts a simulation. Goes to all nodes including self.Initiates a callback to indicate completion of run.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestStep</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">requestStep():Advances a simulation for the specified # of steps.Goes to all nodes including self.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestStop</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">requestStop():Gently stops a simulation after completing current ops.After this op it is save to do 'start' again, and it willresume where it left offGoes to all nodes including self.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestSetupTick</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">requestSetupTick():Asks the Clock to coordinate the assignment of a specificclock tick. Args: Tick#, dt.Goes to all nodes including self.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestReinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">requestReinit():Reinits a simulation: sets to time 0.If simulation is running it stops it first.Goes to all nodes including self.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-71">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>receiveGet</code></strong></td> -<td align="left"><code>bad</code></td> -<td align="left">receiveGet( Uint node#, Uint status, PrepackedBuffer data )Function on master shell that handles the value relayed from worker.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setclock</code></strong></td> -<td align="left"><code>unsigned int,double,bool</code></td> -<td align="left">Assigns clock ticks. Args: tick#, dt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleAck</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Keeps track of # of acks to a blocking shell command. Arg: Source node num.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>create</code></strong></td> -<td align="left"><code>string,Id,Id,string,vector<int></code></td> -<td align="left">create( class, parent, newElm, name, dimensions )</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>delete</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Destroys Element, all its messages, and all its children. Args: Id</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleAddMsg</code></strong></td> -<td align="left"><code>string,unsigned int,ObjId,string,ObjId,string</code></td> -<td align="left">Makes a msg</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleQuit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Stops simulation running and quits the simulator</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>move</code></strong></td> -<td align="left"><code>Id,Id</code></td> -<td align="left">handleMove( Id orig, Id newParent ): moves an Element to a new parent</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleCopy</code></strong></td> -<td align="left"><code>vector<Id>,string,unsigned int,bool,bool</code></td> -<td align="left">handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleUseClock</code></strong></td> -<td align="left"><code>string,string,unsigned int</code></td> -<td align="left">Deals with assignment of path to a given clock.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleSync</code></strong></td> -<td align="left"><code>Id,unsigned int</code></td> -<td align="left">handleSync( Id Element): Synchronizes DataHandler indexing across nodesThe ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleReMesh</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">handleReMesh( Id BaseMesh): Deals with outcome of resizing the meshing in a cellularcompartment (the ChemMesh class). The mesh change has topropagate down to the molecules and reactions managed by this.Mesh. The ElementId is the mesh being synchronized.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleSetParserIdleFlag</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">handleSetParserIdleFlag( bool isParserIdle ): When True, tells the ProcessLoop to wait as the Parser is idle.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleAck</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Keeps track of # of acks to a blocking shell command. Arg: Source node num.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-71">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>master</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Issues commands from master shell to worker shells located on different nodes. Also handles acknowledgements from them.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>worker</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles commands arriving from master shell on node 0.Sends out acknowledgements from them.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clockControl</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Controls the system Clock</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-71">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="simmanager">SimManager</h2> -<h4 id="value-fields-72">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>syncTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">SyncTime is the interval between synchronizing solvers5 msec is a typical value</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>autoPlot</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">When the autoPlot flag is true, the simManager guesses whichplots are of interest, and builds them.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>plotDt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">plotDt is the timestep for plotting variables. As most will bechemical, a default of 1 sec is reasonable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>runTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">runTime is the requested duration of the simulation that is stored in some kinds of model definition files.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>method</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">method is the numerical method used for the calculations.This will set up or even replace the solver with one ableto use the specified method. Currently works only with two solvers: GSL and GSSA.The GSL solver has a variety of ODE methods, by defaultRunge-Kutta-Fehlberg.The GSSA solver currently uses the Gillespie StochasticSystems Algorithm, somewhat optimized over the originalmethod.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>version</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Numerical version number. Used by kkit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>modelFamily</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Family classification of model: <em>kinetic, and </em>neuron are the options so far. In due course expect to see thingslike detailedNetwork, intFireNetwork, sigNeur and so on.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-72">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestMeshStats</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Asks for basic stats for mesh:Total # of entries, and a vector of unique volumes of voxels</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nodeInfo</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Sends out # of nodes to use for meshing, and # of threads to use on each node, to the ChemMesh. These numbers sometimesdiffer from the total # of nodes and threads, because the SimManager may have other portions of the model to allocate.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-72">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>build</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Sets up model, with the specified method. The method may beempty if the intention is that methods be set up through hints in the ChemMesh compartments.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>makeStandardElements</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Sets up the usual infrastructure for a model, with theChemMesh, Stoich, solver and suitable messaging.The argument is the MeshClass to use.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>,vector<unsigned int></code></td> -<td align="left">Handles message from ChemMesh that defines howmeshEntries communicate between nodes.First arg is oldvol, next is list of other nodes, third arg is list number ofmeshEntries to be transferred for each of these nodes, fourth arg is catenated list of meshEntries indices onmy node going to each of the other connected nodes, andlast arg is matching list of meshEntries on other nodes</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>meshStats</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Basic statistics for mesh: Total # of entries, and a vectorof unique volumes of voxels</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-72">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>nodeMeshing</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to ChemMesh to coordinate meshing with paralleldecomposition and with the Stoich</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-72">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="singlemsg">SingleMsg</h2> -<h4 id="value-fields-73">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>i1</code></strong></td> -<td align="left"><code>DataId</code></td> -<td align="left">Index of source object.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>i2</code></strong></td> -<td align="left"><code>DataId</code></td> -<td align="left">Index of dest object.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-73">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-73">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-73">Shared message fields</h4> -<h4 id="lookup-fields-73">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="solverjunction">SolverJunction</h2> -<h4 id="value-fields-74">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numReacs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of cross-compartment reactions on this Junction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numDiffMols</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of molecule species diffusing across this Junction</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numMeshEntries</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of voxels (mesh entries) handled by Junction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>otherCompartment</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of compartment on other side of this Junction. Readily obtained by message traversal, just a utility field.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-74">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>junctionPoolNum</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends out vector of all mol #s needed to compute junction rates.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>junctionPoolDelta</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends out vector of all mol # changes going across junction.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>junctionPoolNum</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Sends out vector of all mol #s needed to compute junction rates.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-74">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleJunctionPoolNum</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleJunctionPoolNum</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleJunctionPoolDelta</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">Handles vector of doubles with pool num changes that arrive at the Junction, by redirecting up to parent StoichPools object</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-74">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>symJunction</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Symmetric shared message between SolverJunctions to handle cross-solver reactions and diffusion. This variant sends only pool mol#s, and is symmetric.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>masterJunction</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the change in pool #, of abutting voxels, and receives the pool# of the same abutting voxels. Thus it operates on the solver that is doing the diffusion calculations. This will typically be the solver that operates at a finer level of detail. The order of detail is Smoldyn > Gillespie > deterministic. For two identical solvers we would typically have one with the finer grid size become the master Junction.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>followerJunction</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the pool #, of its boundary voxels, and receives back changes in the pool# of the same boundary voxels voxels. Thus it operates on the solver that is just tracking the diffusion calculations that the other (master) solver is doing</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-74">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="sparsemsg">SparseMsg</h2> -<h4 id="value-fields-75">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>e1</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>e2</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Id of source Element.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>srcFieldsOnE2</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>destFieldsOnE1</code></strong></td> -<td align="left"><code>vector<string></code></td> -<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numRows</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of rows in matrix.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numColumns</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of columns in matrix.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numEntries</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Entries in matrix.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>probability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">connection probability for random connectivity.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>seed</code></strong></td> -<td align="left"><code>long</code></td> -<td align="left">Random number seed for generating probabilistic connectivity.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-75">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-75">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>setRandomConnectivity</code></strong></td> -<td align="left"><code>double,long</code></td> -<td align="left">Assigns connectivity with specified probability and seed</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>setEntry</code></strong></td> -<td align="left"><code>unsigned int,unsigned int,unsigned int</code></td> -<td align="left">Assigns single row,column value</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>unsetEntry</code></strong></td> -<td align="left"><code>unsigned int,unsigned int</code></td> -<td align="left">Clears single row,column entry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clear</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Clears out the entire matrix</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>transpose</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Transposes the sparse matrix</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-75">Shared message fields</h4> -<h4 id="lookup-fields-75">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="species">Species</h2> -<h4 id="value-fields-76">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>molWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Molecular weight of species</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-76">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sendMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">returns molWt.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-76">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWtRequest</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle requests for molWt.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-76">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>pool</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to pools of this Species type</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-76">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="spherepanel">SpherePanel</h2> -<h4 id="value-fields-77">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-77">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-77">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-77">Shared message fields</h4> -<h4 id="lookup-fields-77">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="spikegen">SpikeGen</h2> -<h4 id="value-fields-78">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>threshold</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Spiking threshold, must cross it going up</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>refractT</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Refractory Time.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>abs_refract</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Absolute refractory time. Synonym for refractT.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>hasFired</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">True if SpikeGen has just fired</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>edgeTriggered</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-78">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>event</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out a trigger for an event.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-78">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-78">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-78">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="stats">Stats</h2> -<h4 id="value-fields-79">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>mean</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Mean of all sampled values.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sdev</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Standard Deviation of all sampled values.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>sum</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sum of all sampled values.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>num</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of all sampled values.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-79">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reduce</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Execute statistics reduction operation on all targets andplace results in this object</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-79">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>trig</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Triggers Reduction operation.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-79">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-79">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="stimulustable">StimulusTable</h2> -<h4 id="value-fields-80">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vec</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">vector with all table entries</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputValue</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output value holding current table entry or output of a calculation</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>startTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>stopTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loopTime</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>stepSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>stepPosition</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>doLoop</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-80">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out tabulated data according to lookup parameters.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-80">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>linearTransform</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Linearly scales and offsets data. Scale first, then offset.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>plainPlot</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadCSV</code></strong></td> -<td align="left"><code>string,int,int,char</code></td> -<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>loadXplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadXplotRange</code></strong></td> -<td align="left"><code>string,string,unsigned int,unsigned int</code></td> -<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>compareXplot</code></strong></td> -<td align="left"><code>string,string,string</code></td> -<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>compareVec</code></strong></td> -<td align="left"><code>vector<double>,string</code></td> -<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clearVec</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request to clear the data vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call, updates internal time stamp.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-80">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-80">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Value of table at specified index</td> -</tr> -</tbody> -</table> -<h2 id="stoich">Stoich</h2> -<h4 id="value-fields-81">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>useOneWayReacs</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nVarPools</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of variable molecule pools in the reac system</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numMeshEntries</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of meshEntries in reac-diff system</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>estimatedDt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Path of reaction system to take over</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-81">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>plugin</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Sends out Stoich Id so that plugins can directly access fields and functions</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nodeDiffBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>poolsReactingAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacRollbacksAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reacRatesAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations <em>V</em> is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-81">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>meshSplit</code></strong></td> -<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td> -<td align="left">Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleReacRatesAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handlePoolsReactingAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleReacRollbacksAcrossBoundary</code></strong></td> -<td align="left"><code>unsigned int,vector<double></code></td> -<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-81">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>boundaryReacOut</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>boundaryReacIn</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-81">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="stoichcore">StoichCore</h2> -<h4 id="value-fields-82">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>useOneWayReacs</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nVarPools</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of variable molecule pools in the reac system</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>estimatedDt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Path of reaction system to take over</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-82">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-82">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-82">Shared message fields</h4> -<h4 id="lookup-fields-82">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="stoichpools">StoichPools</h2> -<p><strong>Author</strong>: Upinder S. Bhalla, 2012, NCBS</p> -<p><strong>Description</strong>: Pure virtual base class for handling reaction pools. GslStoich is derived from this.</p> -<h4 id="value-fields-83">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-83">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-83">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>addJunction</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Add a junction between the current solver and the one whose Id is passed in.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dropJunction</code></strong></td> -<td align="left"><code>Id</code></td> -<td align="left">Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-83">Shared message fields</h4> -<h4 id="lookup-fields-83">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="sumfunc">SumFunc</h2> -<p><strong>Author</strong>: Upi Bhalla</p> -<p><strong>Description</strong>: SumFunc object. Adds up all inputs</p> -<h4 id="value-fields-84">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>result</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Outcome of function computation</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-84">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out sum on each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-84">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-84">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-84">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="surface">Surface</h2> -<h4 id="value-fields-85">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>volume</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">This is something I'll need to write a function to compute.Perhaps have an update routine as it may be hard to compute but is needed often by the molecules.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-85">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>absorb</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">these help the system define non-standard operations for what a molecule does when it hits a surface.The default is reflect.As a molecule may interact with multiple surfaces, it isn't enough to confer a property on the molecule itself. We have to use messages. Perhaps we don't need these, but instead put entities on the surface which the molecule interacts with if it doesn't do the basic reflect operation.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>transmit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Surface lets molecules through</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>jump</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">dunno</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>mixture</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">dunno</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>surface</code></strong></td> -<td align="left"><code>double,double,double</code></td> -<td align="left">Connects up to a compartment, either as interior or exterior Args are volume, area, perimeter</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-85">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-85">Shared message fields</h4> -<h4 id="lookup-fields-85">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="symcompartment">SymCompartment</h2> -<h4 id="value-fields-86">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Cm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane capacitance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Em</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Resting membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Im</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current going through membrane</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inject</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current injection to deliver into compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value for membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Rm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane resistance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ra</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Axial resistance of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diameter</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diameter of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>length</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Length of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y coordinate of start of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x coordinate of end of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y coordinate of end of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z coordinate of end of compartment</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-86">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>axialOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxialOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>raxialOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Ra and Vm on each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sumRaxialOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Ra</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestSumAxial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out request for Ra.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxialOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Ra and Vm on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>sumRaxialOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Ra</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSumAxial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out request for Ra.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Raxial2Out</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Ra and Vm</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sumRaxial2Out</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Ra</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestSumAxial2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out request for Ra.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Raxial2Out</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Ra and Vm</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>sumRaxial2Out</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Ra</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSumAxial2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out request for Ra.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Raxial2Out</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Ra and Vm</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sumRaxial2Out</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Ra</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestSumAxial2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Sends out request for Ra.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-86">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>randInject</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cable</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'process' call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initProc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initReinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleChannel</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles conductance and Reversal potential arguments from Channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRaxial</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles Raxial info: arguments are Ra and Vm.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleAxial</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Axial information. Argument is just Vm.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>raxialSym</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Expects Ra and Vm from other compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>sumRaxial</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Expects Ra from other compartment.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleSumRaxialRequest</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle request to send back Ra to originating compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-86">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>axial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>raxial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxial1</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial shared message between symmetric compartments.It goes from the tail of the current compartment to one closer to the soma.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>CONNECTTAIL</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial shared message between symmetric compartments.It is an alias for raxial1.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxial2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial2 shared message between symmetric compartments.It goes from the head of the current compartment to a compartment further away from the soma</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>CONNECTHEAD</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.It goes from the current compartment to one further from the soma</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>CONNECTCROSS</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.Conceptually, this goes from the tail of the current compartment to the tail of a sibling compartment. However,this works out to the same as CONNECTHEAD in terms of equivalentcircuit.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-86">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="synbase">SynBase</h2> -<h4 id="value-fields-87">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSynapses</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of synapses on SynBase</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-87">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-87">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-87">Shared message fields</h4> -<h4 id="lookup-fields-87">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="synchan">SynChan</h2> -<h4 id="value-fields-88">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSynapses</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of synapses on SynBase</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tau1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Decay time constant for the synaptic conductance, tau1 >= tau2.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>tau2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Rise time constant for the synaptic conductance, tau1 >= tau2.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>normalizeWeights</code></strong></td> -<td align="left"><code>bool</code></td> -<td align="left">Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-88">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-88">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>activation</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sometimes we want to continuously activate the channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>modulator</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Modulate channel response</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-88">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-88">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="synchanbase">SynChanBase</h2> -<h4 id="value-fields-89">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSynapses</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of synapses on SynBase</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-89">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-89">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-89">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-89">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="synapse">Synapse</h2> -<h4 id="value-fields-90">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>weight</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Synaptic weight</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>delay</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Axonal propagation delay to this synapse</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-90">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-90">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>addSpike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles arriving spike messages, by redirecting up to parent SynBase object</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-90">Shared message fields</h4> -<h4 id="lookup-fields-90">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="table">Table</h2> -<h4 id="value-fields-91">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vec</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">vector with all table entries</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputValue</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output value holding current table entry or output of a calculation</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>threshold</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">threshold used when Table acts as a buffer for spikes</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-91">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestData</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Sends request for a field to target object</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-91">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>linearTransform</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Linearly scales and offsets data. Scale first, then offset.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>plainPlot</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadCSV</code></strong></td> -<td align="left"><code>string,int,int,char</code></td> -<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>loadXplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadXplotRange</code></strong></td> -<td align="left"><code>string,string,unsigned int,unsigned int</code></td> -<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>compareXplot</code></strong></td> -<td align="left"><code>string,string,string</code></td> -<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>compareVec</code></strong></td> -<td align="left"><code>vector<double>,string</code></td> -<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clearVec</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request to clear the data vector</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Fills data into the Table.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>spike</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Fills spike timings into the Table. Signal has to exceed thresh</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>recvData</code></strong></td> -<td align="left"><code>bad</code></td> -<td align="left">Handles data sent back following request</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call, updates internal time stamp.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-91">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-91">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Value of table at specified index</td> -</tr> -</tbody> -</table> -<h2 id="tablebase">TableBase</h2> -<h4 id="value-fields-92">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>vec</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">vector with all table entries</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>outputValue</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Output value holding current table entry or output of a calculation</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-92">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-92">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>linearTransform</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Linearly scales and offsets data. Scale first, then offset.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>plainPlot</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadCSV</code></strong></td> -<td align="left"><code>string,int,int,char</code></td> -<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>loadXplot</code></strong></td> -<td align="left"><code>string,string</code></td> -<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>loadXplotRange</code></strong></td> -<td align="left"><code>string,string,unsigned int,unsigned int</code></td> -<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>compareXplot</code></strong></td> -<td align="left"><code>string,string,string</code></td> -<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>compareVec</code></strong></td> -<td align="left"><code>vector<double>,string</code></td> -<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>clearVec</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles request to clear the data vector</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-92">Shared message fields</h4> -<h4 id="lookup-fields-92">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Value of table at specified index</td> -</tr> -</tbody> -</table> -<h2 id="tableentry">TableEntry</h2> -<h4 id="value-fields-93">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>value</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Data value in this entry</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-93">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-93">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-93">Shared message fields</h4> -<h4 id="lookup-fields-93">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="tick">Tick</h2> -<h4 id="value-fields-94">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>dt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Timestep for this tick</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>localdt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Timestep for this tick</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-94">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process0</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 0</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit0</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 0</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process1</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit1</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 1</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process2</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 2</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit2</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 2</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process3</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit3</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 3</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process4</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 4</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit4</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 4</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process5</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 5</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit5</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 5</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process6</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 6</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit6</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 6</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process7</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 7</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit7</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 7</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process8</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 8</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit8</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 8</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process9</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Process for Tick 9</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit9</code></strong></td> -<td align="left"><code>PK8ProcInfo</code></td> -<td align="left">Reinit for Tick 9</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-94">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-94">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc0</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc1</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc2</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc3</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc4</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc5</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc6</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc7</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc8</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc9</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared proc/reinit message</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-94">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="tripanel">TriPanel</h2> -<h4 id="value-fields-95">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>nPts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of points used by panel to specify geometry</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nDims</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Dimensions used by panel to specify geometry</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numNeighbors</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of Neighbors of panel</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>shapeId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Identifier for shape type, as used by Smoldyn</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>coords</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-95">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toNeighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Identifies neighbors of the current panel</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-95">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>neighbor</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles incoming message from neighbor</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-95">Shared message fields</h4> -<h4 id="lookup-fields-95">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">x coordinate identified by index</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">y coordinate identified by index</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">z coordinate identified by index</td> -</tr> -</tbody> -</table> -<h2 id="vectortable">VectorTable</h2> -<h4 id="value-fields-96">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xdivs</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of divisions.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>xmin</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Minimum value in table.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>xmax</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value in table.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>invdx</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximum value in table.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>table</code></strong></td> -<td align="left"><code>vector<double></code></td> -<td align="left">The lookup table.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-96">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-96">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-96">Shared message fields</h4> -<h4 id="lookup-fields-96">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lookupvalue</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Lookup function that performs interpolation to return a value.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>lookupindex</code></strong></td> -<td align="left"><code>unsigned int,double</code></td> -<td align="left">Lookup function that returns value by index.</td> -</tr> -</tbody> -</table> -<h2 id="zbufpool">ZBufPool</h2> -<h4 id="value-fields-97">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-97">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-97">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-97">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-97">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zenz">ZEnz</h2> -<h4 id="value-fields-98">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward reaction from enz + sub to complex</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>k2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse reaction from complex to enz + sub</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant from complex to product + enz</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ratio</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ratio of k2/k3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concK1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-98">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toEnz</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toCplx</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-98">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplxDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of enz-sub complex</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-98">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enz</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enzyme pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplx</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enz-sub complex pool</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-98">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zfuncpool">ZFuncPool</h2> -<h4 id="value-fields-99">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-99">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-99">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input to control value of n_</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-99">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-99">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zmmenz">ZMMenz</h2> -<h4 id="value-fields-100">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-100">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-100">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-100">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-100">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zpool">ZPool</h2> -<h4 id="value-fields-101">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-101">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-101">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-101">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-101">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zreac">ZReac</h2> -<h4 id="value-fields-102">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in # units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in # units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in concentration units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in concentration units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates of reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numProducts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of products of reaction</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-102">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-102">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-102">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-102">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiebufpool">ZombieBufPool</h2> -<h4 id="value-fields-103">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-103">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-103">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-103">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-103">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiecaconc">ZombieCaConc</h2> -<h4 id="value-fields-104">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ca</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Calcium concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>CaBasal</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Basal Calcium concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Ca_base</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Basal Calcium concentration, synonym for CaBasal</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>tau</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Settling time for Ca concentration</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>B</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Volume scaling factor</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>thick</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Thickness of Ca shell.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>ceiling</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>floor</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Floor value for Ca concentration. If Ca < floor, Ca = floor</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-104">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>concOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of Ca in pool</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-104">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>current</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Calcium Ion current, due to be converted to conc.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>currentFraction</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Fraction of total Ion current, that is carried by Ca2+.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>increase</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Any input current that increases the concentration.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>decrease</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Any input current that decreases the concentration.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>basal</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Synonym for assignment of basal conc.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-104">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message to receive Process message from scheduler</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-104">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiecompartment">ZombieCompartment</h2> -<h4 id="value-fields-105">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Cm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane capacitance</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Em</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Resting membrane potential</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Im</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current going through membrane</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>inject</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Current injection to deliver into compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initVm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value for membrane potential</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Rm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Membrane resistance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ra</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Axial resistance of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diameter</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diameter of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>length</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Length of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>x0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">X coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>y0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Y coordinate of start of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>z0</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Z coordinate of start of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>x</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">x coordinate of end of compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">y coordinate of end of compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">z coordinate of end of compartment</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-105">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>VmOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>axialOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>raxialOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-105">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>randInject</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>injectMsg</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cable</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'process' call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles 'reinit' call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>initProc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>initReinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleChannel</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles conductance and Reversal potential arguments from Channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>handleRaxial</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles Raxial info: arguments are Ra and Vm.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleAxial</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Axial information. Argument is just Vm.</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-105">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>init</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>axial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>raxial</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-105">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombieenz">ZombieEnz</h2> -<h4 id="value-fields-106">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward reaction from enz + sub to complex</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>k2</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse reaction from complex to enz + sub</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>k3</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant from complex to product + enz</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ratio</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Ratio of k2/k3</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concK1</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-106">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toEnz</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toCplx</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-106">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplxDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of enz-sub complex</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-106">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enz</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enzyme pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>cplx</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to enz-sub complex pool</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-106">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiefuncpool">ZombieFuncPool</h2> -<h4 id="value-fields-107">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-107">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-107">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input to control value of n_</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-107">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-107">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiehhchannel">ZombieHHChannel</h2> -<h4 id="value-fields-108">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gbar</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Maximal channel conductance</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ek</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reversal potential of channel</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Gk</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel conductance variable</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ik</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current variable</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Xpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for X gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Ypower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Y gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Zpower</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Power for Z gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>instant</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>X</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for X gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Y</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Z</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">State variable for Y gate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>useConcentration</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Flag: when true, use concentration message rather than Vm tocontrol Z gate</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-108">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>channelOut</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends channel variables Gk and Ek to compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>permeability</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Conductance term going out to GHK object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>IkOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-108">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Vm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles Vm message coming in from compartment</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>concen</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Incoming message from Concen object to specific conc to usein the Z gate calculations</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>createGate</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Function to create specified gate.Argument: Gate type [X Y Z]</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-108">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>channel</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>ghk</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Message to Goldman-Hodgkin-Katz object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td> -</tr> -<tr class="even"> -<td align="left"></td> -<td align="left"></td> -<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-108">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiemmenz">ZombieMMenz</h2> -<h4 id="value-fields-109">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Km</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numKm</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Michaelis-Menten constant in number units, volume dependent</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kcat</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant for enzyme, units 1/sec</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-109">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-109">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>enzDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of Enzyme</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product. Dummy.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-109">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to product molecule</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-109">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiepool">ZombiePool</h2> -<h4 id="value-fields-110">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>n</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Number of molecules in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of number of molecules in pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>diffConst</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Diffusion constant of molecule</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>conc</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Concentration of molecules in this pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>concInit</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Initial value of molecular concentration in pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>size</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>speciesId</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-110">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>nOut</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out # of molecules in pool on each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>requestMolWt</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Requests Species object for mol wt</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>requestSize</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Requests Size of pool from matching mesh entry</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-110">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>group</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handle for grouping. Doesn't do anything.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reacDest</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Handles reaction input</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>handleMolWt</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td> -<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-110">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>reac</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>species</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for connecting to species objects</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>mesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for dealing with mesh operations</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-110">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiereac">ZombieReac</h2> -<h4 id="value-fields-111">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in # units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in # units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>Kf</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Forward rate constant, in concentration units</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>Kb</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Reverse rate constant, in concentration units</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>numSubstrates</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of substrates of reaction</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>numProducts</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Number of products of reaction</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-111">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>toSub</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>toPrd</code></strong></td> -<td align="left"><code>double,double</code></td> -<td align="left">Sends out increment of molecules on product each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-111">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>subDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of substrate</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>prdDest</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles # of molecules of product</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>remesh</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-111">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>sub</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>prd</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Connects to substrate pool</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-111">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="zombiesumfunc">ZombieSumFunc</h2> -<h4 id="value-fields-112">Value fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>this</code></strong></td> -<td align="left"><code>Neutral</code></td> -<td align="left">Access function for entire object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>name</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Name of object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>me</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">ObjId for current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>parent</code></strong></td> -<td align="left"><code>ObjId</code></td> -<td align="left">Parent ObjId for current object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>children</code></strong></td> -<td align="left"><code>vector<Id></code></td> -<td align="left">vector of ObjIds listing all children of current object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>path</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">text path for object</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>class</code></strong></td> -<td align="left"><code>string</code></td> -<td align="left">Class Name of object</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>linearSize</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>objectDimensions</code></strong></td> -<td align="left"><code>vector<unsigned int></code></td> -<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>lastDimension</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>localNumField</code></strong></td> -<td align="left"><code>unsigned int</code></td> -<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>pathIndices</code></strong></td> -<td align="left"><code>vector< vector<unsigned int> ></code></td> -<td align="left">Indices of the entire path hierarchy leading up to this Object.</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>msgOut</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages going out from this Element</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>msgIn</code></strong></td> -<td align="left"><code>vector<ObjId></code></td> -<td align="left">Messages coming in to this Element</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>result</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">outcome of summation</td> -</tr> -</tbody> -</table> -<h4 id="source-message-fields-112">Source message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>childMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message to child Elements</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>output</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Sends out sum on each timestep</td> -</tr> -</tbody> -</table> -<h4 id="destination-message-fields-112">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>parentMsg</code></strong></td> -<td align="left"><code>int</code></td> -<td align="left">Message from Parent Element(s)</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>input</code></strong></td> -<td align="left"><code>double</code></td> -<td align="left">Handles input values</td> -</tr> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles process call</td> -</tr> -<tr class="even"> -<td align="left"><strong><code>reinit</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Handles reinit call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-112">Shared message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>proc</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">Shared message for process and reinit</td> -</tr> -</tbody> -</table> -<h4 id="lookup-fields-112">Lookup fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>neighbours</code></strong></td> -<td align="left"><code>string,vector<Id></code></td> -<td align="left">Ids of Elements connected this Element on specified field.</td> -</tr> -</tbody> -</table> -<h2 id="testsched">testSched</h2> -<h4 id="value-fields-113">Value fields</h4> -<h4 id="source-message-fields-113">Source message fields</h4> -<h4 id="destination-message-fields-113">Destination message fields</h4> -<table> -<thead> -<tr class="header"> -<th align="left">Field</th> -<th align="left">Type</th> -<th align="left">Description</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left"><strong><code>process</code></strong></td> -<td align="left"><code>void</code></td> -<td align="left">handles process call</td> -</tr> -</tbody> -</table> -<h4 id="shared-message-fields-113">Shared message fields</h4> -<h4 id="lookup-fields-113">Lookup fields</h4> -<h1 id="moose-functions">MOOSE Functions</h1> -<h2 id="ce">ce</h2> -<p>Set the current working element. 'ce' is an alias of this function</p> -<h2 id="connect">connect</h2> -<p>connect(src, src_field, dest, dest_field, message_type) -> bool</p> -<p>Create a message between <code>src_field</code> on <code>src</code> object to <code>dest_field</code></p> -<p>on <code>dest</code> object.</p> -<h4 id="parameters">Parameters</h4> -<p>src : element</p> -<p>the source object</p> -<p>src_field : str</p> -<p>the source field name. Fields listed under <code>srcFinfo</code> and</p> -<p><code>sharedFinfo</code> qualify for this.</p> -<p>dest : element</p> -<p>the destination object.</p> -<p>dest_field : str</p> -<p>the destination field name. Fields listed under <code>destFinfo</code></p> -<p>and <code>sharedFinfo</code> qualify for this.</p> -<p>message_type : str (optional)</p> -<p>Type of the message. Can be <code>Single</code>, <code>OneToOne</code>, <code>OneToAll</code>.</p> -<p>If not specified, it defaults to <code>Single</code>.</p> -<h4 id="returns">Returns</h4> -<p>element of the message-manager for the newly created message.</p> -<h4 id="example">Example</h4> -<p>Connect the output of a pulse generator to the input of a spike</p> -<p>generator:</p> -<pre><code> ->>> pulsegen = moose.PulseGen('pulsegen') - ->>> spikegen = moose.SpikeGen('spikegen') - ->>> moose.connect(pulsegen, 'outputOut', spikegen, 'Vm') - -1 -</code></pre> -<h2 id="copy">copy</h2> -<p>copy(src, dest, name, n, toGlobal, copyExtMsg) -> bool</p> -<p>Make copies of a moose object.</p> -<h4 id="parameters-1">Parameters</h4> -<p>src : ematrix, element or str</p> -<p>source object.</p> -<p>dest : ematrix, element or str</p> -<p>Destination object to copy into.</p> -<p>name : str</p> -<p>Name of the new object. If omitted, name of the original will be used.</p> -<p>n : int</p> -<p>Number of copies to make.</p> -<p>toGlobal: int</p> -<p>Relevant for parallel environments only. If false, the copies will</p> -<p>reside on local node, otherwise all nodes get the copies.</p> -<p>copyExtMsg: int</p> -<p>If true, messages to/from external objects are also copied.</p> -<h4 id="returns-1">Returns</h4> -<p>ematrix of the copied object</p> -<h2 id="delete">delete</h2> -<p>moose.delete(id)</p> -<p>Delete the underlying moose object. This does not delete any of the</p> -<p>Python objects referring to this ematrix but does invalidate them. Any</p> -<p>attempt to access them will raise a ValueError.</p> -<p>Parameters</p> -<h4 id="section"></h4> -<p>id : ematrix</p> -<p>ematrix of the object to be deleted.</p> -<h2 id="element">element</h2> -<p>moose.element(arg) -> moose object</p> -<p>Convert a path or an object to the appropriate builtin moose class</p> -<p>instance</p> -<h4 id="parameters-2">Parameters</h4> -<p>arg: str or ematrix or moose object</p> -<p>path of the moose element to be converted or another element (possibly</p> -<p>available as a superclass instance).</p> -<h4 id="returns-2">Returns</h4> -<p>An element of the moose builtin class the specified object belongs</p> -<p>to.</p> -<h2 id="exists">exists</h2> -<p>True if there is an object with specified path.</p> -<h2 id="getcwe">getCwe</h2> -<p>Get the current working element. 'pwe' is an alias of this function.</p> -<h2 id="getfield">getField</h2> -<p>getField(element, field, fieldtype) -- Get specified field of specified type from object ematrix.</p> -<h2 id="getfielddict">getFieldDict</h2> -<p>getFieldDict(className, finfoType) -> dict</p> -<p>Get dictionary of field names and types for specified class.</p> -<h4 id="parameters-3">Parameters</h4> -<p>className : str</p> -<p>MOOSE class to find the fields of.</p> -<p>finfoType : str (optional)</p> -<p>Finfo type of the fields to find. If empty or not specified, all</p> -<p>fields will be retrieved.</p> -<p>note: This behaviour is different from <code>getFieldNames</code> where only</p> -<p><code>valueFinfo</code>s are returned when <code>finfoType</code> remains unspecified.</p> -<h4 id="example-1">Example</h4> -<p>List all the source fields on class Neutral:</p> -<pre><code> ->>> moose.getFieldDict('Neutral', 'srcFinfo') - -{'childMsg': 'int'} -</code></pre> -<h2 id="getfieldnames">getFieldNames</h2> -<p>getFieldNames(className, finfoType='valueFinfo') -> tuple</p> -<p>Get a tuple containing the name of all the fields of <code>finfoType</code></p> -<p>kind.</p> -<h4 id="parameters-4">Parameters</h4> -<p>className : string</p> -<p>Name of the class to look up.</p> -<p>finfoType : string</p> -<p>The kind of field (<code>valueFinfo</code>, <code>srcFinfo</code>, <code>destFinfo</code>,</p> -<p><code>lookupFinfo</code>, <code>fieldElementFinfo</code>.).</p> -<h2 id="isrunning">isRunning</h2> -<p>True if the simulation is currently running.</p> -<h2 id="loadmodel">loadModel</h2> -<p>loadModel(filename, modelpath, solverclass) -> moose.ematrix</p> -<p>Load model from a file to a specified path.</p> -<h4 id="parameters-5">Parameters</h4> -<p>filename : str</p> -<p>model description file.</p> -<p>modelpath : str</p> -<p>moose path for the top level element of the model to be created.</p> -<p>solverclass : str</p> -<p>(optional) solver type to be used for simulating the model.</p> -<h4 id="returns-3">Returns</h4> -<p>ematrix instance refering to the loaded model container.</p> -<h2 id="move">move</h2> -<p>Move a ematrix object to a destination.</p> -<h2 id="quit">quit</h2> -<p>Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.</p> -<h2 id="reinit">reinit</h2> -<p>reinit() -> None</p> -<p>Reinitialize simulation.</p> -<p>This function (re)initializes moose simulation. It must be called</p> -<p>before you start the simulation (see moose.start). If you want to</p> -<p>continue simulation after you have called moose.reinit() and</p> -<p>moose.start(), you must NOT call moose.reinit() again. Calling</p> -<p>moose.reinit() again will take the system back to initial setting</p> -<p>(like clear out all data recording tables, set state variables to</p> -<p>their initial values, etc.</p> -<h2 id="savemodel">saveModel</h2> -<p>saveModel(source, fileame)</p> -<p>Save model rooted at <code>source</code> to file <code>filename</code>.</p> -<h4 id="parameters-6">Parameters</h4> -<p>source: ematrix or element or str</p> -<p>root of the model tree</p> -<p>filename: str</p> -<p>destination file to save the model in.</p> -<h4 id="returns-4">Returns</h4> -<p>None</p> -<h2 id="seed">seed</h2> -<p>moose.seed(seedvalue) -> None</p> -<p>Reseed MOOSE random number generator.</p> -<h4 id="parameters-7">Parameters</h4> -<p>seed: int</p> -<p>Optional value to use for seeding. If 0, a random seed is</p> -<p>automatically created using the current system time and other</p> -<p>information. If not specified, it defaults to 0.</p> -<h2 id="setclock">setClock</h2> -<p>Set the dt of a clock.</p> -<h2 id="setcwe">setCwe</h2> -<p>Set the current working element. 'ce' is an alias of this function</p> -<h2 id="start">start</h2> -<p>start(t) -> None</p> -<p>Run simulation for <code>t</code> time. Advances the simulator clock by <code>t</code></p> -<p>time.</p> -<p>After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before</p> -<p>CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the</p> -<p>simulator behaviour will be undefined. Once moose.reinit() has been</p> -<p>called, you can call moose.start(t) as many time as you like. This</p> -<p>will continue the simulation from the last state for <code>t</code> time.</p> -<h4 id="parameters-8">Parameters</h4> -<p>t : float</p> -<p>duration of simulation.</p> -<h4 id="returns-5">Returns</h4> -<p>None</p> -<h4 id="see-also">See also</h4> -<p>moose.reinit : (Re)initialize simulation</p> -<h2 id="stop">stop</h2> -<p>Stop simulation</p> -<h2 id="useclock">useClock</h2> -<p>Schedule objects on a specified clock</p> -<h2 id="wildcardfind">wildcardFind</h2> -<p>moose.wildcardFind(expression) -> tuple of ematrices.</p> -<p>Find an object by wildcard.</p> -<h4 id="parameters-9">Parameters</h4> -<p>expression: str</p> -<p>MOOSE allows wildcard expressions of the form</p> -<p>{PATH}/{WILDCARD}[{CONDITION}]</p> -<p>where {PATH} is valid path in the element tree.</p> -<p>{WILDCARD} can be <code>#</code> or <code>##</code>.</p> -<p><code>#</code> causes the search to be restricted to the children of the</p> -<p>element specified by {PATH}.</p> -<p><code>##</code> makes the search to recursively go through all the descendants</p> -<p>of the {PATH} element.</p> -<p>{CONDITION} can be</p> -<p>TYPE={CLASSNAME} : an element satisfies this condition if it is of</p> -<p>class {CLASSNAME}.</p> -<p>ISA={CLASSNAME} : alias for TYPE={CLASSNAME}</p> -<p>CLASS={CLASSNAME} : alias for TYPE={CLASSNAME}</p> -<p>FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with</p> -<p>{VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=,</p> -<p>!=, >, <, >=, <=).</p> -<p>For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all</p> -<p>the objects under /mymodel whose Vm field is >= -65.</p> -<h2 id="writesbml">writeSBML</h2> -<p>Export biochemical model to an SBML file.</p> -<h2 id="doc">doc</h2> -<p>Display the documentation for class or field in a class.</p> -<h4 id="parameters-10">Parameters</h4> -<p>arg: str or moose class or instance of melement or instance of ematrix</p> -<p>argument can be a string specifying a moose class name and a field</p> -<p>name separated by a dot. e.g., 'Neutral.name'. Prepending <code>moose.</code></p> -<p>is allowed. Thus moose.doc('moose.Neutral.name') is equivalent to</p> -<p>the above.</p> -<p>argument can also be string specifying just a moose class name or</p> -<p>a moose class or a moose object (instance of melement or ematrix</p> -<p>or there subclasses). In that case, the builtin documentation for</p> -<p>the corresponding moose class is displayed.</p> -<p>paged: bool</p> -<p>Whether to display the docs via builtin pager or print and</p> -<p>exit. If not specified, it defaults to False and moose.doc(xyz)</p> -<p>will print help on xyz and return control to command line.</p> -<h2 id="getfielddoc">getfielddoc</h2> -<p>Get the documentation for field specified by</p> -<p>tokens.</p> -<p>tokens should be a two element list/tuple where first element is a</p> -<p>MOOSE class name and second is the field name.</p> -<h2 id="getmoosedoc">getmoosedoc</h2> -<p>Retrieve MOOSE builtin documentation for tokens.</p> -<p>tokens is a list or tuple containing: (classname, [fieldname])</p> -<h2 id="le">le</h2> -<p>List elements.</p> -<h4 id="parameters-11">Parameters</h4> -<p>el: str/melement/ematrix/None</p> -<p>The element or the path under which to look. If <code>None</code>, children</p> -<p>of current working element are displayed.</p> -<h2 id="listmsg">listmsg</h2> -<p>Return a list containing the incoming and outgoing messages of</p> -<p>the given object.</p> -<h2 id="pwe">pwe</h2> -<p>Print present working element. Convenience function for GENESIS</p> -<p>users.</p> -<h2 id="showfield">showfield</h2> -<p>Show the fields of the element, their data types and values in</p> -<p>human readable format. Convenience function for GENESIS users.</p> -<p>Parameters:</p> -<p>elem: str/melement instance</p> -<p>Element or path of an existing element.</p> -<p>field: str</p> -<p>Field to be displayed. If '*', all fields are displayed.</p> -<p>showtype: bool</p> -<p>If True show the data type of each field.</p> -<h2 id="showfields">showfields</h2> -<p>Convenience function. 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" " : "" ) + selector; - } else if ( name ) { - ret.selector = this.selector + "." + name + "(" + selector + ")"; - } - - // Return the newly-formed element set - return ret; - }, - - // Execute a callback for every element in the matched set. - // (You can seed the arguments with an array of args, but this is - // only used internally.) - each: function( callback, args ) { - return jQuery.each( this, callback, args ); - }, - - ready: function( fn ) { - // Attach the listeners - jQuery.bindReady(); - - // Add the callback - readyList.add( fn ); - - return this; - }, - - eq: function( i ) { - i = +i; - return i === -1 ? - this.slice( i ) : - this.slice( i, i + 1 ); - }, - - first: function() { - return this.eq( 0 ); - }, - - last: function() { - return this.eq( -1 ); - }, - - slice: function() { - return this.pushStack( slice.apply( this, arguments ), - "slice", slice.call(arguments).join(",") ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map(this, function( elem, i ) { - return callback.call( elem, i, elem ); - })); - }, - - end: function() { - return this.prevObject || this.constructor(null); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: [].sort, - splice: [].splice -}; - -// Give the init function the jQuery prototype for later instantiation -jQuery.fn.init.prototype = jQuery.fn; - -jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, - target = arguments[0] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - target = arguments[1] || {}; - // skip the boolean and the target - i = 2; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction(target) ) { - target = {}; - } - - // extend jQuery itself if only one argument is passed - if ( length === i ) { - target = this; - --i; - } - - for ( ; i < length; i++ ) { - // Only deal with non-null/undefined values - if ( (options = arguments[ i ]) != null ) { - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) { - if ( copyIsArray ) { - copyIsArray = false; - clone = src && jQuery.isArray(src) ? src : []; - - } else { - clone = src && jQuery.isPlainObject(src) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend({ - noConflict: function( deep ) { - if ( window.$ === jQuery ) { - window.$ = _$; - } - - if ( deep && window.jQuery === jQuery ) { - window.jQuery = _jQuery; - } - - return jQuery; - }, - - // Is the DOM ready to be used? Set to true once it occurs. - isReady: false, - - // A counter to track how many items to wait for before - // the ready event fires. See #6781 - readyWait: 1, - - // Hold (or release) the ready event - holdReady: function( hold ) { - if ( hold ) { - jQuery.readyWait++; - } else { - jQuery.ready( true ); - } - }, - - // Handle when the DOM is ready - ready: function( wait ) { - // Either a released hold or an DOMready/load event and not yet ready - if ( (wait === true && !--jQuery.readyWait) || (wait !== true && !jQuery.isReady) ) { - // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). - if ( !document.body ) { - return setTimeout( jQuery.ready, 1 ); - } - - // Remember that the DOM is ready - jQuery.isReady = true; - - // If a normal DOM Ready event fired, decrement, and wait if need be - if ( wait !== true && --jQuery.readyWait > 0 ) { - return; - } - - // If there are functions bound, to execute - readyList.fireWith( document, [ jQuery ] ); - - // Trigger any bound ready events - if ( jQuery.fn.trigger ) { - jQuery( document ).trigger( "ready" ).off( "ready" ); - } - } - }, - - bindReady: function() { - if ( readyList ) { - return; - } - - readyList = jQuery.Callbacks( "once memory" ); - - // Catch cases where $(document).ready() is called after the - // browser event has already occurred. - if ( document.readyState === "complete" ) { - // Handle it asynchronously to allow scripts the opportunity to delay ready - return setTimeout( jQuery.ready, 1 ); - } - - // Mozilla, Opera and webkit nightlies currently support this event - if ( document.addEventListener ) { - // Use the handy event callback - document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false ); - - // A fallback to window.onload, that will always work - window.addEventListener( "load", jQuery.ready, false ); - - // If IE event model is used - } else if ( document.attachEvent ) { - // ensure firing before onload, - // maybe late but safe also for iframes - document.attachEvent( "onreadystatechange", DOMContentLoaded ); - - // A fallback to window.onload, that will always work - window.attachEvent( "onload", jQuery.ready ); - - // If IE and not a frame - // continually check to see if the document is ready - var toplevel = false; - - try { - toplevel = window.frameElement == null; - } catch(e) {} - - if ( document.documentElement.doScroll && toplevel ) { - doScrollCheck(); - } - } - }, - - // See test/unit/core.js for details concerning isFunction. - // Since version 1.3, DOM methods and functions like alert - // aren't supported. They return false on IE (#2968). - isFunction: function( obj ) { - return jQuery.type(obj) === "function"; - }, - - isArray: Array.isArray || function( obj ) { - return jQuery.type(obj) === "array"; - }, - - isWindow: function( obj ) { - return obj != null && obj == obj.window; - }, - - isNumeric: function( obj ) { - return !isNaN( parseFloat(obj) ) && isFinite( obj ); - }, - - type: function( obj ) { - return obj == null ? - String( obj ) : - class2type[ toString.call(obj) ] || "object"; - }, - - isPlainObject: function( obj ) { - // Must be an Object. - // Because of IE, we also have to check the presence of the constructor property. - // Make sure that DOM nodes and window objects don't pass through, as well - if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) { - return false; - } - - try { - // Not own constructor property must be Object - if ( obj.constructor && - !hasOwn.call(obj, "constructor") && - !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) { - return false; - } - } catch ( e ) { - // IE8,9 Will throw exceptions on certain host objects #9897 - return false; - } - - // Own properties are enumerated firstly, so to speed up, - // if last one is own, then all properties are own. - - var key; - for ( key in obj ) {} - - return key === undefined || hasOwn.call( obj, key ); - }, - - isEmptyObject: function( obj ) { - for ( var name in obj ) { - return false; - } - return true; - }, - - error: function( msg ) { - throw new Error( msg ); - }, - - parseJSON: function( data ) { - if ( typeof data !== "string" || !data ) { - return null; - } - - // Make sure leading/trailing whitespace is removed (IE can't handle it) - data = jQuery.trim( data ); - - // Attempt to parse using the native JSON parser first - if ( window.JSON && window.JSON.parse ) { - return window.JSON.parse( data ); - } - - // Make sure the incoming data is actual JSON - // Logic borrowed from http://json.org/json2.js - if ( rvalidchars.test( data.replace( rvalidescape, "@" ) - .replace( rvalidtokens, "]" ) - .replace( rvalidbraces, "")) ) { - - return ( new Function( "return " + data ) )(); - - } - jQuery.error( "Invalid JSON: " + data ); - }, - - // Cross-browser xml parsing - parseXML: function( data ) { - if ( typeof data !== "string" || !data ) { - return null; - } - var xml, tmp; - try { - if ( window.DOMParser ) { // Standard - tmp = new DOMParser(); - xml = tmp.parseFromString( data , "text/xml" ); - } else { // IE - xml = new ActiveXObject( "Microsoft.XMLDOM" ); - xml.async = "false"; - xml.loadXML( data ); - } - } catch( e ) { - xml = undefined; - } - if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) { - jQuery.error( "Invalid XML: " + data ); - } - return xml; - }, - - noop: function() {}, - - // Evaluates a script in a global context - // Workarounds based on findings by Jim Driscoll - // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context - globalEval: function( data ) { - if ( data && rnotwhite.test( data ) ) { - // We use execScript on Internet Explorer - // We use an anonymous function so that context is window - // rather than jQuery in Firefox - ( window.execScript || function( data ) { - window[ "eval" ].call( window, data ); - } )( data ); - } - }, - - // Convert dashed to camelCase; used by the css and data modules - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toUpperCase() === name.toUpperCase(); - }, - - // args is for internal usage only - each: function( object, callback, args ) { - var name, i = 0, - length = object.length, - isObj = length === undefined || jQuery.isFunction( object ); - - if ( args ) { - if ( isObj ) { - for ( name in object ) { - if ( callback.apply( object[ name ], args ) === false ) { - break; - } - } - } else { - for ( ; i < length; ) { - if ( callback.apply( object[ i++ ], args ) === false ) { - break; - } - } - } - - // A special, fast, case for the most common use of each - } else { - if ( isObj ) { - for ( name in object ) { - if ( callback.call( object[ name ], name, object[ name ] ) === false ) { - break; - } - } - } else { - for ( ; i < length; ) { - if ( callback.call( object[ i ], i, object[ i++ ] ) === false ) { - break; - } - } - } - } - - return object; - }, - - // Use native String.trim function wherever possible - trim: trim ? - function( text ) { - return text == null ? - "" : - trim.call( text ); - } : - - // Otherwise use our own trimming functionality - function( text ) { - return text == null ? - "" : - text.toString().replace( trimLeft, "" ).replace( trimRight, "" ); - }, - - // results is for internal usage only - makeArray: function( array, results ) { - var ret = results || []; - - if ( array != null ) { - // The window, strings (and functions) also have 'length' - // Tweaked logic slightly to handle Blackberry 4.7 RegExp issues #6930 - var type = jQuery.type( array ); - - if ( array.length == null || type === "string" || type === "function" || type === "regexp" || jQuery.isWindow( array ) ) { - push.call( ret, array ); - } else { - jQuery.merge( ret, array ); - } - } - - return ret; - }, - - inArray: function( elem, array, i ) { - var len; - - if ( array ) { - if ( indexOf ) { - return indexOf.call( array, elem, i ); - } - - len = array.length; - i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0; - - for ( ; i < len; i++ ) { - // Skip accessing in sparse arrays - if ( i in array && array[ i ] === elem ) { - return i; - } - } - } - - return -1; - }, - - merge: function( first, second ) { - var i = first.length, - j = 0; - - if ( typeof second.length === "number" ) { - for ( var l = second.length; j < l; j++ ) { - first[ i++ ] = second[ j ]; - } - - } else { - while ( second[j] !== undefined ) { - first[ i++ ] = second[ j++ ]; - } - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, inv ) { - var ret = [], retVal; - inv = !!inv; - - // Go through the array, only saving the items - // that pass the validator function - for ( var i = 0, length = elems.length; i < length; i++ ) { - retVal = !!callback( elems[ i ], i ); - if ( inv !== retVal ) { - ret.push( elems[ i ] ); - } - } - - return ret; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var value, key, ret = [], - i = 0, - length = elems.length, - // jquery objects are treated as arrays - isArray = elems instanceof jQuery || length !== undefined && typeof length === "number" && ( ( length > 0 && elems[ 0 ] && elems[ length -1 ] ) || length === 0 || jQuery.isArray( elems ) ) ; - - // Go through the array, translating each of the items to their - if ( isArray ) { - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret[ ret.length ] = value; - } - } - - // Go through every key on the object, - } else { - for ( key in elems ) { - value = callback( elems[ key ], key, arg ); - - if ( value != null ) { - ret[ ret.length ] = value; - } - } - } - - // Flatten any nested arrays - return ret.concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - if ( typeof context === "string" ) { - var tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - var args = slice.call( arguments, 2 ), - proxy = function() { - return fn.apply( context, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || proxy.guid || jQuery.guid++; - - return proxy; - }, - - // Mutifunctional method to get and set values to a collection - // The value/s can optionally be executed if it's a function - access: function( elems, fn, key, value, chainable, emptyGet, pass ) { - var exec, - bulk = key == null, - i = 0, - length = elems.length; - - // Sets many values - if ( key && typeof key === "object" ) { - for ( i in key ) { - jQuery.access( elems, fn, i, key[i], 1, emptyGet, value ); - } - chainable = 1; - - // Sets one value - } else if ( value !== undefined ) { - // Optionally, function values get executed if exec is true - exec = pass === undefined && jQuery.isFunction( value ); - - if ( bulk ) { - // Bulk operations only iterate when executing function values - if ( exec ) { - exec = fn; - fn = function( elem, key, value ) { - return exec.call( jQuery( elem ), value ); - }; - - // Otherwise they run against the entire set - } else { - fn.call( elems, value ); - fn = null; - } - } - - if ( fn ) { - for (; i < length; i++ ) { - fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass ); - } - } - - chainable = 1; - } - - return chainable ? - elems : - - // Gets - bulk ? - fn.call( elems ) : - length ? fn( elems[0], key ) : emptyGet; - }, - - now: function() { - return ( new Date() ).getTime(); - }, - - // Use of jQuery.browser is frowned upon. - // More details: http://docs.jquery.com/Utilities/jQuery.browser - uaMatch: function( ua ) { - ua = ua.toLowerCase(); - - var match = rwebkit.exec( ua ) || - ropera.exec( ua ) || - rmsie.exec( ua ) || - ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || - []; - - return { browser: match[1] || "", version: match[2] || "0" }; - }, - - sub: function() { - function jQuerySub( selector, context ) { - return new jQuerySub.fn.init( selector, context ); - } - jQuery.extend( true, jQuerySub, this ); - jQuerySub.superclass = this; - jQuerySub.fn = jQuerySub.prototype = this(); - jQuerySub.fn.constructor = jQuerySub; - jQuerySub.sub = this.sub; - jQuerySub.fn.init = function init( selector, context ) { - if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) { - context = jQuerySub( context ); - } - - return jQuery.fn.init.call( this, selector, context, rootjQuerySub ); - }; - jQuerySub.fn.init.prototype = jQuerySub.fn; - var rootjQuerySub = jQuerySub(document); - return jQuerySub; - }, - - browser: {} -}); - -// Populate the class2type map -jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -}); - -browserMatch = jQuery.uaMatch( userAgent ); -if ( browserMatch.browser ) { - jQuery.browser[ browserMatch.browser ] = true; - jQuery.browser.version = browserMatch.version; -} - -// Deprecated, use jQuery.browser.webkit instead -if ( jQuery.browser.webkit ) { - jQuery.browser.safari = true; -} - -// IE doesn't match non-breaking spaces with \s -if ( rnotwhite.test( "\xA0" ) ) { - trimLeft = /^[\s\xA0]+/; - trimRight = /[\s\xA0]+$/; -} - -// All jQuery objects should point back to these -rootjQuery = jQuery(document); - -// Cleanup functions for the document ready method -if ( document.addEventListener ) { - DOMContentLoaded = function() { - document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); - jQuery.ready(); - }; - -} else if ( document.attachEvent ) { - DOMContentLoaded = function() { - // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). - if ( document.readyState === "complete" ) { - document.detachEvent( "onreadystatechange", DOMContentLoaded ); - jQuery.ready(); - } - }; -} - -// The DOM ready check for Internet Explorer -function doScrollCheck() { - if ( jQuery.isReady ) { - return; - } - - try { - // If IE is used, use the trick by Diego Perini - // http://javascript.nwbox.com/IEContentLoaded/ - document.documentElement.doScroll("left"); - } catch(e) { - setTimeout( doScrollCheck, 1 ); - return; - } - - // and execute any waiting functions - jQuery.ready(); -} - -return jQuery; - -})(); - - -// String to Object flags format cache -var flagsCache = {}; - -// Convert String-formatted flags into Object-formatted ones and store in cache -function createFlags( flags ) { - var object = flagsCache[ flags ] = {}, - i, length; - flags = flags.split( /\s+/ ); - for ( i = 0, length = flags.length; i < length; i++ ) { - object[ flags[i] ] = true; - } - return object; -} - -/* - * Create a callback list using the following parameters: - * - * flags: an optional list of space-separated flags that will change how - * the callback list behaves - * - * By default a callback list will act like an event callback list and can be - * "fired" multiple times. - * - * Possible flags: - * - * once: will ensure the callback list can only be fired once (like a Deferred) - * - * memory: will keep track of previous values and will call any callback added - * after the list has been fired right away with the latest "memorized" - * values (like a Deferred) - * - * unique: will ensure a callback can only be added once (no duplicate in the list) - * - * stopOnFalse: interrupt callings when a callback returns false - * - */ -jQuery.Callbacks = function( flags ) { - - // Convert flags from String-formatted to Object-formatted - // (we check in cache first) - flags = flags ? ( flagsCache[ flags ] || createFlags( flags ) ) : {}; - - var // Actual callback list - list = [], - // Stack of fire calls for repeatable lists - stack = [], - // Last fire value (for non-forgettable lists) - memory, - // Flag to know if list was already fired - fired, - // Flag to know if list is currently firing - firing, - // First callback to fire (used internally by add and fireWith) - firingStart, - // End of the loop when firing - firingLength, - // Index of currently firing callback (modified by remove if needed) - firingIndex, - // Add one or several callbacks to the list - add = function( args ) { - var i, - length, - elem, - type, - actual; - for ( i = 0, length = args.length; i < length; i++ ) { - elem = args[ i ]; - type = jQuery.type( elem ); - if ( type === "array" ) { - // Inspect recursively - add( elem ); - } else if ( type === "function" ) { - // Add if not in unique mode and callback is not in - if ( !flags.unique || !self.has( elem ) ) { - list.push( elem ); - } - } - } - }, - // Fire callbacks - fire = function( context, args ) { - args = args || []; - memory = !flags.memory || [ context, args ]; - fired = true; - firing = true; - firingIndex = firingStart || 0; - firingStart = 0; - firingLength = list.length; - for ( ; list && firingIndex < firingLength; firingIndex++ ) { - if ( list[ firingIndex ].apply( context, args ) === false && flags.stopOnFalse ) { - memory = true; // Mark as halted - break; - } - } - firing = false; - if ( list ) { - if ( !flags.once ) { - if ( stack && stack.length ) { - memory = stack.shift(); - self.fireWith( memory[ 0 ], memory[ 1 ] ); - } - } else if ( memory === true ) { - self.disable(); - } else { - list = []; - } - } - }, - // Actual Callbacks object - self = { - // Add a callback or a collection of callbacks to the list - add: function() { - if ( list ) { - var length = list.length; - add( arguments ); - // Do we need to add the callbacks to the - // current firing batch? - if ( firing ) { - firingLength = list.length; - // With memory, if we're not firing then - // we should call right away, unless previous - // firing was halted (stopOnFalse) - } else if ( memory && memory !== true ) { - firingStart = length; - fire( memory[ 0 ], memory[ 1 ] ); - } - } - return this; - }, - // Remove a callback from the list - remove: function() { - if ( list ) { - var args = arguments, - argIndex = 0, - argLength = args.length; - for ( ; argIndex < argLength ; argIndex++ ) { - for ( var i = 0; i < list.length; i++ ) { - if ( args[ argIndex ] === list[ i ] ) { - // Handle firingIndex and firingLength - if ( firing ) { - if ( i <= firingLength ) { - firingLength--; - if ( i <= firingIndex ) { - firingIndex--; - } - } - } - // Remove the element - list.splice( i--, 1 ); - // If we have some unicity property then - // we only need to do this once - if ( flags.unique ) { - break; - } - } - } - } - } - return this; - }, - // Control if a given callback is in the list - has: function( fn ) { - if ( list ) { - var i = 0, - length = list.length; - for ( ; i < length; i++ ) { - if ( fn === list[ i ] ) { - return true; - } - } - } - return false; - }, - // Remove all callbacks from the list - empty: function() { - list = []; - return this; - }, - // Have the list do nothing anymore - disable: function() { - list = stack = memory = undefined; - return this; - }, - // Is it disabled? - disabled: function() { - return !list; - }, - // Lock the list in its current state - lock: function() { - stack = undefined; - if ( !memory || memory === true ) { - self.disable(); - } - return this; - }, - // Is it locked? - locked: function() { - return !stack; - }, - // Call all callbacks with the given context and arguments - fireWith: function( context, args ) { - if ( stack ) { - if ( firing ) { - if ( !flags.once ) { - stack.push( [ context, args ] ); - } - } else if ( !( flags.once && memory ) ) { - fire( context, args ); - } - } - return this; - }, - // Call all the callbacks with the given arguments - fire: function() { - self.fireWith( this, arguments ); - return this; - }, - // To know if the callbacks have already been called at least once - fired: function() { - return !!fired; - } - }; - - return self; -}; - - - - -var // Static reference to slice - sliceDeferred = [].slice; - -jQuery.extend({ - - Deferred: function( func ) { - var doneList = jQuery.Callbacks( "once memory" ), - failList = jQuery.Callbacks( "once memory" ), - progressList = jQuery.Callbacks( "memory" ), - state = "pending", - lists = { - resolve: doneList, - reject: failList, - notify: progressList - }, - promise = { - done: doneList.add, - fail: failList.add, - progress: progressList.add, - - state: function() { - return state; - }, - - // Deprecated - isResolved: doneList.fired, - isRejected: failList.fired, - - then: function( doneCallbacks, failCallbacks, progressCallbacks ) { - deferred.done( doneCallbacks ).fail( failCallbacks ).progress( progressCallbacks ); - return this; - }, - always: function() { - deferred.done.apply( deferred, arguments ).fail.apply( deferred, arguments ); - return this; - }, - pipe: function( fnDone, fnFail, fnProgress ) { - return jQuery.Deferred(function( newDefer ) { - jQuery.each( { - done: [ fnDone, "resolve" ], - fail: [ fnFail, "reject" ], - progress: [ fnProgress, "notify" ] - }, function( handler, data ) { - var fn = data[ 0 ], - action = data[ 1 ], - returned; - if ( jQuery.isFunction( fn ) ) { - deferred[ handler ](function() { - returned = fn.apply( this, arguments ); - if ( returned && jQuery.isFunction( returned.promise ) ) { - returned.promise().then( newDefer.resolve, newDefer.reject, newDefer.notify ); - } else { - newDefer[ action + "With" ]( this === deferred ? newDefer : this, [ returned ] ); - } - }); - } else { - deferred[ handler ]( newDefer[ action ] ); - } - }); - }).promise(); - }, - // Get a promise for this deferred - // If obj is provided, the promise aspect is added to the object - promise: function( obj ) { - if ( obj == null ) { - obj = promise; - } else { - for ( var key in promise ) { - obj[ key ] = promise[ key ]; - } - } - return obj; - } - }, - deferred = promise.promise({}), - key; - - for ( key in lists ) { - deferred[ key ] = lists[ key ].fire; - deferred[ key + "With" ] = lists[ key ].fireWith; - } - - // Handle state - deferred.done( function() { - state = "resolved"; - }, failList.disable, progressList.lock ).fail( function() { - state = "rejected"; - }, doneList.disable, progressList.lock ); - - // Call given func if any - if ( func ) { - func.call( deferred, deferred ); - } - - // All done! - return deferred; - }, - - // Deferred helper - when: function( firstParam ) { - var args = sliceDeferred.call( arguments, 0 ), - i = 0, - length = args.length, - pValues = new Array( length ), - count = length, - pCount = length, - deferred = length <= 1 && firstParam && jQuery.isFunction( firstParam.promise ) ? - firstParam : - jQuery.Deferred(), - promise = deferred.promise(); - function resolveFunc( i ) { - return function( value ) { - args[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; - if ( !( --count ) ) { - deferred.resolveWith( deferred, args ); - } - }; - } - function progressFunc( i ) { - return function( value ) { - pValues[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; - deferred.notifyWith( promise, pValues ); - }; - } - if ( length > 1 ) { - for ( ; i < length; i++ ) { - if ( args[ i ] && args[ i ].promise && jQuery.isFunction( args[ i ].promise ) ) { - args[ i ].promise().then( resolveFunc(i), deferred.reject, progressFunc(i) ); - } else { - --count; - } - } - if ( !count ) { - deferred.resolveWith( deferred, args ); - } - } else if ( deferred !== firstParam ) { - deferred.resolveWith( deferred, length ? [ firstParam ] : [] ); - } - return promise; - } -}); - - - - -jQuery.support = (function() { - - var support, - all, - a, - select, - opt, - input, - fragment, - tds, - events, - eventName, - i, - isSupported, - div = document.createElement( "div" ), - documentElement = document.documentElement; - - // Preliminary tests - div.setAttribute("className", "t"); - div.innerHTML = " <link/><table></table><a href='/a' style='top:1px;float:left;opacity:.55;'>a</a><input type='checkbox'/>"; - - all = div.getElementsByTagName( "*" ); - a = div.getElementsByTagName( "a" )[ 0 ]; - - // Can't get basic test support - if ( !all || !all.length || !a ) { - return {}; - } - - // First batch of supports tests - select = document.createElement( "select" ); - opt = select.appendChild( document.createElement("option") ); - input = div.getElementsByTagName( "input" )[ 0 ]; - - support = { - // IE strips leading whitespace when .innerHTML is used - leadingWhitespace: ( div.firstChild.nodeType === 3 ), - - // Make sure that tbody elements aren't automatically inserted - // IE will insert them into empty tables - tbody: !div.getElementsByTagName("tbody").length, - - // Make sure that link elements get serialized correctly by innerHTML - // This requires a wrapper element in IE - htmlSerialize: !!div.getElementsByTagName("link").length, - - // Get the style information from getAttribute - // (IE uses .cssText instead) - style: /top/.test( a.getAttribute("style") ), - - // Make sure that URLs aren't manipulated - // (IE normalizes it by default) - hrefNormalized: ( a.getAttribute("href") === "/a" ), - - // Make sure that element opacity exists - // (IE uses filter instead) - // Use a regex to work around a WebKit issue. See #5145 - opacity: /^0.55/.test( a.style.opacity ), - - // Verify style float existence - // (IE uses styleFloat instead of cssFloat) - cssFloat: !!a.style.cssFloat, - - // Make sure that if no value is specified for a checkbox - // that it defaults to "on". - // (WebKit defaults to "" instead) - checkOn: ( input.value === "on" ), - - // Make sure that a selected-by-default option has a working selected property. - // (WebKit defaults to false instead of true, IE too, if it's in an optgroup) - optSelected: opt.selected, - - // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7) - getSetAttribute: div.className !== "t", - - // Tests for enctype support on a form(#6743) - enctype: !!document.createElement("form").enctype, - - // Makes sure cloning an html5 element does not cause problems - // Where outerHTML is undefined, this still works - html5Clone: document.createElement("nav").cloneNode( true ).outerHTML !== "<:nav></:nav>", - - // Will be defined later - submitBubbles: true, - changeBubbles: true, - focusinBubbles: false, - deleteExpando: true, - noCloneEvent: true, - inlineBlockNeedsLayout: false, - shrinkWrapBlocks: false, - reliableMarginRight: true, - pixelMargin: true - }; - - // jQuery.boxModel DEPRECATED in 1.3, use jQuery.support.boxModel instead - jQuery.boxModel = support.boxModel = (document.compatMode === "CSS1Compat"); - - // Make sure checked status is properly cloned - input.checked = true; - support.noCloneChecked = input.cloneNode( true ).checked; - - // Make sure that the options inside disabled selects aren't marked as disabled - // (WebKit marks them as disabled) - select.disabled = true; - support.optDisabled = !opt.disabled; - - // Test to see if it's possible to delete an expando from an element - // Fails in Internet Explorer - try { - delete div.test; - } catch( e ) { - support.deleteExpando = false; - } - - if ( !div.addEventListener && div.attachEvent && div.fireEvent ) { - div.attachEvent( "onclick", function() { - // Cloning a node shouldn't copy over any - // bound event handlers (IE does this) - support.noCloneEvent = false; - }); - div.cloneNode( true ).fireEvent( "onclick" ); - } - - // Check if a radio maintains its value - // after being appended to the DOM - input = document.createElement("input"); - input.value = "t"; - input.setAttribute("type", "radio"); - support.radioValue = input.value === "t"; - - input.setAttribute("checked", "checked"); - - // #11217 - WebKit loses check when the name is after the checked attribute - input.setAttribute( "name", "t" ); - - div.appendChild( input ); - fragment = document.createDocumentFragment(); - fragment.appendChild( div.lastChild ); - - // WebKit doesn't clone checked state correctly in fragments - support.checkClone = fragment.cloneNode( true ).cloneNode( true ).lastChild.checked; - - // Check if a disconnected checkbox will retain its checked - // value of true after appended to the DOM (IE6/7) - support.appendChecked = input.checked; - - fragment.removeChild( input ); - fragment.appendChild( div ); - - // Technique from Juriy Zaytsev - // http://perfectionkills.com/detecting-event-support-without-browser-sniffing/ - // We only care about the case where non-standard event systems - // are used, namely in IE. Short-circuiting here helps us to - // avoid an eval call (in setAttribute) which can cause CSP - // to go haywire. See: https://developer.mozilla.org/en/Security/CSP - if ( div.attachEvent ) { - for ( i in { - submit: 1, - change: 1, - focusin: 1 - }) { - eventName = "on" + i; - isSupported = ( eventName in div ); - if ( !isSupported ) { - div.setAttribute( eventName, "return;" ); - isSupported = ( typeof div[ eventName ] === "function" ); - } - support[ i + "Bubbles" ] = isSupported; - } - } - - fragment.removeChild( div ); - - // Null elements to avoid leaks in IE - fragment = select = opt = div = input = null; - - // Run tests that need a body at doc ready - jQuery(function() { - var container, outer, inner, table, td, offsetSupport, - marginDiv, conMarginTop, style, html, positionTopLeftWidthHeight, - paddingMarginBorderVisibility, paddingMarginBorder, - body = document.getElementsByTagName("body")[0]; - - if ( !body ) { - // Return for frameset docs that don't have a body - return; - } - - conMarginTop = 1; - paddingMarginBorder = "padding:0;margin:0;border:"; - positionTopLeftWidthHeight = "position:absolute;top:0;left:0;width:1px;height:1px;"; - paddingMarginBorderVisibility = paddingMarginBorder + "0;visibility:hidden;"; - style = "style='" + positionTopLeftWidthHeight + paddingMarginBorder + "5px solid #000;"; - html = "<div " + style + "display:block;'><div style='" + paddingMarginBorder + "0;display:block;overflow:hidden;'></div></div>" + - "<table " + style + "' cellpadding='0' cellspacing='0'>" + - "<tr><td></td></tr></table>"; - - container = document.createElement("div"); - container.style.cssText = paddingMarginBorderVisibility + "width:0;height:0;position:static;top:0;margin-top:" + conMarginTop + "px"; - body.insertBefore( container, body.firstChild ); - - // Construct the test element - div = document.createElement("div"); - container.appendChild( div ); - - // Check if table cells still have offsetWidth/Height when they are set - // to display:none and there are still other visible table cells in a - // table row; if so, offsetWidth/Height are not reliable for use when - // determining if an element has been hidden directly using - // display:none (it is still safe to use offsets if a parent element is - // hidden; don safety goggles and see bug #4512 for more information). - // (only IE 8 fails this test) - div.innerHTML = "<table><tr><td style='" + paddingMarginBorder + "0;display:none'></td><td>t</td></tr></table>"; - tds = div.getElementsByTagName( "td" ); - isSupported = ( tds[ 0 ].offsetHeight === 0 ); - - tds[ 0 ].style.display = ""; - tds[ 1 ].style.display = "none"; - - // Check if empty table cells still have offsetWidth/Height - // (IE <= 8 fail this test) - support.reliableHiddenOffsets = isSupported && ( tds[ 0 ].offsetHeight === 0 ); - - // Check if div with explicit width and no margin-right incorrectly - // gets computed margin-right based on width of container. For more - // info see bug #3333 - // Fails in WebKit before Feb 2011 nightlies - // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right - if ( window.getComputedStyle ) { - div.innerHTML = ""; - marginDiv = document.createElement( "div" ); - marginDiv.style.width = "0"; - marginDiv.style.marginRight = "0"; - div.style.width = "2px"; - div.appendChild( marginDiv ); - support.reliableMarginRight = - ( parseInt( ( window.getComputedStyle( marginDiv, null ) || { marginRight: 0 } ).marginRight, 10 ) || 0 ) === 0; - } - - if ( typeof div.style.zoom !== "undefined" ) { - // Check if natively block-level elements act like inline-block - // elements when setting their display to 'inline' and giving - // them layout - // (IE < 8 does this) - div.innerHTML = ""; - div.style.width = div.style.padding = "1px"; - div.style.border = 0; - div.style.overflow = "hidden"; - div.style.display = "inline"; - div.style.zoom = 1; - support.inlineBlockNeedsLayout = ( div.offsetWidth === 3 ); - - // Check if elements with layout shrink-wrap their children - // (IE 6 does this) - div.style.display = "block"; - div.style.overflow = "visible"; - div.innerHTML = "<div style='width:5px;'></div>"; - support.shrinkWrapBlocks = ( div.offsetWidth !== 3 ); - } - - div.style.cssText = positionTopLeftWidthHeight + paddingMarginBorderVisibility; - div.innerHTML = html; - - outer = div.firstChild; - inner = outer.firstChild; - td = outer.nextSibling.firstChild.firstChild; - - offsetSupport = { - doesNotAddBorder: ( inner.offsetTop !== 5 ), - doesAddBorderForTableAndCells: ( td.offsetTop === 5 ) - }; - - inner.style.position = "fixed"; - inner.style.top = "20px"; - - // safari subtracts parent border width here which is 5px - offsetSupport.fixedPosition = ( inner.offsetTop === 20 || inner.offsetTop === 15 ); - inner.style.position = inner.style.top = ""; - - outer.style.overflow = "hidden"; - outer.style.position = "relative"; - - offsetSupport.subtractsBorderForOverflowNotVisible = ( inner.offsetTop === -5 ); - offsetSupport.doesNotIncludeMarginInBodyOffset = ( body.offsetTop !== conMarginTop ); - - if ( window.getComputedStyle ) { - div.style.marginTop = "1%"; - support.pixelMargin = ( window.getComputedStyle( div, null ) || { marginTop: 0 } ).marginTop !== "1%"; - } - - if ( typeof container.style.zoom !== "undefined" ) { - container.style.zoom = 1; - } - - body.removeChild( container ); - marginDiv = div = container = null; - - jQuery.extend( support, offsetSupport ); - }); - - return support; -})(); - - - - -var rbrace = /^(?:\{.*\}|\[.*\])$/, - rmultiDash = /([A-Z])/g; - -jQuery.extend({ - cache: {}, - - // Please use with caution - uuid: 0, - - // Unique for each copy of jQuery on the page - // Non-digits removed to match rinlinejQuery - expando: "jQuery" + ( jQuery.fn.jquery + Math.random() ).replace( /\D/g, "" ), - - // The following elements throw uncatchable exceptions if you - // attempt to add expando properties to them. - noData: { - "embed": true, - // Ban all objects except for Flash (which handle expandos) - "object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000", - "applet": true - }, - - hasData: function( elem ) { - elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ]; - return !!elem && !isEmptyDataObject( elem ); - }, - - data: function( elem, name, data, pvt /* Internal Use Only */ ) { - if ( !jQuery.acceptData( elem ) ) { - return; - } - - var privateCache, thisCache, ret, - internalKey = jQuery.expando, - getByName = typeof name === "string", - - // We have to handle DOM nodes and JS objects differently because IE6-7 - // can't GC object references properly across the DOM-JS boundary - isNode = elem.nodeType, - - // Only DOM nodes need the global jQuery cache; JS object data is - // attached directly to the object so GC can occur automatically - cache = isNode ? jQuery.cache : elem, - - // Only defining an ID for JS objects if its cache already exists allows - // the code to shortcut on the same path as a DOM node with no cache - id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey, - isEvents = name === "events"; - - // Avoid doing any more work than we need to when trying to get data on an - // object that has no data at all - if ( (!id || !cache[id] || (!isEvents && !pvt && !cache[id].data)) && getByName && data === undefined ) { - return; - } - - if ( !id ) { - // Only DOM nodes need a new unique ID for each element since their data - // ends up in the global cache - if ( isNode ) { - elem[ internalKey ] = id = ++jQuery.uuid; - } else { - id = internalKey; - } - } - - if ( !cache[ id ] ) { - cache[ id ] = {}; - - // Avoids exposing jQuery metadata on plain JS objects when the object - // is serialized using JSON.stringify - if ( !isNode ) { - cache[ id ].toJSON = jQuery.noop; - } - } - - // An object can be passed to jQuery.data instead of a key/value pair; this gets - // shallow copied over onto the existing cache - if ( typeof name === "object" || typeof name === "function" ) { - if ( pvt ) { - cache[ id ] = jQuery.extend( cache[ id ], name ); - } else { - cache[ id ].data = jQuery.extend( cache[ id ].data, name ); - } - } - - privateCache = thisCache = cache[ id ]; - - // jQuery data() is stored in a separate object inside the object's internal data - // cache in order to avoid key collisions between internal data and user-defined - // data. - if ( !pvt ) { - if ( !thisCache.data ) { - thisCache.data = {}; - } - - thisCache = thisCache.data; - } - - if ( data !== undefined ) { - thisCache[ jQuery.camelCase( name ) ] = data; - } - - // Users should not attempt to inspect the internal events object using jQuery.data, - // it is undocumented and subject to change. But does anyone listen? No. - if ( isEvents && !thisCache[ name ] ) { - return privateCache.events; - } - - // Check for both converted-to-camel and non-converted data property names - // If a data property was specified - if ( getByName ) { - - // First Try to find as-is property data - ret = thisCache[ name ]; - - // Test for null|undefined property data - if ( ret == null ) { - - // Try to find the camelCased property - ret = thisCache[ jQuery.camelCase( name ) ]; - } - } else { - ret = thisCache; - } - - return ret; - }, - - removeData: function( elem, name, pvt /* Internal Use Only */ ) { - if ( !jQuery.acceptData( elem ) ) { - return; - } - - var thisCache, i, l, - - // Reference to internal data cache key - internalKey = jQuery.expando, - - isNode = elem.nodeType, - - // See jQuery.data for more information - cache = isNode ? jQuery.cache : elem, - - // See jQuery.data for more information - id = isNode ? elem[ internalKey ] : internalKey; - - // If there is already no cache entry for this object, there is no - // purpose in continuing - if ( !cache[ id ] ) { - return; - } - - if ( name ) { - - thisCache = pvt ? cache[ id ] : cache[ id ].data; - - if ( thisCache ) { - - // Support array or space separated string names for data keys - if ( !jQuery.isArray( name ) ) { - - // try the string as a key before any manipulation - if ( name in thisCache ) { - name = [ name ]; - } else { - - // split the camel cased version by spaces unless a key with the spaces exists - name = jQuery.camelCase( name ); - if ( name in thisCache ) { - name = [ name ]; - } else { - name = name.split( " " ); - } - } - } - - for ( i = 0, l = name.length; i < l; i++ ) { - delete thisCache[ name[i] ]; - } - - // If there is no data left in the cache, we want to continue - // and let the cache object itself get destroyed - if ( !( pvt ? isEmptyDataObject : jQuery.isEmptyObject )( thisCache ) ) { - return; - } - } - } - - // See jQuery.data for more information - if ( !pvt ) { - delete cache[ id ].data; - - // Don't destroy the parent cache unless the internal data object - // had been the only thing left in it - if ( !isEmptyDataObject(cache[ id ]) ) { - return; - } - } - - // Browsers that fail expando deletion also refuse to delete expandos on - // the window, but it will allow it on all other JS objects; other browsers - // don't care - // Ensure that `cache` is not a window object #10080 - if ( jQuery.support.deleteExpando || !cache.setInterval ) { - delete cache[ id ]; - } else { - cache[ id ] = null; - } - - // We destroyed the cache and need to eliminate the expando on the node to avoid - // false lookups in the cache for entries that no longer exist - if ( isNode ) { - // IE does not allow us to delete expando properties from nodes, - // nor does it have a removeAttribute function on Document nodes; - // we must handle all of these cases - if ( jQuery.support.deleteExpando ) { - delete elem[ internalKey ]; - } else if ( elem.removeAttribute ) { - elem.removeAttribute( internalKey ); - } else { - elem[ internalKey ] = null; - } - } - }, - - // For internal use only. - _data: function( elem, name, data ) { - return jQuery.data( elem, name, data, true ); - }, - - // A method for determining if a DOM node can handle the data expando - acceptData: function( elem ) { - if ( elem.nodeName ) { - var match = jQuery.noData[ elem.nodeName.toLowerCase() ]; - - if ( match ) { - return !(match === true || elem.getAttribute("classid") !== match); - } - } - - return true; - } -}); - -jQuery.fn.extend({ - data: function( key, value ) { - var parts, part, attr, name, l, - elem = this[0], - i = 0, - data = null; - - // Gets all values - if ( key === undefined ) { - if ( this.length ) { - data = jQuery.data( elem ); - - if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) { - attr = elem.attributes; - for ( l = attr.length; i < l; i++ ) { - name = attr[i].name; - - if ( name.indexOf( "data-" ) === 0 ) { - name = jQuery.camelCase( name.substring(5) ); - - dataAttr( elem, name, data[ name ] ); - } - } - jQuery._data( elem, "parsedAttrs", true ); - } - } - - return data; - } - - // Sets multiple values - if ( typeof key === "object" ) { - return this.each(function() { - jQuery.data( this, key ); - }); - } - - parts = key.split( ".", 2 ); - parts[1] = parts[1] ? "." + parts[1] : ""; - part = parts[1] + "!"; - - return jQuery.access( this, function( value ) { - - if ( value === undefined ) { - data = this.triggerHandler( "getData" + part, [ parts[0] ] ); - - // Try to fetch any internally stored data first - if ( data === undefined && elem ) { - data = jQuery.data( elem, key ); - data = dataAttr( elem, key, data ); - } - - return data === undefined && parts[1] ? - this.data( parts[0] ) : - data; - } - - parts[1] = value; - this.each(function() { - var self = jQuery( this ); - - self.triggerHandler( "setData" + part, parts ); - jQuery.data( this, key, value ); - self.triggerHandler( "changeData" + part, parts ); - }); - }, null, value, arguments.length > 1, null, false ); - }, - - removeData: function( key ) { - return this.each(function() { - jQuery.removeData( this, key ); - }); - } -}); - -function dataAttr( elem, key, data ) { - // If nothing was found internally, try to fetch any - // data from the HTML5 data-* attribute - if ( data === undefined && elem.nodeType === 1 ) { - - var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase(); - - data = elem.getAttribute( name ); - - if ( typeof data === "string" ) { - try { - data = data === "true" ? true : - data === "false" ? false : - data === "null" ? null : - jQuery.isNumeric( data ) ? +data : - rbrace.test( data ) ? jQuery.parseJSON( data ) : - data; - } catch( e ) {} - - // Make sure we set the data so it isn't changed later - jQuery.data( elem, key, data ); - - } else { - data = undefined; - } - } - - return data; -} - -// checks a cache object for emptiness -function isEmptyDataObject( obj ) { - for ( var name in obj ) { - - // if the public data object is empty, the private is still empty - if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) { - continue; - } - if ( name !== "toJSON" ) { - return false; - } - } - - return true; -} - - - - -function handleQueueMarkDefer( elem, type, src ) { - var deferDataKey = type + "defer", - queueDataKey = type + "queue", - markDataKey = type + "mark", - defer = jQuery._data( elem, deferDataKey ); - if ( defer && - ( src === "queue" || !jQuery._data(elem, queueDataKey) ) && - ( src === "mark" || !jQuery._data(elem, markDataKey) ) ) { - // Give room for hard-coded callbacks to fire first - // and eventually mark/queue something else on the element - setTimeout( function() { - if ( !jQuery._data( elem, queueDataKey ) && - !jQuery._data( elem, markDataKey ) ) { - jQuery.removeData( elem, deferDataKey, true ); - defer.fire(); - } - }, 0 ); - } -} - -jQuery.extend({ - - _mark: function( elem, type ) { - if ( elem ) { - type = ( type || "fx" ) + "mark"; - jQuery._data( elem, type, (jQuery._data( elem, type ) || 0) + 1 ); - } - }, - - _unmark: function( force, elem, type ) { - if ( force !== true ) { - type = elem; - elem = force; - force = false; - } - if ( elem ) { - type = type || "fx"; - var key = type + "mark", - count = force ? 0 : ( (jQuery._data( elem, key ) || 1) - 1 ); - if ( count ) { - jQuery._data( elem, key, count ); - } else { - jQuery.removeData( elem, key, true ); - handleQueueMarkDefer( elem, type, "mark" ); - } - } - }, - - queue: function( elem, type, data ) { - var q; - if ( elem ) { - type = ( type || "fx" ) + "queue"; - q = jQuery._data( elem, type ); - - // Speed up dequeue by getting out quickly if this is just a lookup - if ( data ) { - if ( !q || jQuery.isArray(data) ) { - q = jQuery._data( elem, type, jQuery.makeArray(data) ); - } else { - q.push( data ); - } - } - return q || []; - } - }, - - dequeue: function( elem, type ) { - type = type || "fx"; - - var queue = jQuery.queue( elem, type ), - fn = queue.shift(), - hooks = {}; - - // If the fx queue is dequeued, always remove the progress sentinel - if ( fn === "inprogress" ) { - fn = queue.shift(); - } - - if ( fn ) { - // Add a progress sentinel to prevent the fx queue from being - // automatically dequeued - if ( type === "fx" ) { - queue.unshift( "inprogress" ); - } - - jQuery._data( elem, type + ".run", hooks ); - fn.call( elem, function() { - jQuery.dequeue( elem, type ); - }, hooks ); - } - - if ( !queue.length ) { - jQuery.removeData( elem, type + "queue " + type + ".run", true ); - handleQueueMarkDefer( elem, type, "queue" ); - } - } -}); - -jQuery.fn.extend({ - queue: function( type, data ) { - var setter = 2; - - if ( typeof type !== "string" ) { - data = type; - type = "fx"; - setter--; - } - - if ( arguments.length < setter ) { - return jQuery.queue( this[0], type ); - } - - return data === undefined ? - this : - this.each(function() { - var queue = jQuery.queue( this, type, data ); - - if ( type === "fx" && queue[0] !== "inprogress" ) { - jQuery.dequeue( this, type ); - } - }); - }, - dequeue: function( type ) { - return this.each(function() { - jQuery.dequeue( this, type ); - }); - }, - // Based off of the plugin by Clint Helfers, with permission. - // http://blindsignals.com/index.php/2009/07/jquery-delay/ - delay: function( time, type ) { - time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; - type = type || "fx"; - - return this.queue( type, function( next, hooks ) { - var timeout = setTimeout( next, time ); - hooks.stop = function() { - clearTimeout( timeout ); - }; - }); - }, - clearQueue: function( type ) { - return this.queue( type || "fx", [] ); - }, - // Get a promise resolved when queues of a certain type - // are emptied (fx is the type by default) - promise: function( type, object ) { - if ( typeof type !== "string" ) { - object = type; - type = undefined; - } - type = type || "fx"; - var defer = jQuery.Deferred(), - elements = this, - i = elements.length, - count = 1, - deferDataKey = type + "defer", - queueDataKey = type + "queue", - markDataKey = type + "mark", - tmp; - function resolve() { - if ( !( --count ) ) { - defer.resolveWith( elements, [ elements ] ); - } - } - while( i-- ) { - if (( tmp = jQuery.data( elements[ i ], deferDataKey, undefined, true ) || - ( jQuery.data( elements[ i ], queueDataKey, undefined, true ) || - jQuery.data( elements[ i ], markDataKey, undefined, true ) ) && - jQuery.data( elements[ i ], deferDataKey, jQuery.Callbacks( "once memory" ), true ) )) { - count++; - tmp.add( resolve ); - } - } - resolve(); - return defer.promise( object ); - } -}); - - - - -var rclass = /[\n\t\r]/g, - rspace = /\s+/, - rreturn = /\r/g, - rtype = /^(?:button|input)$/i, - rfocusable = /^(?:button|input|object|select|textarea)$/i, - rclickable = /^a(?:rea)?$/i, - rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i, - getSetAttribute = jQuery.support.getSetAttribute, - nodeHook, boolHook, fixSpecified; - -jQuery.fn.extend({ - attr: function( name, value ) { - return jQuery.access( this, jQuery.attr, name, value, arguments.length > 1 ); - }, - - removeAttr: function( name ) { - return this.each(function() { - jQuery.removeAttr( this, name ); - }); - }, - - prop: function( name, value ) { - return jQuery.access( this, jQuery.prop, name, value, arguments.length > 1 ); - }, - - removeProp: function( name ) { - name = jQuery.propFix[ name ] || name; - return this.each(function() { - // try/catch handles cases where IE balks (such as removing a property on window) - try { - this[ name ] = undefined; - delete this[ name ]; - } catch( e ) {} - }); - }, - - addClass: function( value ) { - var classNames, i, l, elem, - setClass, c, cl; - - if ( jQuery.isFunction( value ) ) { - return this.each(function( j ) { - jQuery( this ).addClass( value.call(this, j, this.className) ); - }); - } - - if ( value && typeof value === "string" ) { - classNames = value.split( rspace ); - - for ( i = 0, l = this.length; i < l; i++ ) { - elem = this[ i ]; - - if ( elem.nodeType === 1 ) { - if ( !elem.className && classNames.length === 1 ) { - elem.className = value; - - } else { - setClass = " " + elem.className + " "; - - for ( c = 0, cl = classNames.length; c < cl; c++ ) { - if ( !~setClass.indexOf( " " + classNames[ c ] + " " ) ) { - setClass += classNames[ c ] + " "; - } - } - elem.className = jQuery.trim( setClass ); - } - } - } - } - - return this; - }, - - removeClass: function( value ) { - var classNames, i, l, elem, className, c, cl; - - if ( jQuery.isFunction( value ) ) { - return this.each(function( j ) { - jQuery( this ).removeClass( value.call(this, j, this.className) ); - }); - } - - if ( (value && typeof value === "string") || value === undefined ) { - classNames = ( value || "" ).split( rspace ); - - for ( i = 0, l = this.length; i < l; i++ ) { - elem = this[ i ]; - - if ( elem.nodeType === 1 && elem.className ) { - if ( value ) { - className = (" " + elem.className + " ").replace( rclass, " " ); - for ( c = 0, cl = classNames.length; c < cl; c++ ) { - className = className.replace(" " + classNames[ c ] + " ", " "); - } - elem.className = jQuery.trim( className ); - - } else { - elem.className = ""; - } - } - } - } - - return this; - }, - - toggleClass: function( value, stateVal ) { - var type = typeof value, - isBool = typeof stateVal === "boolean"; - - if ( jQuery.isFunction( value ) ) { - return this.each(function( i ) { - jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal ); - }); - } - - return this.each(function() { - if ( type === "string" ) { - // toggle individual class names - var className, - i = 0, - self = jQuery( this ), - state = stateVal, - classNames = value.split( rspace ); - - while ( (className = classNames[ i++ ]) ) { - // check each className given, space seperated list - state = isBool ? state : !self.hasClass( className ); - self[ state ? "addClass" : "removeClass" ]( className ); - } - - } else if ( type === "undefined" || type === "boolean" ) { - if ( this.className ) { - // store className if set - jQuery._data( this, "__className__", this.className ); - } - - // toggle whole className - this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || ""; - } - }); - }, - - hasClass: function( selector ) { - var className = " " + selector + " ", - i = 0, - l = this.length; - for ( ; i < l; i++ ) { - if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) > -1 ) { - return true; - } - } - - return false; - }, - - val: function( value ) { - var hooks, ret, isFunction, - elem = this[0]; - - if ( !arguments.length ) { - if ( elem ) { - hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ]; - - if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) { - return ret; - } - - ret = elem.value; - - return typeof ret === "string" ? - // handle most common string cases - ret.replace(rreturn, "") : - // handle cases where value is null/undef or number - ret == null ? "" : ret; - } - - return; - } - - isFunction = jQuery.isFunction( value ); - - return this.each(function( i ) { - var self = jQuery(this), val; - - if ( this.nodeType !== 1 ) { - return; - } - - if ( isFunction ) { - val = value.call( this, i, self.val() ); - } else { - val = value; - } - - // Treat null/undefined as ""; convert numbers to string - if ( val == null ) { - val = ""; - } else if ( typeof val === "number" ) { - val += ""; - } else if ( jQuery.isArray( val ) ) { - val = jQuery.map(val, function ( value ) { - return value == null ? "" : value + ""; - }); - } - - hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; - - // If set returns undefined, fall back to normal setting - if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) { - this.value = val; - } - }); - } -}); - -jQuery.extend({ - valHooks: { - option: { - get: function( elem ) { - // attributes.value is undefined in Blackberry 4.7 but - // uses .value. See #6932 - var val = elem.attributes.value; - return !val || val.specified ? elem.value : elem.text; - } - }, - select: { - get: function( elem ) { - var value, i, max, option, - index = elem.selectedIndex, - values = [], - options = elem.options, - one = elem.type === "select-one"; - - // Nothing was selected - if ( index < 0 ) { - return null; - } - - // Loop through all the selected options - i = one ? index : 0; - max = one ? index + 1 : options.length; - for ( ; i < max; i++ ) { - option = options[ i ]; - - // Don't return options that are disabled or in a disabled optgroup - if ( option.selected && (jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null) && - (!option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" )) ) { - - // Get the specific value for the option - value = jQuery( option ).val(); - - // We don't need an array for one selects - if ( one ) { - return value; - } - - // Multi-Selects return an array - values.push( value ); - } - } - - // Fixes Bug #2551 -- select.val() broken in IE after form.reset() - if ( one && !values.length && options.length ) { - return jQuery( options[ index ] ).val(); - } - - return values; - }, - - set: function( elem, value ) { - var values = jQuery.makeArray( value ); - - jQuery(elem).find("option").each(function() { - this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0; - }); - - if ( !values.length ) { - elem.selectedIndex = -1; - } - return values; - } - } - }, - - attrFn: { - val: true, - css: true, - html: true, - text: true, - data: true, - width: true, - height: true, - offset: true - }, - - attr: function( elem, name, value, pass ) { - var ret, hooks, notxml, - nType = elem.nodeType; - - // don't get/set attributes on text, comment and attribute nodes - if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - if ( pass && name in jQuery.attrFn ) { - return jQuery( elem )[ name ]( value ); - } - - // Fallback to prop when attributes are not supported - if ( typeof elem.getAttribute === "undefined" ) { - return jQuery.prop( elem, name, value ); - } - - notxml = nType !== 1 || !jQuery.isXMLDoc( elem ); - - // All attributes are lowercase - // Grab necessary hook if one is defined - if ( notxml ) { - name = name.toLowerCase(); - hooks = jQuery.attrHooks[ name ] || ( rboolean.test( name ) ? boolHook : nodeHook ); - } - - if ( value !== undefined ) { - - if ( value === null ) { - jQuery.removeAttr( elem, name ); - return; - - } else if ( hooks && "set" in hooks && notxml && (ret = hooks.set( elem, value, name )) !== undefined ) { - return ret; - - } else { - elem.setAttribute( name, "" + value ); - return value; - } - - } else if ( hooks && "get" in hooks && notxml && (ret = hooks.get( elem, name )) !== null ) { - return ret; - - } else { - - ret = elem.getAttribute( name ); - - // Non-existent attributes return null, we normalize to undefined - return ret === null ? - undefined : - ret; - } - }, - - removeAttr: function( elem, value ) { - var propName, attrNames, name, l, isBool, - i = 0; - - if ( value && elem.nodeType === 1 ) { - attrNames = value.toLowerCase().split( rspace ); - l = attrNames.length; - - for ( ; i < l; i++ ) { - name = attrNames[ i ]; - - if ( name ) { - propName = jQuery.propFix[ name ] || name; - isBool = rboolean.test( name ); - - // See #9699 for explanation of this approach (setting first, then removal) - // Do not do this for boolean attributes (see #10870) - if ( !isBool ) { - jQuery.attr( elem, name, "" ); - } - elem.removeAttribute( getSetAttribute ? name : propName ); - - // Set corresponding property to false for boolean attributes - if ( isBool && propName in elem ) { - elem[ propName ] = false; - } - } - } - } - }, - - attrHooks: { - type: { - set: function( elem, value ) { - // We can't allow the type property to be changed (since it causes problems in IE) - if ( rtype.test( elem.nodeName ) && elem.parentNode ) { - jQuery.error( "type property can't be changed" ); - } else if ( !jQuery.support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) { - // Setting the type on a radio button after the value resets the value in IE6-9 - // Reset value to it's default in case type is set after value - // This is for element creation - var val = elem.value; - elem.setAttribute( "type", value ); - if ( val ) { - elem.value = val; - } - return value; - } - } - }, - // Use the value property for back compat - // Use the nodeHook for button elements in IE6/7 (#1954) - value: { - get: function( elem, name ) { - if ( nodeHook && jQuery.nodeName( elem, "button" ) ) { - return nodeHook.get( elem, name ); - } - return name in elem ? - elem.value : - null; - }, - set: function( elem, value, name ) { - if ( nodeHook && jQuery.nodeName( elem, "button" ) ) { - return nodeHook.set( elem, value, name ); - } - // Does not return so that setAttribute is also used - elem.value = value; - } - } - }, - - propFix: { - tabindex: "tabIndex", - readonly: "readOnly", - "for": "htmlFor", - "class": "className", - maxlength: "maxLength", - cellspacing: "cellSpacing", - cellpadding: "cellPadding", - rowspan: "rowSpan", - colspan: "colSpan", - usemap: "useMap", - frameborder: "frameBorder", - contenteditable: "contentEditable" - }, - - prop: function( elem, name, value ) { - var ret, hooks, notxml, - nType = elem.nodeType; - - // don't get/set properties on text, comment and attribute nodes - if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { - return; - } - - notxml = nType !== 1 || !jQuery.isXMLDoc( elem ); - - if ( notxml ) { - // Fix name and attach hooks - name = jQuery.propFix[ name ] || name; - hooks = jQuery.propHooks[ name ]; - } - - if ( value !== undefined ) { - if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) { - return ret; - - } else { - return ( elem[ name ] = value ); - } - - } else { - if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) { - return ret; - - } else { - return elem[ name ]; - } - } - }, - - propHooks: { - tabIndex: { - get: function( elem ) { - // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set - // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ - var attributeNode = elem.getAttributeNode("tabindex"); - - return attributeNode && attributeNode.specified ? - parseInt( attributeNode.value, 10 ) : - rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ? - 0 : - undefined; - } - } - } -}); - -// Add the tabIndex propHook to attrHooks for back-compat (different case is intentional) -jQuery.attrHooks.tabindex = jQuery.propHooks.tabIndex; - -// Hook for boolean attributes -boolHook = { - get: function( elem, name ) { - // Align boolean attributes with corresponding properties - // Fall back to attribute presence where some booleans are not supported - var attrNode, - property = jQuery.prop( elem, name ); - return property === true || typeof property !== "boolean" && ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ? - name.toLowerCase() : - undefined; - }, - set: function( elem, value, name ) { - var propName; - if ( value === false ) { - // Remove boolean attributes when set to false - jQuery.removeAttr( elem, name ); - } else { - // value is true since we know at this point it's type boolean and not false - // Set boolean attributes to the same name and set the DOM property - propName = jQuery.propFix[ name ] || name; - if ( propName in elem ) { - // Only set the IDL specifically if it already exists on the element - elem[ propName ] = true; - } - - elem.setAttribute( name, name.toLowerCase() ); - } - return name; - } -}; - -// IE6/7 do not support getting/setting some attributes with get/setAttribute -if ( !getSetAttribute ) { - - fixSpecified = { - name: true, - id: true, - coords: true - }; - - // Use this for any attribute in IE6/7 - // This fixes almost every IE6/7 issue - nodeHook = jQuery.valHooks.button = { - get: function( elem, name ) { - var ret; - ret = elem.getAttributeNode( name ); - return ret && ( fixSpecified[ name ] ? ret.nodeValue !== "" : ret.specified ) ? - ret.nodeValue : - undefined; - }, - set: function( elem, value, name ) { - // Set the existing or create a new attribute node - var ret = elem.getAttributeNode( name ); - if ( !ret ) { - ret = document.createAttribute( name ); - elem.setAttributeNode( ret ); - } - return ( ret.nodeValue = value + "" ); - } - }; - - // Apply the nodeHook to tabindex - jQuery.attrHooks.tabindex.set = nodeHook.set; - - // Set width and height to auto instead of 0 on empty string( Bug #8150 ) - // This is for removals - jQuery.each([ "width", "height" ], function( i, name ) { - jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], { - set: function( elem, value ) { - if ( value === "" ) { - elem.setAttribute( name, "auto" ); - return value; - } - } - }); - }); - - // Set contenteditable to false on removals(#10429) - // Setting to empty string throws an error as an invalid value - jQuery.attrHooks.contenteditable = { - get: nodeHook.get, - set: function( elem, value, name ) { - if ( value === "" ) { - value = "false"; - } - nodeHook.set( elem, value, name ); - } - }; -} - - -// Some attributes require a special call on IE -if ( !jQuery.support.hrefNormalized ) { - jQuery.each([ "href", "src", "width", "height" ], function( i, name ) { - jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], { - get: function( elem ) { - var ret = elem.getAttribute( name, 2 ); - return ret === null ? undefined : ret; - } - }); - }); -} - -if ( !jQuery.support.style ) { - jQuery.attrHooks.style = { - get: function( elem ) { - // Return undefined in the case of empty string - // Normalize to lowercase since IE uppercases css property names - return elem.style.cssText.toLowerCase() || undefined; - }, - set: function( elem, value ) { - return ( elem.style.cssText = "" + value ); - } - }; -} - -// Safari mis-reports the default selected property of an option -// Accessing the parent's selectedIndex property fixes it -if ( !jQuery.support.optSelected ) { - jQuery.propHooks.selected = jQuery.extend( jQuery.propHooks.selected, { - get: function( elem ) { - var parent = elem.parentNode; - - if ( parent ) { - parent.selectedIndex; - - // Make sure that it also works with optgroups, see #5701 - if ( parent.parentNode ) { - parent.parentNode.selectedIndex; - } - } - return null; - } - }); -} - -// IE6/7 call enctype encoding -if ( !jQuery.support.enctype ) { - jQuery.propFix.enctype = "encoding"; -} - -// Radios and checkboxes getter/setter -if ( !jQuery.support.checkOn ) { - jQuery.each([ "radio", "checkbox" ], function() { - jQuery.valHooks[ this ] = { - get: function( elem ) { - // Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified - return elem.getAttribute("value") === null ? "on" : elem.value; - } - }; - }); -} -jQuery.each([ "radio", "checkbox" ], function() { - jQuery.valHooks[ this ] = jQuery.extend( jQuery.valHooks[ this ], { - set: function( elem, value ) { - if ( jQuery.isArray( value ) ) { - return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 ); - } - } - }); -}); - - - - -var rformElems = /^(?:textarea|input|select)$/i, - rtypenamespace = /^([^\.]*)?(?:\.(.+))?$/, - rhoverHack = /(?:^|\s)hover(\.\S+)?\b/, - rkeyEvent = /^key/, - rmouseEvent = /^(?:mouse|contextmenu)|click/, - rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, - rquickIs = /^(\w*)(?:#([\w\-]+))?(?:\.([\w\-]+))?$/, - quickParse = function( selector ) { - var quick = rquickIs.exec( selector ); - if ( quick ) { - // 0 1 2 3 - // [ _, tag, id, class ] - quick[1] = ( quick[1] || "" ).toLowerCase(); - quick[3] = quick[3] && new RegExp( "(?:^|\\s)" + quick[3] + "(?:\\s|$)" ); - } - return quick; - }, - quickIs = function( elem, m ) { - var attrs = elem.attributes || {}; - return ( - (!m[1] || elem.nodeName.toLowerCase() === m[1]) && - (!m[2] || (attrs.id || {}).value === m[2]) && - (!m[3] || m[3].test( (attrs[ "class" ] || {}).value )) - ); - }, - hoverHack = function( events ) { - return jQuery.event.special.hover ? events : events.replace( rhoverHack, "mouseenter$1 mouseleave$1" ); - }; - -/* - * Helper functions for managing events -- not part of the public interface. - * Props to Dean Edwards' addEvent library for many of the ideas. - */ -jQuery.event = { - - add: function( elem, types, handler, data, selector ) { - - var elemData, eventHandle, events, - t, tns, type, namespaces, handleObj, - handleObjIn, quick, handlers, special; - - // Don't attach events to noData or text/comment nodes (allow plain objects tho) - if ( elem.nodeType === 3 || elem.nodeType === 8 || !types || !handler || !(elemData = jQuery._data( elem )) ) { - return; - } - - // Caller can pass in an object of custom data in lieu of the handler - if ( handler.handler ) { - handleObjIn = handler; - handler = handleObjIn.handler; - selector = handleObjIn.selector; - } - - // Make sure that the handler has a unique ID, used to find/remove it later - if ( !handler.guid ) { - handler.guid = jQuery.guid++; - } - - // Init the element's event structure and main handler, if this is the first - events = elemData.events; - if ( !events ) { - elemData.events = events = {}; - } - eventHandle = elemData.handle; - if ( !eventHandle ) { - elemData.handle = eventHandle = function( e ) { - // Discard the second event of a jQuery.event.trigger() and - // when an event is called after a page has unloaded - return typeof jQuery !== "undefined" && (!e || jQuery.event.triggered !== e.type) ? - jQuery.event.dispatch.apply( eventHandle.elem, arguments ) : - undefined; - }; - // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events - eventHandle.elem = elem; - } - - // Handle multiple events separated by a space - // jQuery(...).bind("mouseover mouseout", fn); - types = jQuery.trim( hoverHack(types) ).split( " " ); - for ( t = 0; t < types.length; t++ ) { - - tns = rtypenamespace.exec( types[t] ) || []; - type = tns[1]; - namespaces = ( tns[2] || "" ).split( "." ).sort(); - - // If event changes its type, use the special event handlers for the changed type - special = jQuery.event.special[ type ] || {}; - - // If selector defined, determine special event api type, otherwise given type - type = ( selector ? special.delegateType : special.bindType ) || type; - - // Update special based on newly reset type - special = jQuery.event.special[ type ] || {}; - - // handleObj is passed to all event handlers - handleObj = jQuery.extend({ - type: type, - origType: tns[1], - data: data, - handler: handler, - guid: handler.guid, - selector: selector, - quick: selector && quickParse( selector ), - namespace: namespaces.join(".") - }, handleObjIn ); - - // Init the event handler queue if we're the first - handlers = events[ type ]; - if ( !handlers ) { - handlers = events[ type ] = []; - handlers.delegateCount = 0; - - // Only use addEventListener/attachEvent if the special events handler returns false - if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) { - // Bind the global event handler to the element - if ( elem.addEventListener ) { - elem.addEventListener( type, eventHandle, false ); - - } else if ( elem.attachEvent ) { - elem.attachEvent( "on" + type, eventHandle ); - } - } - } - - if ( special.add ) { - special.add.call( elem, handleObj ); - - if ( !handleObj.handler.guid ) { - handleObj.handler.guid = handler.guid; - } - } - - // Add to the element's handler list, delegates in front - if ( selector ) { - handlers.splice( handlers.delegateCount++, 0, handleObj ); - } else { - handlers.push( handleObj ); - } - - // Keep track of which events have ever been used, for event optimization - jQuery.event.global[ type ] = true; - } - - // Nullify elem to prevent memory leaks in IE - elem = null; - }, - - global: {}, - - // Detach an event or set of events from an element - remove: function( elem, types, handler, selector, mappedTypes ) { - - var elemData = jQuery.hasData( elem ) && jQuery._data( elem ), - t, tns, type, origType, namespaces, origCount, - j, events, special, handle, eventType, handleObj; - - if ( !elemData || !(events = elemData.events) ) { - return; - } - - // Once for each type.namespace in types; type may be omitted - types = jQuery.trim( hoverHack( types || "" ) ).split(" "); - for ( t = 0; t < types.length; t++ ) { - tns = rtypenamespace.exec( types[t] ) || []; - type = origType = tns[1]; - namespaces = tns[2]; - - // Unbind all events (on this namespace, if provided) for the element - if ( !type ) { - for ( type in events ) { - jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); - } - continue; - } - - special = jQuery.event.special[ type ] || {}; - type = ( selector? special.delegateType : special.bindType ) || type; - eventType = events[ type ] || []; - origCount = eventType.length; - namespaces = namespaces ? new RegExp("(^|\\.)" + namespaces.split(".").sort().join("\\.(?:.*\\.)?") + "(\\.|$)") : null; - - // Remove matching events - for ( j = 0; j < eventType.length; j++ ) { - handleObj = eventType[ j ]; - - if ( ( mappedTypes || origType === handleObj.origType ) && - ( !handler || handler.guid === handleObj.guid ) && - ( !namespaces || namespaces.test( handleObj.namespace ) ) && - ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) { - eventType.splice( j--, 1 ); - - if ( handleObj.selector ) { - eventType.delegateCount--; - } - if ( special.remove ) { - special.remove.call( elem, handleObj ); - } - } - } - - // Remove generic event handler if we removed something and no more handlers exist - // (avoids potential for endless recursion during removal of special event handlers) - if ( eventType.length === 0 && origCount !== eventType.length ) { - if ( !special.teardown || special.teardown.call( elem, namespaces ) === false ) { - jQuery.removeEvent( elem, type, elemData.handle ); - } - - delete events[ type ]; - } - } - - // Remove the expando if it's no longer used - if ( jQuery.isEmptyObject( events ) ) { - handle = elemData.handle; - if ( handle ) { - handle.elem = null; - } - - // removeData also checks for emptiness and clears the expando if empty - // so use it instead of delete - jQuery.removeData( elem, [ "events", "handle" ], true ); - } - }, - - // Events that are safe to short-circuit if no handlers are attached. - // Native DOM events should not be added, they may have inline handlers. - customEvent: { - "getData": true, - "setData": true, - "changeData": true - }, - - trigger: function( event, data, elem, onlyHandlers ) { - // Don't do events on text and comment nodes - if ( elem && (elem.nodeType === 3 || elem.nodeType === 8) ) { - return; - } - - // Event object or event type - var type = event.type || event, - namespaces = [], - cache, exclusive, i, cur, old, ontype, special, handle, eventPath, bubbleType; - - // focus/blur morphs to focusin/out; ensure we're not firing them right now - if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { - return; - } - - if ( type.indexOf( "!" ) >= 0 ) { - // Exclusive events trigger only for the exact event (no namespaces) - type = type.slice(0, -1); - exclusive = true; - } - - if ( type.indexOf( "." ) >= 0 ) { - // Namespaced trigger; create a regexp to match event type in handle() - namespaces = type.split("."); - type = namespaces.shift(); - namespaces.sort(); - } - - if ( (!elem || jQuery.event.customEvent[ type ]) && !jQuery.event.global[ type ] ) { - // No jQuery handlers for this event type, and it can't have inline handlers - return; - } - - // Caller can pass in an Event, Object, or just an event type string - event = typeof event === "object" ? - // jQuery.Event object - event[ jQuery.expando ] ? event : - // Object literal - new jQuery.Event( type, event ) : - // Just the event type (string) - new jQuery.Event( type ); - - event.type = type; - event.isTrigger = true; - event.exclusive = exclusive; - event.namespace = namespaces.join( "." ); - event.namespace_re = event.namespace? new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.)?") + "(\\.|$)") : null; - ontype = type.indexOf( ":" ) < 0 ? "on" + type : ""; - - // Handle a global trigger - if ( !elem ) { - - // TODO: Stop taunting the data cache; remove global events and always attach to document - cache = jQuery.cache; - for ( i in cache ) { - if ( cache[ i ].events && cache[ i ].events[ type ] ) { - jQuery.event.trigger( event, data, cache[ i ].handle.elem, true ); - } - } - return; - } - - // Clean up the event in case it is being reused - event.result = undefined; - if ( !event.target ) { - event.target = elem; - } - - // Clone any incoming data and prepend the event, creating the handler arg list - data = data != null ? jQuery.makeArray( data ) : []; - data.unshift( event ); - - // Allow special events to draw outside the lines - special = jQuery.event.special[ type ] || {}; - if ( special.trigger && special.trigger.apply( elem, data ) === false ) { - return; - } - - // Determine event propagation path in advance, per W3C events spec (#9951) - // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) - eventPath = [[ elem, special.bindType || type ]]; - if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { - - bubbleType = special.delegateType || type; - cur = rfocusMorph.test( bubbleType + type ) ? elem : elem.parentNode; - old = null; - for ( ; cur; cur = cur.parentNode ) { - eventPath.push([ cur, bubbleType ]); - old = cur; - } - - // Only add window if we got to document (e.g., not plain obj or detached DOM) - if ( old && old === elem.ownerDocument ) { - eventPath.push([ old.defaultView || old.parentWindow || window, bubbleType ]); - } - } - - // Fire handlers on the event path - for ( i = 0; i < eventPath.length && !event.isPropagationStopped(); i++ ) { - - cur = eventPath[i][0]; - event.type = eventPath[i][1]; - - handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" ); - if ( handle ) { - handle.apply( cur, data ); - } - // Note that this is a bare JS function and not a jQuery handler - handle = ontype && cur[ ontype ]; - if ( handle && jQuery.acceptData( cur ) && handle.apply( cur, data ) === false ) { - event.preventDefault(); - } - } - event.type = type; - - // If nobody prevented the default action, do it now - if ( !onlyHandlers && !event.isDefaultPrevented() ) { - - if ( (!special._default || special._default.apply( elem.ownerDocument, data ) === false) && - !(type === "click" && jQuery.nodeName( elem, "a" )) && jQuery.acceptData( elem ) ) { - - // Call a native DOM method on the target with the same name name as the event. - // Can't use an .isFunction() check here because IE6/7 fails that test. - // Don't do default actions on window, that's where global variables be (#6170) - // IE<9 dies on focus/blur to hidden element (#1486) - if ( ontype && elem[ type ] && ((type !== "focus" && type !== "blur") || event.target.offsetWidth !== 0) && !jQuery.isWindow( elem ) ) { - - // Don't re-trigger an onFOO event when we call its FOO() method - old = elem[ ontype ]; - - if ( old ) { - elem[ ontype ] = null; - } - - // Prevent re-triggering of the same event, since we already bubbled it above - jQuery.event.triggered = type; - elem[ type ](); - jQuery.event.triggered = undefined; - - if ( old ) { - elem[ ontype ] = old; - } - } - } - } - - return event.result; - }, - - dispatch: function( event ) { - - // Make a writable jQuery.Event from the native event object - event = jQuery.event.fix( event || window.event ); - - var handlers = ( (jQuery._data( this, "events" ) || {} )[ event.type ] || []), - delegateCount = handlers.delegateCount, - args = [].slice.call( arguments, 0 ), - run_all = !event.exclusive && !event.namespace, - special = jQuery.event.special[ event.type ] || {}, - handlerQueue = [], - i, j, cur, jqcur, ret, selMatch, matched, matches, handleObj, sel, related; - - // Use the fix-ed jQuery.Event rather than the (read-only) native event - args[0] = event; - event.delegateTarget = this; - - // Call the preDispatch hook for the mapped type, and let it bail if desired - if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { - return; - } - - // Determine handlers that should run if there are delegated events - // Avoid non-left-click bubbling in Firefox (#3861) - if ( delegateCount && !(event.button && event.type === "click") ) { - - // Pregenerate a single jQuery object for reuse with .is() - jqcur = jQuery(this); - jqcur.context = this.ownerDocument || this; - - for ( cur = event.target; cur != this; cur = cur.parentNode || this ) { - - // Don't process events on disabled elements (#6911, #8165) - if ( cur.disabled !== true ) { - selMatch = {}; - matches = []; - jqcur[0] = cur; - for ( i = 0; i < delegateCount; i++ ) { - handleObj = handlers[ i ]; - sel = handleObj.selector; - - if ( selMatch[ sel ] === undefined ) { - selMatch[ sel ] = ( - handleObj.quick ? quickIs( cur, handleObj.quick ) : jqcur.is( sel ) - ); - } - if ( selMatch[ sel ] ) { - matches.push( handleObj ); - } - } - if ( matches.length ) { - handlerQueue.push({ elem: cur, matches: matches }); - } - } - } - } - - // Add the remaining (directly-bound) handlers - if ( handlers.length > delegateCount ) { - handlerQueue.push({ elem: this, matches: handlers.slice( delegateCount ) }); - } - - // Run delegates first; they may want to stop propagation beneath us - for ( i = 0; i < handlerQueue.length && !event.isPropagationStopped(); i++ ) { - matched = handlerQueue[ i ]; - event.currentTarget = matched.elem; - - for ( j = 0; j < matched.matches.length && !event.isImmediatePropagationStopped(); j++ ) { - handleObj = matched.matches[ j ]; - - // Triggered event must either 1) be non-exclusive and have no namespace, or - // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace). - if ( run_all || (!event.namespace && !handleObj.namespace) || event.namespace_re && event.namespace_re.test( handleObj.namespace ) ) { - - event.data = handleObj.data; - event.handleObj = handleObj; - - ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler ) - .apply( matched.elem, args ); - - if ( ret !== undefined ) { - event.result = ret; - if ( ret === false ) { - event.preventDefault(); - event.stopPropagation(); - } - } - } - } - } - - // Call the postDispatch hook for the mapped type - if ( special.postDispatch ) { - special.postDispatch.call( this, event ); - } - - return event.result; - }, - - // Includes some event props shared by KeyEvent and MouseEvent - // *** attrChange attrName relatedNode srcElement are not normalized, non-W3C, deprecated, will be removed in 1.8 *** - props: "attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "), - - fixHooks: {}, - - keyHooks: { - props: "char charCode key keyCode".split(" "), - filter: function( event, original ) { - - // Add which for key events - if ( event.which == null ) { - event.which = original.charCode != null ? original.charCode : original.keyCode; - } - - return event; - } - }, - - mouseHooks: { - props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "), - filter: function( event, original ) { - var eventDoc, doc, body, - button = original.button, - fromElement = original.fromElement; - - // Calculate pageX/Y if missing and clientX/Y available - if ( event.pageX == null && original.clientX != null ) { - eventDoc = event.target.ownerDocument || document; - doc = eventDoc.documentElement; - body = eventDoc.body; - - event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 ); - event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 ); - } - - // Add relatedTarget, if necessary - if ( !event.relatedTarget && fromElement ) { - event.relatedTarget = fromElement === event.target ? original.toElement : fromElement; - } - - // Add which for click: 1 === left; 2 === middle; 3 === right - // Note: button is not normalized, so don't use it - if ( !event.which && button !== undefined ) { - event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) ); - } - - return event; - } - }, - - fix: function( event ) { - if ( event[ jQuery.expando ] ) { - return event; - } - - // Create a writable copy of the event object and normalize some properties - var i, prop, - originalEvent = event, - fixHook = jQuery.event.fixHooks[ event.type ] || {}, - copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props; - - event = jQuery.Event( originalEvent ); - - for ( i = copy.length; i; ) { - prop = copy[ --i ]; - event[ prop ] = originalEvent[ prop ]; - } - - // Fix target property, if necessary (#1925, IE 6/7/8 & Safari2) - if ( !event.target ) { - event.target = originalEvent.srcElement || document; - } - - // Target should not be a text node (#504, Safari) - if ( event.target.nodeType === 3 ) { - event.target = event.target.parentNode; - } - - // For mouse/key events; add metaKey if it's not there (#3368, IE6/7/8) - if ( event.metaKey === undefined ) { - event.metaKey = event.ctrlKey; - } - - return fixHook.filter? fixHook.filter( event, originalEvent ) : event; - }, - - special: { - ready: { - // Make sure the ready event is setup - setup: jQuery.bindReady - }, - - load: { - // Prevent triggered image.load events from bubbling to window.load - noBubble: true - }, - - focus: { - delegateType: "focusin" - }, - blur: { - delegateType: "focusout" - }, - - beforeunload: { - setup: function( data, namespaces, eventHandle ) { - // We only want to do this special case on windows - if ( jQuery.isWindow( this ) ) { - this.onbeforeunload = eventHandle; - } - }, - - teardown: function( namespaces, eventHandle ) { - if ( this.onbeforeunload === eventHandle ) { - this.onbeforeunload = null; - } - } - } - }, - - simulate: function( type, elem, event, bubble ) { - // Piggyback on a donor event to simulate a different one. - // Fake originalEvent to avoid donor's stopPropagation, but if the - // simulated event prevents default then we do the same on the donor. - var e = jQuery.extend( - new jQuery.Event(), - event, - { type: type, - isSimulated: true, - originalEvent: {} - } - ); - if ( bubble ) { - jQuery.event.trigger( e, null, elem ); - } else { - jQuery.event.dispatch.call( elem, e ); - } - if ( e.isDefaultPrevented() ) { - event.preventDefault(); - } - } -}; - -// Some plugins are using, but it's undocumented/deprecated and will be removed. -// The 1.7 special event interface should provide all the hooks needed now. -jQuery.event.handle = jQuery.event.dispatch; - -jQuery.removeEvent = document.removeEventListener ? - function( elem, type, handle ) { - if ( elem.removeEventListener ) { - elem.removeEventListener( type, handle, false ); - } - } : - function( elem, type, handle ) { - if ( elem.detachEvent ) { - elem.detachEvent( "on" + type, handle ); - } - }; - -jQuery.Event = function( src, props ) { - // Allow instantiation without the 'new' keyword - if ( !(this instanceof jQuery.Event) ) { - return new jQuery.Event( src, props ); - } - - // Event object - if ( src && src.type ) { - this.originalEvent = src; - this.type = src.type; - - // Events bubbling up the document may have been marked as prevented - // by a handler lower down the tree; reflect the correct value. - this.isDefaultPrevented = ( src.defaultPrevented || src.returnValue === false || - src.getPreventDefault && src.getPreventDefault() ) ? returnTrue : returnFalse; - - // Event type - } else { - this.type = src; - } - - // Put explicitly provided properties onto the event object - if ( props ) { - jQuery.extend( this, props ); - } - - // Create a timestamp if incoming event doesn't have one - this.timeStamp = src && src.timeStamp || jQuery.now(); - - // Mark it as fixed - this[ jQuery.expando ] = true; -}; - -function returnFalse() { - return false; -} -function returnTrue() { - return true; -} - -// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding -// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html -jQuery.Event.prototype = { - preventDefault: function() { - this.isDefaultPrevented = returnTrue; - - var e = this.originalEvent; - if ( !e ) { - return; - } - - // if preventDefault exists run it on the original event - if ( e.preventDefault ) { - e.preventDefault(); - - // otherwise set the returnValue property of the original event to false (IE) - } else { - e.returnValue = false; - } - }, - stopPropagation: function() { - this.isPropagationStopped = returnTrue; - - var e = this.originalEvent; - if ( !e ) { - return; - } - // if stopPropagation exists run it on the original event - if ( e.stopPropagation ) { - e.stopPropagation(); - } - // otherwise set the cancelBubble property of the original event to true (IE) - e.cancelBubble = true; - }, - stopImmediatePropagation: function() { - this.isImmediatePropagationStopped = returnTrue; - this.stopPropagation(); - }, - isDefaultPrevented: returnFalse, - isPropagationStopped: returnFalse, - isImmediatePropagationStopped: returnFalse -}; - -// Create mouseenter/leave events using mouseover/out and event-time checks -jQuery.each({ - mouseenter: "mouseover", - mouseleave: "mouseout" -}, function( orig, fix ) { - jQuery.event.special[ orig ] = { - delegateType: fix, - bindType: fix, - - handle: function( event ) { - var target = this, - related = event.relatedTarget, - handleObj = event.handleObj, - selector = handleObj.selector, - ret; - - // For mousenter/leave call the handler if related is outside the target. - // NB: No relatedTarget if the mouse left/entered the browser window - if ( !related || (related !== target && !jQuery.contains( target, related )) ) { - event.type = handleObj.origType; - ret = handleObj.handler.apply( this, arguments ); - event.type = fix; - } - return ret; - } - }; -}); - -// IE submit delegation -if ( !jQuery.support.submitBubbles ) { - - jQuery.event.special.submit = { - setup: function() { - // Only need this for delegated form submit events - if ( jQuery.nodeName( this, "form" ) ) { - return false; - } - - // Lazy-add a submit handler when a descendant form may potentially be submitted - jQuery.event.add( this, "click._submit keypress._submit", function( e ) { - // Node name check avoids a VML-related crash in IE (#9807) - var elem = e.target, - form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined; - if ( form && !form._submit_attached ) { - jQuery.event.add( form, "submit._submit", function( event ) { - event._submit_bubble = true; - }); - form._submit_attached = true; - } - }); - // return undefined since we don't need an event listener - }, - - postDispatch: function( event ) { - // If form was submitted by the user, bubble the event up the tree - if ( event._submit_bubble ) { - delete event._submit_bubble; - if ( this.parentNode && !event.isTrigger ) { - jQuery.event.simulate( "submit", this.parentNode, event, true ); - } - } - }, - - teardown: function() { - // Only need this for delegated form submit events - if ( jQuery.nodeName( this, "form" ) ) { - return false; - } - - // Remove delegated handlers; cleanData eventually reaps submit handlers attached above - jQuery.event.remove( this, "._submit" ); - } - }; -} - -// IE change delegation and checkbox/radio fix -if ( !jQuery.support.changeBubbles ) { - - jQuery.event.special.change = { - - setup: function() { - - if ( rformElems.test( this.nodeName ) ) { - // IE doesn't fire change on a check/radio until blur; trigger it on click - // after a propertychange. Eat the blur-change in special.change.handle. - // This still fires onchange a second time for check/radio after blur. - if ( this.type === "checkbox" || this.type === "radio" ) { - jQuery.event.add( this, "propertychange._change", function( event ) { - if ( event.originalEvent.propertyName === "checked" ) { - this._just_changed = true; - } - }); - jQuery.event.add( this, "click._change", function( event ) { - if ( this._just_changed && !event.isTrigger ) { - this._just_changed = false; - jQuery.event.simulate( "change", this, event, true ); - } - }); - } - return false; - } - // Delegated event; lazy-add a change handler on descendant inputs - jQuery.event.add( this, "beforeactivate._change", function( e ) { - var elem = e.target; - - if ( rformElems.test( elem.nodeName ) && !elem._change_attached ) { - jQuery.event.add( elem, "change._change", function( event ) { - if ( this.parentNode && !event.isSimulated && !event.isTrigger ) { - jQuery.event.simulate( "change", this.parentNode, event, true ); - } - }); - elem._change_attached = true; - } - }); - }, - - handle: function( event ) { - var elem = event.target; - - // Swallow native change events from checkbox/radio, we already triggered them above - if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) { - return event.handleObj.handler.apply( this, arguments ); - } - }, - - teardown: function() { - jQuery.event.remove( this, "._change" ); - - return rformElems.test( this.nodeName ); - } - }; -} - -// Create "bubbling" focus and blur events -if ( !jQuery.support.focusinBubbles ) { - jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { - - // Attach a single capturing handler while someone wants focusin/focusout - var attaches = 0, - handler = function( event ) { - jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true ); - }; - - jQuery.event.special[ fix ] = { - setup: function() { - if ( attaches++ === 0 ) { - document.addEventListener( orig, handler, true ); - } - }, - teardown: function() { - if ( --attaches === 0 ) { - document.removeEventListener( orig, handler, true ); - } - } - }; - }); -} - -jQuery.fn.extend({ - - on: function( types, selector, data, fn, /*INTERNAL*/ one ) { - var origFn, type; - - // Types can be a map of types/handlers - if ( typeof types === "object" ) { - // ( types-Object, selector, data ) - if ( typeof selector !== "string" ) { // && selector != null - // ( types-Object, data ) - data = data || selector; - selector = undefined; - } - for ( type in types ) { - this.on( type, selector, data, types[ type ], one ); - } - return this; - } - - if ( data == null && fn == null ) { - // ( types, fn ) - fn = selector; - data = selector = undefined; - } else if ( fn == null ) { - if ( typeof selector === "string" ) { - // ( types, selector, fn ) - fn = data; - data = undefined; - } else { - // ( types, data, fn ) - fn = data; - data = selector; - selector = undefined; - } - } - if ( fn === false ) { - fn = returnFalse; - } else if ( !fn ) { - return this; - } - - if ( one === 1 ) { - origFn = fn; - fn = function( event ) { - // Can use an empty set, since event contains the info - jQuery().off( event ); - return origFn.apply( this, arguments ); - }; - // Use same guid so caller can remove using origFn - fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); - } - return this.each( function() { - jQuery.event.add( this, types, fn, data, selector ); - }); - }, - one: function( types, selector, data, fn ) { - return this.on( types, selector, data, fn, 1 ); - }, - off: function( types, selector, fn ) { - if ( types && types.preventDefault && types.handleObj ) { - // ( event ) dispatched jQuery.Event - var handleObj = types.handleObj; - jQuery( types.delegateTarget ).off( - handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType, - handleObj.selector, - handleObj.handler - ); - return this; - } - if ( typeof types === "object" ) { - // ( types-object [, selector] ) - for ( var type in types ) { - this.off( type, selector, types[ type ] ); - } - return this; - } - if ( selector === false || typeof selector === "function" ) { - // ( types [, fn] ) - fn = selector; - selector = undefined; - } - if ( fn === false ) { - fn = returnFalse; - } - return this.each(function() { - jQuery.event.remove( this, types, fn, selector ); - }); - }, - - bind: function( types, data, fn ) { - return this.on( types, null, data, fn ); - }, - unbind: function( types, fn ) { - return this.off( types, null, fn ); - }, - - live: function( types, data, fn ) { - jQuery( this.context ).on( types, this.selector, data, fn ); - return this; - }, - die: function( types, fn ) { - jQuery( this.context ).off( types, this.selector || "**", fn ); - return this; - }, - - delegate: function( selector, types, data, fn ) { - return this.on( types, selector, data, fn ); - }, - undelegate: function( selector, types, fn ) { - // ( namespace ) or ( selector, types [, fn] ) - return arguments.length == 1? this.off( selector, "**" ) : this.off( types, selector, fn ); - }, - - trigger: function( type, data ) { - return this.each(function() { - jQuery.event.trigger( type, data, this ); - }); - }, - triggerHandler: function( type, data ) { - if ( this[0] ) { - return jQuery.event.trigger( type, data, this[0], true ); - } - }, - - toggle: function( fn ) { - // Save reference to arguments for access in closure - var args = arguments, - guid = fn.guid || jQuery.guid++, - i = 0, - toggler = function( event ) { - // Figure out which function to execute - var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i; - jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 ); - - // Make sure that clicks stop - event.preventDefault(); - - // and execute the function - return args[ lastToggle ].apply( this, arguments ) || false; - }; - - // link all the functions, so any of them can unbind this click handler - toggler.guid = guid; - while ( i < args.length ) { - args[ i++ ].guid = guid; - } - - return this.click( toggler ); - }, - - hover: function( fnOver, fnOut ) { - return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); - } -}); - -jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " + - "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + - "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) { - - // Handle event binding - jQuery.fn[ name ] = function( data, fn ) { - if ( fn == null ) { - fn = data; - data = null; - } - - return arguments.length > 0 ? - this.on( name, null, data, fn ) : - this.trigger( name ); - }; - - if ( jQuery.attrFn ) { - jQuery.attrFn[ name ] = true; - } - - if ( rkeyEvent.test( name ) ) { - jQuery.event.fixHooks[ name ] = jQuery.event.keyHooks; - } - - if ( rmouseEvent.test( name ) ) { - jQuery.event.fixHooks[ name ] = jQuery.event.mouseHooks; - } -}); - - - -/*! - * Sizzle CSS Selector Engine - * Copyright 2011, The Dojo Foundation - * Released under the MIT, BSD, and GPL Licenses. - * More information: http://sizzlejs.com/ - */ -(function(){ - -var chunker = /((?:\((?:\([^()]+\)|[^()]+)+\)|\[(?:\[[^\[\]]*\]|['"][^'"]*['"]|[^\[\]'"]+)+\]|\\.|[^ >+~,(\[\\]+)+|[>+~])(\s*,\s*)?((?:.|\r|\n)*)/g, - expando = "sizcache" + (Math.random() + '').replace('.', ''), - done = 0, - toString = Object.prototype.toString, - hasDuplicate = false, - baseHasDuplicate = true, - rBackslash = /\\/g, - rReturn = /\r\n/g, - rNonWord = /\W/; - -// Here we check if the JavaScript engine is using some sort of -// optimization where it does not always call our comparision -// function. If that is the case, discard the hasDuplicate value. -// Thus far that includes Google Chrome. -[0, 0].sort(function() { - baseHasDuplicate = false; - return 0; -}); - -var Sizzle = function( selector, context, results, seed ) { - results = results || []; - context = context || document; - - var origContext = context; - - if ( context.nodeType !== 1 && context.nodeType !== 9 ) { - return []; - } - - if ( !selector || typeof selector !== "string" ) { - return results; - } - - var m, set, checkSet, extra, ret, cur, pop, i, - prune = true, - contextXML = Sizzle.isXML( context ), - parts = [], - soFar = selector; - - // Reset the position of the chunker regexp (start from head) - do { - chunker.exec( "" ); - m = chunker.exec( soFar ); - - if ( m ) { - soFar = m[3]; - - parts.push( m[1] ); - - if ( m[2] ) { - extra = m[3]; - break; - } - } - } while ( m ); - - if ( parts.length > 1 && origPOS.exec( selector ) ) { - - if ( parts.length === 2 && Expr.relative[ parts[0] ] ) { - set = posProcess( parts[0] + parts[1], context, seed ); - - } else { - set = Expr.relative[ parts[0] ] ? - [ context ] : - Sizzle( parts.shift(), context ); - - while ( parts.length ) { - selector = parts.shift(); - - if ( Expr.relative[ selector ] ) { - selector += parts.shift(); - } - - set = posProcess( selector, set, seed ); - } - } - - } else { - // Take a shortcut and set the context if the root selector is an ID - // (but not if it'll be faster if the inner selector is an ID) - if ( !seed && parts.length > 1 && context.nodeType === 9 && !contextXML && - Expr.match.ID.test(parts[0]) && !Expr.match.ID.test(parts[parts.length - 1]) ) { - - ret = Sizzle.find( parts.shift(), context, contextXML ); - context = ret.expr ? - Sizzle.filter( ret.expr, ret.set )[0] : - ret.set[0]; - } - - if ( context ) { - ret = seed ? - { expr: parts.pop(), set: makeArray(seed) } : - Sizzle.find( parts.pop(), parts.length === 1 && (parts[0] === "~" || parts[0] === "+") && context.parentNode ? context.parentNode : context, contextXML ); - - set = ret.expr ? - Sizzle.filter( ret.expr, ret.set ) : - ret.set; - - if ( parts.length > 0 ) { - checkSet = makeArray( set ); - - } else { - prune = false; - } - - while ( parts.length ) { - cur = parts.pop(); - pop = cur; - - if ( !Expr.relative[ cur ] ) { - cur = ""; - } else { - pop = parts.pop(); - } - - if ( pop == null ) { - pop = context; - } - - Expr.relative[ cur ]( checkSet, pop, contextXML ); - } - - } else { - checkSet = parts = []; - } - } - - if ( !checkSet ) { - checkSet = set; - } - - if ( !checkSet ) { - Sizzle.error( cur || selector ); - } - - if ( toString.call(checkSet) === "[object Array]" ) { - if ( !prune ) { - results.push.apply( results, checkSet ); - - } else if ( context && context.nodeType === 1 ) { - for ( i = 0; checkSet[i] != null; i++ ) { - if ( checkSet[i] && (checkSet[i] === true || checkSet[i].nodeType === 1 && Sizzle.contains(context, checkSet[i])) ) { - results.push( set[i] ); - } - } - - } else { - for ( i = 0; checkSet[i] != null; i++ ) { - if ( checkSet[i] && checkSet[i].nodeType === 1 ) { - results.push( set[i] ); - } - } - } - - } else { - makeArray( checkSet, results ); - } - - if ( extra ) { - Sizzle( extra, origContext, results, seed ); - Sizzle.uniqueSort( results ); - } - - return results; -}; - -Sizzle.uniqueSort = function( results ) { - if ( sortOrder ) { - hasDuplicate = baseHasDuplicate; - results.sort( sortOrder ); - - if ( hasDuplicate ) { - for ( var i = 1; i < results.length; i++ ) { - if ( results[i] === results[ i - 1 ] ) { - results.splice( i--, 1 ); - } - } - } - } - - return results; -}; - -Sizzle.matches = function( expr, set ) { - return Sizzle( expr, null, null, set ); -}; - -Sizzle.matchesSelector = function( node, expr ) { - return Sizzle( expr, null, null, [node] ).length > 0; -}; - -Sizzle.find = function( expr, context, isXML ) { - var set, i, len, match, type, left; - - if ( !expr ) { - return []; - } - - for ( i = 0, len = Expr.order.length; i < len; i++ ) { - type = Expr.order[i]; - - if ( (match = Expr.leftMatch[ type ].exec( expr )) ) { - left = match[1]; - match.splice( 1, 1 ); - - if ( left.substr( left.length - 1 ) !== "\\" ) { - match[1] = (match[1] || "").replace( rBackslash, "" ); - set = Expr.find[ type ]( match, context, isXML ); - - if ( set != null ) { - expr = expr.replace( Expr.match[ type ], "" ); - break; - } - } - } - } - - if ( !set ) { - set = typeof context.getElementsByTagName !== "undefined" ? - context.getElementsByTagName( "*" ) : - []; - } - - return { set: set, expr: expr }; -}; - -Sizzle.filter = function( expr, set, inplace, not ) { - var match, anyFound, - type, found, item, filter, left, - i, pass, - old = expr, - result = [], - curLoop = set, - isXMLFilter = set && set[0] && Sizzle.isXML( set[0] ); - - while ( expr && set.length ) { - for ( type in Expr.filter ) { - if ( (match = Expr.leftMatch[ type ].exec( expr )) != null && match[2] ) { - filter = Expr.filter[ type ]; - left = match[1]; - - anyFound = false; - - match.splice(1,1); - - if ( left.substr( left.length - 1 ) === "\\" ) { - continue; - } - - if ( curLoop === result ) { - result = []; - } - - if ( Expr.preFilter[ type ] ) { - match = Expr.preFilter[ type ]( match, curLoop, inplace, result, not, isXMLFilter ); - - if ( !match ) { - anyFound = found = true; - - } else if ( match === true ) { - continue; - } - } - - if ( match ) { - for ( i = 0; (item = curLoop[i]) != null; i++ ) { - if ( item ) { - found = filter( item, match, i, curLoop ); - pass = not ^ found; - - if ( inplace && found != null ) { - if ( pass ) { - anyFound = true; - - } else { - curLoop[i] = false; - } - - } else if ( pass ) { - result.push( item ); - anyFound = true; - } - } - } - } - - if ( found !== undefined ) { - if ( !inplace ) { - curLoop = result; - } - - expr = expr.replace( Expr.match[ type ], "" ); - - if ( !anyFound ) { - return []; - } - - break; - } - } - } - - // Improper expression - if ( expr === old ) { - if ( anyFound == null ) { - Sizzle.error( expr ); - - } else { - break; - } - } - - old = expr; - } - - return curLoop; -}; - -Sizzle.error = function( msg ) { - throw new Error( "Syntax error, unrecognized expression: " + msg ); -}; - -/** - * Utility function for retreiving the text value of an array of DOM nodes - * @param {Array|Element} elem - */ -var getText = Sizzle.getText = function( elem ) { - var i, node, - nodeType = elem.nodeType, - ret = ""; - - if ( nodeType ) { - if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { - // Use textContent || innerText for elements - if ( typeof elem.textContent === 'string' ) { - return elem.textContent; - } else if ( typeof elem.innerText === 'string' ) { - // Replace IE's carriage returns - return elem.innerText.replace( rReturn, '' ); - } else { - // Traverse it's children - for ( elem = elem.firstChild; elem; elem = elem.nextSibling) { - ret += getText( elem ); - } - } - } else if ( nodeType === 3 || nodeType === 4 ) { - return elem.nodeValue; - } - } else { - - // If no nodeType, this is expected to be an array - for ( i = 0; (node = elem[i]); i++ ) { - // Do not traverse comment nodes - if ( node.nodeType !== 8 ) { - ret += getText( node ); - } - } - } - return ret; -}; - -var Expr = Sizzle.selectors = { - order: [ "ID", "NAME", "TAG" ], - - match: { - ID: /#((?:[\w\u00c0-\uFFFF\-]|\\.)+)/, - CLASS: /\.((?:[\w\u00c0-\uFFFF\-]|\\.)+)/, - NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF\-]|\\.)+)['"]*\]/, - ATTR: /\[\s*((?:[\w\u00c0-\uFFFF\-]|\\.)+)\s*(?:(\S?=)\s*(?:(['"])(.*?)\3|(#?(?:[\w\u00c0-\uFFFF\-]|\\.)*)|)|)\s*\]/, - TAG: /^((?:[\w\u00c0-\uFFFF\*\-]|\\.)+)/, - CHILD: /:(only|nth|last|first)-child(?:\(\s*(even|odd|(?:[+\-]?\d+|(?:[+\-]?\d*)?n\s*(?:[+\-]\s*\d+)?))\s*\))?/, - POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:\((\d*)\))?(?=[^\-]|$)/, - PSEUDO: /:((?:[\w\u00c0-\uFFFF\-]|\\.)+)(?:\((['"]?)((?:\([^\)]+\)|[^\(\)]*)+)\2\))?/ - }, - - leftMatch: {}, - - attrMap: { - "class": "className", - "for": "htmlFor" - }, - - attrHandle: { - href: function( elem ) { - return elem.getAttribute( "href" ); - }, - type: function( elem ) { - return elem.getAttribute( "type" ); - } - }, - - relative: { - "+": function(checkSet, part){ - var isPartStr = typeof part === "string", - isTag = isPartStr && !rNonWord.test( part ), - isPartStrNotTag = isPartStr && !isTag; - - if ( isTag ) { - part = part.toLowerCase(); - } - - for ( var i = 0, l = checkSet.length, elem; i < l; i++ ) { - if ( (elem = checkSet[i]) ) { - while ( (elem = elem.previousSibling) && elem.nodeType !== 1 ) {} - - checkSet[i] = isPartStrNotTag || elem && elem.nodeName.toLowerCase() === part ? - elem || false : - elem === part; - } - } - - if ( isPartStrNotTag ) { - Sizzle.filter( part, checkSet, true ); - } - }, - - ">": function( checkSet, part ) { - var elem, - isPartStr = typeof part === "string", - i = 0, - l = checkSet.length; - - if ( isPartStr && !rNonWord.test( part ) ) { - part = part.toLowerCase(); - - for ( ; i < l; i++ ) { - elem = checkSet[i]; - - if ( elem ) { - var parent = elem.parentNode; - checkSet[i] = parent.nodeName.toLowerCase() === part ? parent : false; - } - } - - } else { - for ( ; i < l; i++ ) { - elem = checkSet[i]; - - if ( elem ) { - checkSet[i] = isPartStr ? - elem.parentNode : - elem.parentNode === part; - } - } - - if ( isPartStr ) { - Sizzle.filter( part, checkSet, true ); - } - } - }, - - "": function(checkSet, part, isXML){ - var nodeCheck, - doneName = done++, - checkFn = dirCheck; - - if ( typeof part === "string" && !rNonWord.test( part ) ) { - part = part.toLowerCase(); - nodeCheck = part; - checkFn = dirNodeCheck; - } - - checkFn( "parentNode", part, doneName, checkSet, nodeCheck, isXML ); - }, - - "~": function( checkSet, part, isXML ) { - var nodeCheck, - doneName = done++, - checkFn = dirCheck; - - if ( typeof part === "string" && !rNonWord.test( part ) ) { - part = part.toLowerCase(); - nodeCheck = part; - checkFn = dirNodeCheck; - } - - checkFn( "previousSibling", part, doneName, checkSet, nodeCheck, isXML ); - } - }, - - find: { - ID: function( match, context, isXML ) { - if ( typeof context.getElementById !== "undefined" && !isXML ) { - var m = context.getElementById(match[1]); - // Check parentNode to catch when Blackberry 4.6 returns - // nodes that are no longer in the document #6963 - return m && m.parentNode ? [m] : []; - } - }, - - NAME: function( match, context ) { - if ( typeof context.getElementsByName !== "undefined" ) { - var ret = [], - results = context.getElementsByName( match[1] ); - - for ( var i = 0, l = results.length; i < l; i++ ) { - if ( results[i].getAttribute("name") === match[1] ) { - ret.push( results[i] ); - } - } - - return ret.length === 0 ? null : ret; - } - }, - - TAG: function( match, context ) { - if ( typeof context.getElementsByTagName !== "undefined" ) { - return context.getElementsByTagName( match[1] ); - } - } - }, - preFilter: { - CLASS: function( match, curLoop, inplace, result, not, isXML ) { - match = " " + match[1].replace( rBackslash, "" ) + " "; - - if ( isXML ) { - return match; - } - - for ( var i = 0, elem; (elem = curLoop[i]) != null; i++ ) { - if ( elem ) { - if ( not ^ (elem.className && (" " + elem.className + " ").replace(/[\t\n\r]/g, " ").indexOf(match) >= 0) ) { - if ( !inplace ) { - result.push( elem ); - } - - } else if ( inplace ) { - curLoop[i] = false; - } - } - } - - return false; - }, - - ID: function( match ) { - return match[1].replace( rBackslash, "" ); - }, - - TAG: function( match, curLoop ) { - return match[1].replace( rBackslash, "" ).toLowerCase(); - }, - - CHILD: function( match ) { - if ( match[1] === "nth" ) { - if ( !match[2] ) { - Sizzle.error( match[0] ); - } - - match[2] = match[2].replace(/^\+|\s*/g, ''); - - // parse equations like 'even', 'odd', '5', '2n', '3n+2', '4n-1', '-n+6' - var test = /(-?)(\d*)(?:n([+\-]?\d*))?/.exec( - match[2] === "even" && "2n" || match[2] === "odd" && "2n+1" || - !/\D/.test( match[2] ) && "0n+" + match[2] || match[2]); - - // calculate the numbers (first)n+(last) including if they are negative - match[2] = (test[1] + (test[2] || 1)) - 0; - match[3] = test[3] - 0; - } - else if ( match[2] ) { - Sizzle.error( match[0] ); - } - - // TODO: Move to normal caching system - match[0] = done++; - - return match; - }, - - ATTR: function( match, curLoop, inplace, result, not, isXML ) { - var name = match[1] = match[1].replace( rBackslash, "" ); - - if ( !isXML && Expr.attrMap[name] ) { - match[1] = Expr.attrMap[name]; - } - - // Handle if an un-quoted value was used - match[4] = ( match[4] || match[5] || "" ).replace( rBackslash, "" ); - - if ( match[2] === "~=" ) { - match[4] = " " + match[4] + " "; - } - - return match; - }, - - PSEUDO: function( match, curLoop, inplace, result, not ) { - if ( match[1] === "not" ) { - // If we're dealing with a complex expression, or a simple one - if ( ( chunker.exec(match[3]) || "" ).length > 1 || /^\w/.test(match[3]) ) { - match[3] = Sizzle(match[3], null, null, curLoop); - - } else { - var ret = Sizzle.filter(match[3], curLoop, inplace, true ^ not); - - if ( !inplace ) { - result.push.apply( result, ret ); - } - - return false; - } - - } else if ( Expr.match.POS.test( match[0] ) || Expr.match.CHILD.test( match[0] ) ) { - return true; - } - - return match; - }, - - POS: function( match ) { - match.unshift( true ); - - return match; - } - }, - - filters: { - enabled: function( elem ) { - return elem.disabled === false && elem.type !== "hidden"; - }, - - disabled: function( elem ) { - return elem.disabled === true; - }, - - checked: function( elem ) { - return elem.checked === true; - }, - - selected: function( elem ) { - // Accessing this property makes selected-by-default - // options in Safari work properly - if ( elem.parentNode ) { - elem.parentNode.selectedIndex; - } - - return elem.selected === true; - }, - - parent: function( elem ) { - return !!elem.firstChild; - }, - - empty: function( elem ) { - return !elem.firstChild; - }, - - has: function( elem, i, match ) { - return !!Sizzle( match[3], elem ).length; - }, - - header: function( elem ) { - return (/h\d/i).test( elem.nodeName ); - }, - - text: function( elem ) { - var attr = elem.getAttribute( "type" ), type = elem.type; - // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc) - // use getAttribute instead to test this case - return elem.nodeName.toLowerCase() === "input" && "text" === type && ( attr === type || attr === null ); - }, - - radio: function( elem ) { - return elem.nodeName.toLowerCase() === "input" && "radio" === elem.type; - }, - - checkbox: function( elem ) { - return elem.nodeName.toLowerCase() === "input" && "checkbox" === elem.type; - }, - - file: function( elem ) { - return elem.nodeName.toLowerCase() === "input" && "file" === elem.type; - }, - - password: function( elem ) { - return elem.nodeName.toLowerCase() === "input" && "password" === elem.type; - }, - - submit: function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && "submit" === elem.type; - }, - - image: function( elem ) { - return elem.nodeName.toLowerCase() === "input" && "image" === elem.type; - }, - - reset: function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && "reset" === elem.type; - }, - - button: function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && "button" === elem.type || name === "button"; - }, - - input: function( elem ) { - return (/input|select|textarea|button/i).test( elem.nodeName ); - }, - - focus: function( elem ) { - return elem === elem.ownerDocument.activeElement; - } - }, - setFilters: { - first: function( elem, i ) { - return i === 0; - }, - - last: function( elem, i, match, array ) { - return i === array.length - 1; - }, - - even: function( elem, i ) { - return i % 2 === 0; - }, - - odd: function( elem, i ) { - return i % 2 === 1; - }, - - lt: function( elem, i, match ) { - return i < match[3] - 0; - }, - - gt: function( elem, i, match ) { - return i > match[3] - 0; - }, - - nth: function( elem, i, match ) { - return match[3] - 0 === i; - }, - - eq: function( elem, i, match ) { - return match[3] - 0 === i; - } - }, - filter: { - PSEUDO: function( elem, match, i, array ) { - var name = match[1], - filter = Expr.filters[ name ]; - - if ( filter ) { - return filter( elem, i, match, array ); - - } else if ( name === "contains" ) { - return (elem.textContent || elem.innerText || getText([ elem ]) || "").indexOf(match[3]) >= 0; - - } else if ( name === "not" ) { - var not = match[3]; - - for ( var j = 0, l = not.length; j < l; j++ ) { - if ( not[j] === elem ) { - return false; - } - } - - return true; - - } else { - Sizzle.error( name ); - } - }, - - CHILD: function( elem, match ) { - var first, last, - doneName, parent, cache, - count, diff, - type = match[1], - node = elem; - - switch ( type ) { - case "only": - case "first": - while ( (node = node.previousSibling) ) { - if ( node.nodeType === 1 ) { - return false; - } - } - - if ( type === "first" ) { - return true; - } - - node = elem; - - /* falls through */ - case "last": - while ( (node = node.nextSibling) ) { - if ( node.nodeType === 1 ) { - return false; - } - } - - return true; - - case "nth": - first = match[2]; - last = match[3]; - - if ( first === 1 && last === 0 ) { - return true; - } - - doneName = match[0]; - parent = elem.parentNode; - - if ( parent && (parent[ expando ] !== doneName || !elem.nodeIndex) ) { - count = 0; - - for ( node = parent.firstChild; node; node = node.nextSibling ) { - if ( node.nodeType === 1 ) { - node.nodeIndex = ++count; - } - } - - parent[ expando ] = doneName; - } - - diff = elem.nodeIndex - last; - - if ( first === 0 ) { - return diff === 0; - - } else { - return ( diff % first === 0 && diff / first >= 0 ); - } - } - }, - - ID: function( elem, match ) { - return elem.nodeType === 1 && elem.getAttribute("id") === match; - }, - - TAG: function( elem, match ) { - return (match === "*" && elem.nodeType === 1) || !!elem.nodeName && elem.nodeName.toLowerCase() === match; - }, - - CLASS: function( elem, match ) { - return (" " + (elem.className || elem.getAttribute("class")) + " ") - .indexOf( match ) > -1; - }, - - ATTR: function( elem, match ) { - var name = match[1], - result = Sizzle.attr ? - Sizzle.attr( elem, name ) : - Expr.attrHandle[ name ] ? - Expr.attrHandle[ name ]( elem ) : - elem[ name ] != null ? - elem[ name ] : - elem.getAttribute( name ), - value = result + "", - type = match[2], - check = match[4]; - - return result == null ? - type === "!=" : - !type && Sizzle.attr ? - result != null : - type === "=" ? - value === check : - type === "*=" ? - value.indexOf(check) >= 0 : - type === "~=" ? - (" " + value + " ").indexOf(check) >= 0 : - !check ? - value && result !== false : - type === "!=" ? - value !== check : - type === "^=" ? - value.indexOf(check) === 0 : - type === "$=" ? - value.substr(value.length - check.length) === check : - type === "|=" ? - value === check || value.substr(0, check.length + 1) === check + "-" : - false; - }, - - POS: function( elem, match, i, array ) { - var name = match[2], - filter = Expr.setFilters[ name ]; - - if ( filter ) { - return filter( elem, i, match, array ); - } - } - } -}; - -var origPOS = Expr.match.POS, - fescape = function(all, num){ - return "\\" + (num - 0 + 1); - }; - -for ( var type in Expr.match ) { - Expr.match[ type ] = new RegExp( Expr.match[ type ].source + (/(?![^\[]*\])(?![^\(]*\))/.source) ); - Expr.leftMatch[ type ] = new RegExp( /(^(?:.|\r|\n)*?)/.source + Expr.match[ type ].source.replace(/\\(\d+)/g, fescape) ); -} -// Expose origPOS -// "global" as in regardless of relation to brackets/parens -Expr.match.globalPOS = origPOS; - -var makeArray = function( array, results ) { - array = Array.prototype.slice.call( array, 0 ); - - if ( results ) { - results.push.apply( results, array ); - return results; - } - - return array; -}; - -// Perform a simple check to determine if the browser is capable of -// converting a NodeList to an array using builtin methods. -// Also verifies that the returned array holds DOM nodes -// (which is not the case in the Blackberry browser) -try { - Array.prototype.slice.call( document.documentElement.childNodes, 0 )[0].nodeType; - -// Provide a fallback method if it does not work -} catch( e ) { - makeArray = function( array, results ) { - var i = 0, - ret = results || []; - - if ( toString.call(array) === "[object Array]" ) { - Array.prototype.push.apply( ret, array ); - - } else { - if ( typeof array.length === "number" ) { - for ( var l = array.length; i < l; i++ ) { - ret.push( array[i] ); - } - - } else { - for ( ; array[i]; i++ ) { - ret.push( array[i] ); - } - } - } - - return ret; - }; -} - -var sortOrder, siblingCheck; - -if ( document.documentElement.compareDocumentPosition ) { - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - return 0; - } - - if ( !a.compareDocumentPosition || !b.compareDocumentPosition ) { - return a.compareDocumentPosition ? -1 : 1; - } - - return a.compareDocumentPosition(b) & 4 ? -1 : 1; - }; - -} else { - sortOrder = function( a, b ) { - // The nodes are identical, we can exit early - if ( a === b ) { - hasDuplicate = true; - return 0; - - // Fallback to using sourceIndex (in IE) if it's available on both nodes - } else if ( a.sourceIndex && b.sourceIndex ) { - return a.sourceIndex - b.sourceIndex; - } - - var al, bl, - ap = [], - bp = [], - aup = a.parentNode, - bup = b.parentNode, - cur = aup; - - // If the nodes are siblings (or identical) we can do a quick check - if ( aup === bup ) { - return siblingCheck( a, b ); - - // If no parents were found then the nodes are disconnected - } else if ( !aup ) { - return -1; - - } else if ( !bup ) { - return 1; - } - - // Otherwise they're somewhere else in the tree so we need - // to build up a full list of the parentNodes for comparison - while ( cur ) { - ap.unshift( cur ); - cur = cur.parentNode; - } - - cur = bup; - - while ( cur ) { - bp.unshift( cur ); - cur = cur.parentNode; - } - - al = ap.length; - bl = bp.length; - - // Start walking down the tree looking for a discrepancy - for ( var i = 0; i < al && i < bl; i++ ) { - if ( ap[i] !== bp[i] ) { - return siblingCheck( ap[i], bp[i] ); - } - } - - // We ended someplace up the tree so do a sibling check - return i === al ? - siblingCheck( a, bp[i], -1 ) : - siblingCheck( ap[i], b, 1 ); - }; - - siblingCheck = function( a, b, ret ) { - if ( a === b ) { - return ret; - } - - var cur = a.nextSibling; - - while ( cur ) { - if ( cur === b ) { - return -1; - } - - cur = cur.nextSibling; - } - - return 1; - }; -} - -// Check to see if the browser returns elements by name when -// querying by getElementById (and provide a workaround) -(function(){ - // We're going to inject a fake input element with a specified name - var form = document.createElement("div"), - id = "script" + (new Date()).getTime(), - root = document.documentElement; - - form.innerHTML = "<a name='" + id + "'/>"; - - // Inject it into the root element, check its status, and remove it quickly - root.insertBefore( form, root.firstChild ); - - // The workaround has to do additional checks after a getElementById - // Which slows things down for other browsers (hence the branching) - if ( document.getElementById( id ) ) { - Expr.find.ID = function( match, context, isXML ) { - if ( typeof context.getElementById !== "undefined" && !isXML ) { - var m = context.getElementById(match[1]); - - return m ? - m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ? - [m] : - undefined : - []; - } - }; - - Expr.filter.ID = function( elem, match ) { - var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); - - return elem.nodeType === 1 && node && node.nodeValue === match; - }; - } - - root.removeChild( form ); - - // release memory in IE - root = form = null; -})(); - -(function(){ - // Check to see if the browser returns only elements - // when doing getElementsByTagName("*") - - // Create a fake element - var div = document.createElement("div"); - div.appendChild( document.createComment("") ); - - // Make sure no comments are found - if ( div.getElementsByTagName("*").length > 0 ) { - Expr.find.TAG = function( match, context ) { - var results = context.getElementsByTagName( match[1] ); - - // Filter out possible comments - if ( match[1] === "*" ) { - var tmp = []; - - for ( var i = 0; results[i]; i++ ) { - if ( results[i].nodeType === 1 ) { - tmp.push( results[i] ); - } - } - - results = tmp; - } - - return results; - }; - } - - // Check to see if an attribute returns normalized href attributes - div.innerHTML = "<a href='#'></a>"; - - if ( div.firstChild && typeof div.firstChild.getAttribute !== "undefined" && - div.firstChild.getAttribute("href") !== "#" ) { - - Expr.attrHandle.href = function( elem ) { - return elem.getAttribute( "href", 2 ); - }; - } - - // release memory in IE - div = null; -})(); - -if ( document.querySelectorAll ) { - (function(){ - var oldSizzle = Sizzle, - div = document.createElement("div"), - id = "__sizzle__"; - - div.innerHTML = "<p class='TEST'></p>"; - - // Safari can't handle uppercase or unicode characters when - // in quirks mode. - if ( div.querySelectorAll && div.querySelectorAll(".TEST").length === 0 ) { - return; - } - - Sizzle = function( query, context, extra, seed ) { - context = context || document; - - // Only use querySelectorAll on non-XML documents - // (ID selectors don't work in non-HTML documents) - if ( !seed && !Sizzle.isXML(context) ) { - // See if we find a selector to speed up - var match = /^(\w+$)|^\.([\w\-]+$)|^#([\w\-]+$)/.exec( query ); - - if ( match && (context.nodeType === 1 || context.nodeType === 9) ) { - // Speed-up: Sizzle("TAG") - if ( match[1] ) { - return makeArray( context.getElementsByTagName( query ), extra ); - - // Speed-up: Sizzle(".CLASS") - } else if ( match[2] && Expr.find.CLASS && context.getElementsByClassName ) { - return makeArray( context.getElementsByClassName( match[2] ), extra ); - } - } - - if ( context.nodeType === 9 ) { - // Speed-up: Sizzle("body") - // The body element only exists once, optimize finding it - if ( query === "body" && context.body ) { - return makeArray( [ context.body ], extra ); - - // Speed-up: Sizzle("#ID") - } else if ( match && match[3] ) { - var elem = context.getElementById( match[3] ); - - // Check parentNode to catch when Blackberry 4.6 returns - // nodes that are no longer in the document #6963 - if ( elem && elem.parentNode ) { - // Handle the case where IE and Opera return items - // by name instead of ID - if ( elem.id === match[3] ) { - return makeArray( [ elem ], extra ); - } - - } else { - return makeArray( [], extra ); - } - } - - try { - return makeArray( context.querySelectorAll(query), extra ); - } catch(qsaError) {} - - // qSA works strangely on Element-rooted queries - // We can work around this by specifying an extra ID on the root - // and working up from there (Thanks to Andrew Dupont for the technique) - // IE 8 doesn't work on object elements - } else if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) { - var oldContext = context, - old = context.getAttribute( "id" ), - nid = old || id, - hasParent = context.parentNode, - relativeHierarchySelector = /^\s*[+~]/.test( query ); - - if ( !old ) { - context.setAttribute( "id", nid ); - } else { - nid = nid.replace( /'/g, "\\$&" ); - } - if ( relativeHierarchySelector && hasParent ) { - context = context.parentNode; - } - - try { - if ( !relativeHierarchySelector || hasParent ) { - return makeArray( context.querySelectorAll( "[id='" + nid + "'] " + query ), extra ); - } - - } catch(pseudoError) { - } finally { - if ( !old ) { - oldContext.removeAttribute( "id" ); - } - } - } - } - - return oldSizzle(query, context, extra, seed); - }; - - for ( var prop in oldSizzle ) { - Sizzle[ prop ] = oldSizzle[ prop ]; - } - - // release memory in IE - div = null; - })(); -} - -(function(){ - var html = document.documentElement, - matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector; - - if ( matches ) { - // Check to see if it's possible to do matchesSelector - // on a disconnected node (IE 9 fails this) - var disconnectedMatch = !matches.call( document.createElement( "div" ), "div" ), - pseudoWorks = false; - - try { - // This should fail with an exception - // Gecko does not error, returns false instead - matches.call( document.documentElement, "[test!='']:sizzle" ); - - } catch( pseudoError ) { - pseudoWorks = true; - } - - Sizzle.matchesSelector = function( node, expr ) { - // Make sure that attribute selectors are quoted - expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']"); - - if ( !Sizzle.isXML( node ) ) { - try { - if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) { - var ret = matches.call( node, expr ); - - // IE 9's matchesSelector returns false on disconnected nodes - if ( ret || !disconnectedMatch || - // As well, disconnected nodes are said to be in a document - // fragment in IE 9, so check for that - node.document && node.document.nodeType !== 11 ) { - return ret; - } - } - } catch(e) {} - } - - return Sizzle(expr, null, null, [node]).length > 0; - }; - } -})(); - -(function(){ - var div = document.createElement("div"); - - div.innerHTML = "<div class='test e'></div><div class='test'></div>"; - - // Opera can't find a second classname (in 9.6) - // Also, make sure that getElementsByClassName actually exists - if ( !div.getElementsByClassName || div.getElementsByClassName("e").length === 0 ) { - return; - } - - // Safari caches class attributes, doesn't catch changes (in 3.2) - div.lastChild.className = "e"; - - if ( div.getElementsByClassName("e").length === 1 ) { - return; - } - - Expr.order.splice(1, 0, "CLASS"); - Expr.find.CLASS = function( match, context, isXML ) { - if ( typeof context.getElementsByClassName !== "undefined" && !isXML ) { - return context.getElementsByClassName(match[1]); - } - }; - - // release memory in IE - div = null; -})(); - -function dirNodeCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - - if ( elem ) { - var match = false; - - elem = elem[dir]; - - while ( elem ) { - if ( elem[ expando ] === doneName ) { - match = checkSet[elem.sizset]; - break; - } - - if ( elem.nodeType === 1 && !isXML ){ - elem[ expando ] = doneName; - elem.sizset = i; - } - - if ( elem.nodeName.toLowerCase() === cur ) { - match = elem; - break; - } - - elem = elem[dir]; - } - - checkSet[i] = match; - } - } -} - -function dirCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - - if ( elem ) { - var match = false; - - elem = elem[dir]; - - while ( elem ) { - if ( elem[ expando ] === doneName ) { - match = checkSet[elem.sizset]; - break; - } - - if ( elem.nodeType === 1 ) { - if ( !isXML ) { - elem[ expando ] = doneName; - elem.sizset = i; - } - - if ( typeof cur !== "string" ) { - if ( elem === cur ) { - match = true; - break; - } - - } else if ( Sizzle.filter( cur, [elem] ).length > 0 ) { - match = elem; - break; - } - } - - elem = elem[dir]; - } - - checkSet[i] = match; - } - } -} - -if ( document.documentElement.contains ) { - Sizzle.contains = function( a, b ) { - return a !== b && (a.contains ? a.contains(b) : true); - }; - -} else if ( document.documentElement.compareDocumentPosition ) { - Sizzle.contains = function( a, b ) { - return !!(a.compareDocumentPosition(b) & 16); - }; - -} else { - Sizzle.contains = function() { - return false; - }; -} - -Sizzle.isXML = function( elem ) { - // documentElement is verified for cases where it doesn't yet exist - // (such as loading iframes in IE - #4833) - var documentElement = (elem ? elem.ownerDocument || elem : 0).documentElement; - - return documentElement ? documentElement.nodeName !== "HTML" : false; -}; - -var posProcess = function( selector, context, seed ) { - var match, - tmpSet = [], - later = "", - root = context.nodeType ? [context] : context; - - // Position selectors must be done after the filter - // And so must :not(positional) so we move all PSEUDOs to the end - while ( (match = Expr.match.PSEUDO.exec( selector )) ) { - later += match[0]; - selector = selector.replace( Expr.match.PSEUDO, "" ); - } - - selector = Expr.relative[selector] ? selector + "*" : selector; - - for ( var i = 0, l = root.length; i < l; i++ ) { - Sizzle( selector, root[i], tmpSet, seed ); - } - - return Sizzle.filter( later, tmpSet ); -}; - -// EXPOSE -// Override sizzle attribute retrieval -Sizzle.attr = jQuery.attr; -Sizzle.selectors.attrMap = {}; -jQuery.find = Sizzle; -jQuery.expr = Sizzle.selectors; -jQuery.expr[":"] = jQuery.expr.filters; -jQuery.unique = Sizzle.uniqueSort; -jQuery.text = Sizzle.getText; -jQuery.isXMLDoc = Sizzle.isXML; -jQuery.contains = Sizzle.contains; - - -})(); - - -var runtil = /Until$/, - rparentsprev = /^(?:parents|prevUntil|prevAll)/, - // Note: This RegExp should be improved, or likely pulled from Sizzle - rmultiselector = /,/, - isSimple = /^.[^:#\[\.,]*$/, - slice = Array.prototype.slice, - POS = jQuery.expr.match.globalPOS, - // methods guaranteed to produce a unique set when starting from a unique set - guaranteedUnique = { - children: true, - contents: true, - next: true, - prev: true - }; - -jQuery.fn.extend({ - find: function( selector ) { - var self = this, - i, l; - - if ( typeof selector !== "string" ) { - return jQuery( selector ).filter(function() { - for ( i = 0, l = self.length; i < l; i++ ) { - if ( jQuery.contains( self[ i ], this ) ) { - return true; - } - } - }); - } - - var ret = this.pushStack( "", "find", selector ), - length, n, r; - - for ( i = 0, l = this.length; i < l; i++ ) { - length = ret.length; - jQuery.find( selector, this[i], ret ); - - if ( i > 0 ) { - // Make sure that the results are unique - for ( n = length; n < ret.length; n++ ) { - for ( r = 0; r < length; r++ ) { - if ( ret[r] === ret[n] ) { - ret.splice(n--, 1); - break; - } - } - } - } - } - - return ret; - }, - - has: function( target ) { - var targets = jQuery( target ); - return this.filter(function() { - for ( var i = 0, l = targets.length; i < l; i++ ) { - if ( jQuery.contains( this, targets[i] ) ) { - return true; - } - } - }); - }, - - not: function( selector ) { - return this.pushStack( winnow(this, selector, false), "not", selector); - }, - - filter: function( selector ) { - return this.pushStack( winnow(this, selector, true), "filter", selector ); - }, - - is: function( selector ) { - return !!selector && ( - typeof selector === "string" ? - // If this is a positional selector, check membership in the returned set - // so $("p:first").is("p:last") won't return true for a doc with two "p". - POS.test( selector ) ? - jQuery( selector, this.context ).index( this[0] ) >= 0 : - jQuery.filter( selector, this ).length > 0 : - this.filter( selector ).length > 0 ); - }, - - closest: function( selectors, context ) { - var ret = [], i, l, cur = this[0]; - - // Array (deprecated as of jQuery 1.7) - if ( jQuery.isArray( selectors ) ) { - var level = 1; - - while ( cur && cur.ownerDocument && cur !== context ) { - for ( i = 0; i < selectors.length; i++ ) { - - if ( jQuery( cur ).is( selectors[ i ] ) ) { - ret.push({ selector: selectors[ i ], elem: cur, level: level }); - } - } - - cur = cur.parentNode; - level++; - } - - return ret; - } - - // String - var pos = POS.test( selectors ) || typeof selectors !== "string" ? - jQuery( selectors, context || this.context ) : - 0; - - for ( i = 0, l = this.length; i < l; i++ ) { - cur = this[i]; - - while ( cur ) { - if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) { - ret.push( cur ); - break; - - } else { - cur = cur.parentNode; - if ( !cur || !cur.ownerDocument || cur === context || cur.nodeType === 11 ) { - break; - } - } - } - } - - ret = ret.length > 1 ? jQuery.unique( ret ) : ret; - - return this.pushStack( ret, "closest", selectors ); - }, - - // Determine the position of an element within - // the matched set of elements - index: function( elem ) { - - // No argument, return index in parent - if ( !elem ) { - return ( this[0] && this[0].parentNode ) ? this.prevAll().length : -1; - } - - // index in selector - if ( typeof elem === "string" ) { - return jQuery.inArray( this[0], jQuery( elem ) ); - } - - // Locate the position of the desired element - return jQuery.inArray( - // If it receives a jQuery object, the first element is used - elem.jquery ? elem[0] : elem, this ); - }, - - add: function( selector, context ) { - var set = typeof selector === "string" ? - jQuery( selector, context ) : - jQuery.makeArray( selector && selector.nodeType ? [ selector ] : selector ), - all = jQuery.merge( this.get(), set ); - - return this.pushStack( isDisconnected( set[0] ) || isDisconnected( all[0] ) ? - all : - jQuery.unique( all ) ); - }, - - andSelf: function() { - return this.add( this.prevObject ); - } -}); - -// A painfully simple check to see if an element is disconnected -// from a document (should be improved, where feasible). -function isDisconnected( node ) { - return !node || !node.parentNode || node.parentNode.nodeType === 11; -} - -jQuery.each({ - parent: function( elem ) { - var parent = elem.parentNode; - return parent && parent.nodeType !== 11 ? parent : null; - }, - parents: function( elem ) { - return jQuery.dir( elem, "parentNode" ); - }, - parentsUntil: function( elem, i, until ) { - return jQuery.dir( elem, "parentNode", until ); - }, - next: function( elem ) { - return jQuery.nth( elem, 2, "nextSibling" ); - }, - prev: function( elem ) { - return jQuery.nth( elem, 2, "previousSibling" ); - }, - nextAll: function( elem ) { - return jQuery.dir( elem, "nextSibling" ); - }, - prevAll: function( elem ) { - return jQuery.dir( elem, "previousSibling" ); - }, - nextUntil: function( elem, i, until ) { - return jQuery.dir( elem, "nextSibling", until ); - }, - prevUntil: function( elem, i, until ) { - return jQuery.dir( elem, "previousSibling", until ); - }, - siblings: function( elem ) { - return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem ); - }, - children: function( elem ) { - return jQuery.sibling( elem.firstChild ); - }, - contents: function( elem ) { - return jQuery.nodeName( elem, "iframe" ) ? - elem.contentDocument || elem.contentWindow.document : - jQuery.makeArray( elem.childNodes ); - } -}, function( name, fn ) { - jQuery.fn[ name ] = function( until, selector ) { - var ret = jQuery.map( this, fn, until ); - - if ( !runtil.test( name ) ) { - selector = until; - } - - if ( selector && typeof selector === "string" ) { - ret = jQuery.filter( selector, ret ); - } - - ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret; - - if ( (this.length > 1 || rmultiselector.test( selector )) && rparentsprev.test( name ) ) { - ret = ret.reverse(); - } - - return this.pushStack( ret, name, slice.call( arguments ).join(",") ); - }; -}); - -jQuery.extend({ - filter: function( expr, elems, not ) { - if ( not ) { - expr = ":not(" + expr + ")"; - } - - return elems.length === 1 ? - jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] : - jQuery.find.matches(expr, elems); - }, - - dir: function( elem, dir, until ) { - var matched = [], - cur = elem[ dir ]; - - while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) { - if ( cur.nodeType === 1 ) { - matched.push( cur ); - } - cur = cur[dir]; - } - return matched; - }, - - nth: function( cur, result, dir, elem ) { - result = result || 1; - var num = 0; - - for ( ; cur; cur = cur[dir] ) { - if ( cur.nodeType === 1 && ++num === result ) { - break; - } - } - - return cur; - }, - - sibling: function( n, elem ) { - var r = []; - - for ( ; n; n = n.nextSibling ) { - if ( n.nodeType === 1 && n !== elem ) { - r.push( n ); - } - } - - return r; - } -}); - -// Implement the identical functionality for filter and not -function winnow( elements, qualifier, keep ) { - - // Can't pass null or undefined to indexOf in Firefox 4 - // Set to 0 to skip string check - qualifier = qualifier || 0; - - if ( jQuery.isFunction( qualifier ) ) { - return jQuery.grep(elements, function( elem, i ) { - var retVal = !!qualifier.call( elem, i, elem ); - return retVal === keep; - }); - - } else if ( qualifier.nodeType ) { - return jQuery.grep(elements, function( elem, i ) { - return ( elem === qualifier ) === keep; - }); - - } else if ( typeof qualifier === "string" ) { - var filtered = jQuery.grep(elements, function( elem ) { - return elem.nodeType === 1; - }); - - if ( isSimple.test( qualifier ) ) { - return jQuery.filter(qualifier, filtered, !keep); - } else { - qualifier = jQuery.filter( qualifier, filtered ); - } - } - - return jQuery.grep(elements, function( elem, i ) { - return ( jQuery.inArray( elem, qualifier ) >= 0 ) === keep; - }); -} - - - - -function createSafeFragment( document ) { - var list = nodeNames.split( "|" ), - safeFrag = document.createDocumentFragment(); - - if ( safeFrag.createElement ) { - while ( list.length ) { - safeFrag.createElement( - list.pop() - ); - } - } - return safeFrag; -} - -var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" + - "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video", - rinlinejQuery = / jQuery\d+="(?:\d+|null)"/g, - rleadingWhitespace = /^\s+/, - rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/ig, - rtagName = /<([\w:]+)/, - rtbody = /<tbody/i, - rhtml = /<|&#?\w+;/, - rnoInnerhtml = /<(?:script|style)/i, - rnocache = /<(?:script|object|embed|option|style)/i, - rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"), - // checked="checked" or checked - rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, - rscriptType = /\/(java|ecma)script/i, - rcleanScript = /^\s*<!(?:\[CDATA\[|\-\-)/, - wrapMap = { - option: [ 1, "<select multiple='multiple'>", "</select>" ], - legend: [ 1, "<fieldset>", "</fieldset>" ], - thead: [ 1, "<table>", "</table>" ], - tr: [ 2, "<table><tbody>", "</tbody></table>" ], - td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ], - col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ], - area: [ 1, "<map>", "</map>" ], - _default: [ 0, "", "" ] - }, - safeFragment = createSafeFragment( document ); - -wrapMap.optgroup = wrapMap.option; -wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; -wrapMap.th = wrapMap.td; - -// IE can't serialize <link> and <script> tags normally -if ( !jQuery.support.htmlSerialize ) { - wrapMap._default = [ 1, "div<div>", "</div>" ]; -} - -jQuery.fn.extend({ - text: function( value ) { - return jQuery.access( this, function( value ) { - return value === undefined ? - jQuery.text( this ) : - this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) ); - }, null, value, arguments.length ); - }, - - wrapAll: function( html ) { - if ( jQuery.isFunction( html ) ) { - return this.each(function(i) { - jQuery(this).wrapAll( html.call(this, i) ); - }); - } - - if ( this[0] ) { - // The elements to wrap the target around - var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true); - - if ( this[0].parentNode ) { - wrap.insertBefore( this[0] ); - } - - wrap.map(function() { - var elem = this; - - while ( elem.firstChild && elem.firstChild.nodeType === 1 ) { - elem = elem.firstChild; - } - - return elem; - }).append( this ); - } - - return this; - }, - - wrapInner: function( html ) { - if ( jQuery.isFunction( html ) ) { - return this.each(function(i) { - jQuery(this).wrapInner( html.call(this, i) ); - }); - } - - return this.each(function() { - var self = jQuery( this ), - contents = self.contents(); - - if ( contents.length ) { - contents.wrapAll( html ); - - } else { - self.append( html ); - } - }); - }, - - wrap: function( html ) { - var isFunction = jQuery.isFunction( html ); - - return this.each(function(i) { - jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html ); - }); - }, - - unwrap: function() { - return this.parent().each(function() { - if ( !jQuery.nodeName( this, "body" ) ) { - jQuery( this ).replaceWith( this.childNodes ); - } - }).end(); - }, - - append: function() { - return this.domManip(arguments, true, function( elem ) { - if ( this.nodeType === 1 ) { - this.appendChild( elem ); - } - }); - }, - - prepend: function() { - return this.domManip(arguments, true, function( elem ) { - if ( this.nodeType === 1 ) { - this.insertBefore( elem, this.firstChild ); - } - }); - }, - - before: function() { - if ( this[0] && this[0].parentNode ) { - return this.domManip(arguments, false, function( elem ) { - this.parentNode.insertBefore( elem, this ); - }); - } else if ( arguments.length ) { - var set = jQuery.clean( arguments ); - set.push.apply( set, this.toArray() ); - return this.pushStack( set, "before", arguments ); - } - }, - - after: function() { - if ( this[0] && this[0].parentNode ) { - return this.domManip(arguments, false, function( elem ) { - this.parentNode.insertBefore( elem, this.nextSibling ); - }); - } else if ( arguments.length ) { - var set = this.pushStack( this, "after", arguments ); - set.push.apply( set, jQuery.clean(arguments) ); - return set; - } - }, - - // keepData is for internal use only--do not document - remove: function( selector, keepData ) { - for ( var i = 0, elem; (elem = this[i]) != null; i++ ) { - if ( !selector || jQuery.filter( selector, [ elem ] ).length ) { - if ( !keepData && elem.nodeType === 1 ) { - jQuery.cleanData( elem.getElementsByTagName("*") ); - jQuery.cleanData( [ elem ] ); - } - - if ( elem.parentNode ) { - elem.parentNode.removeChild( elem ); - } - } - } - - return this; - }, - - empty: function() { - for ( var i = 0, elem; (elem = this[i]) != null; i++ ) { - // Remove element nodes and prevent memory leaks - if ( elem.nodeType === 1 ) { - jQuery.cleanData( elem.getElementsByTagName("*") ); - } - - // Remove any remaining nodes - while ( elem.firstChild ) { - elem.removeChild( elem.firstChild ); - } - } - - return this; - }, - - clone: function( dataAndEvents, deepDataAndEvents ) { - dataAndEvents = dataAndEvents == null ? false : dataAndEvents; - deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; - - return this.map( function () { - return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); - }); - }, - - html: function( value ) { - return jQuery.access( this, function( value ) { - var elem = this[0] || {}, - i = 0, - l = this.length; - - if ( value === undefined ) { - return elem.nodeType === 1 ? - elem.innerHTML.replace( rinlinejQuery, "" ) : - null; - } - - - if ( typeof value === "string" && !rnoInnerhtml.test( value ) && - ( jQuery.support.leadingWhitespace || !rleadingWhitespace.test( value ) ) && - !wrapMap[ ( rtagName.exec( value ) || ["", ""] )[1].toLowerCase() ] ) { - - value = value.replace( rxhtmlTag, "<$1></$2>" ); - - try { - for (; i < l; i++ ) { - // Remove element nodes and prevent memory leaks - elem = this[i] || {}; - if ( elem.nodeType === 1 ) { - jQuery.cleanData( elem.getElementsByTagName( "*" ) ); - elem.innerHTML = value; - } - } - - elem = 0; - - // If using innerHTML throws an exception, use the fallback method - } catch(e) {} - } - - if ( elem ) { - this.empty().append( value ); - } - }, null, value, arguments.length ); - }, - - replaceWith: function( value ) { - if ( this[0] && this[0].parentNode ) { - // Make sure that the elements are removed from the DOM before they are inserted - // this can help fix replacing a parent with child elements - if ( jQuery.isFunction( value ) ) { - return this.each(function(i) { - var self = jQuery(this), old = self.html(); - self.replaceWith( value.call( this, i, old ) ); - }); - } - - if ( typeof value !== "string" ) { - value = jQuery( value ).detach(); - } - - return this.each(function() { - var next = this.nextSibling, - parent = this.parentNode; - - jQuery( this ).remove(); - - if ( next ) { - jQuery(next).before( value ); - } else { - jQuery(parent).append( value ); - } - }); - } else { - return this.length ? - this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ) : - this; - } - }, - - detach: function( selector ) { - return this.remove( selector, true ); - }, - - domManip: function( args, table, callback ) { - var results, first, fragment, parent, - value = args[0], - scripts = []; - - // We can't cloneNode fragments that contain checked, in WebKit - if ( !jQuery.support.checkClone && arguments.length === 3 && typeof value === "string" && rchecked.test( value ) ) { - return this.each(function() { - jQuery(this).domManip( args, table, callback, true ); - }); - } - - if ( jQuery.isFunction(value) ) { - return this.each(function(i) { - var self = jQuery(this); - args[0] = value.call(this, i, table ? self.html() : undefined); - self.domManip( args, table, callback ); - }); - } - - if ( this[0] ) { - parent = value && value.parentNode; - - // If we're in a fragment, just use that instead of building a new one - if ( jQuery.support.parentNode && parent && parent.nodeType === 11 && parent.childNodes.length === this.length ) { - results = { fragment: parent }; - - } else { - results = jQuery.buildFragment( args, this, scripts ); - } - - fragment = results.fragment; - - if ( fragment.childNodes.length === 1 ) { - first = fragment = fragment.firstChild; - } else { - first = fragment.firstChild; - } - - if ( first ) { - table = table && jQuery.nodeName( first, "tr" ); - - for ( var i = 0, l = this.length, lastIndex = l - 1; i < l; i++ ) { - callback.call( - table ? - root(this[i], first) : - this[i], - // Make sure that we do not leak memory by inadvertently discarding - // the original fragment (which might have attached data) instead of - // using it; in addition, use the original fragment object for the last - // item instead of first because it can end up being emptied incorrectly - // in certain situations (Bug #8070). - // Fragments from the fragment cache must always be cloned and never used - // in place. - results.cacheable || ( l > 1 && i < lastIndex ) ? - jQuery.clone( fragment, true, true ) : - fragment - ); - } - } - - if ( scripts.length ) { - jQuery.each( scripts, function( i, elem ) { - if ( elem.src ) { - jQuery.ajax({ - type: "GET", - global: false, - url: elem.src, - async: false, - dataType: "script" - }); - } else { - jQuery.globalEval( ( elem.text || elem.textContent || elem.innerHTML || "" ).replace( rcleanScript, "/*$0*/" ) ); - } - - if ( elem.parentNode ) { - elem.parentNode.removeChild( elem ); - } - }); - } - } - - return this; - } -}); - -function root( elem, cur ) { - return jQuery.nodeName(elem, "table") ? - (elem.getElementsByTagName("tbody")[0] || - elem.appendChild(elem.ownerDocument.createElement("tbody"))) : - elem; -} - -function cloneCopyEvent( src, dest ) { - - if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) { - return; - } - - var type, i, l, - oldData = jQuery._data( src ), - curData = jQuery._data( dest, oldData ), - events = oldData.events; - - if ( events ) { - delete curData.handle; - curData.events = {}; - - for ( type in events ) { - for ( i = 0, l = events[ type ].length; i < l; i++ ) { - jQuery.event.add( dest, type, events[ type ][ i ] ); - } - } - } - - // make the cloned public data object a copy from the original - if ( curData.data ) { - curData.data = jQuery.extend( {}, curData.data ); - } -} - -function cloneFixAttributes( src, dest ) { - var nodeName; - - // We do not need to do anything for non-Elements - if ( dest.nodeType !== 1 ) { - return; - } - - // clearAttributes removes the attributes, which we don't want, - // but also removes the attachEvent events, which we *do* want - if ( dest.clearAttributes ) { - dest.clearAttributes(); - } - - // mergeAttributes, in contrast, only merges back on the - // original attributes, not the events - if ( dest.mergeAttributes ) { - dest.mergeAttributes( src ); - } - - nodeName = dest.nodeName.toLowerCase(); - - // IE6-8 fail to clone children inside object elements that use - // the proprietary classid attribute value (rather than the type - // attribute) to identify the type of content to display - if ( nodeName === "object" ) { - dest.outerHTML = src.outerHTML; - - } else if ( nodeName === "input" && (src.type === "checkbox" || src.type === "radio") ) { - // IE6-8 fails to persist the checked state of a cloned checkbox - // or radio button. Worse, IE6-7 fail to give the cloned element - // a checked appearance if the defaultChecked value isn't also set - if ( src.checked ) { - dest.defaultChecked = dest.checked = src.checked; - } - - // IE6-7 get confused and end up setting the value of a cloned - // checkbox/radio button to an empty string instead of "on" - if ( dest.value !== src.value ) { - dest.value = src.value; - } - - // IE6-8 fails to return the selected option to the default selected - // state when cloning options - } else if ( nodeName === "option" ) { - dest.selected = src.defaultSelected; - - // IE6-8 fails to set the defaultValue to the correct value when - // cloning other types of input fields - } else if ( nodeName === "input" || nodeName === "textarea" ) { - dest.defaultValue = src.defaultValue; - - // IE blanks contents when cloning scripts - } else if ( nodeName === "script" && dest.text !== src.text ) { - dest.text = src.text; - } - - // Event data gets referenced instead of copied if the expando - // gets copied too - dest.removeAttribute( jQuery.expando ); - - // Clear flags for bubbling special change/submit events, they must - // be reattached when the newly cloned events are first activated - dest.removeAttribute( "_submit_attached" ); - dest.removeAttribute( "_change_attached" ); -} - -jQuery.buildFragment = function( args, nodes, scripts ) { - var fragment, cacheable, cacheresults, doc, - first = args[ 0 ]; - - // nodes may contain either an explicit document object, - // a jQuery collection or context object. - // If nodes[0] contains a valid object to assign to doc - if ( nodes && nodes[0] ) { - doc = nodes[0].ownerDocument || nodes[0]; - } - - // Ensure that an attr object doesn't incorrectly stand in as a document object - // Chrome and Firefox seem to allow this to occur and will throw exception - // Fixes #8950 - if ( !doc.createDocumentFragment ) { - doc = document; - } - - // Only cache "small" (1/2 KB) HTML strings that are associated with the main document - // Cloning options loses the selected state, so don't cache them - // IE 6 doesn't like it when you put <object> or <embed> elements in a fragment - // Also, WebKit does not clone 'checked' attributes on cloneNode, so don't cache - // Lastly, IE6,7,8 will not correctly reuse cached fragments that were created from unknown elems #10501 - if ( args.length === 1 && typeof first === "string" && first.length < 512 && doc === document && - first.charAt(0) === "<" && !rnocache.test( first ) && - (jQuery.support.checkClone || !rchecked.test( first )) && - (jQuery.support.html5Clone || !rnoshimcache.test( first )) ) { - - cacheable = true; - - cacheresults = jQuery.fragments[ first ]; - if ( cacheresults && cacheresults !== 1 ) { - fragment = cacheresults; - } - } - - if ( !fragment ) { - fragment = doc.createDocumentFragment(); - jQuery.clean( args, doc, fragment, scripts ); - } - - if ( cacheable ) { - jQuery.fragments[ first ] = cacheresults ? fragment : 1; - } - - return { fragment: fragment, cacheable: cacheable }; -}; - -jQuery.fragments = {}; - -jQuery.each({ - appendTo: "append", - prependTo: "prepend", - insertBefore: "before", - insertAfter: "after", - replaceAll: "replaceWith" -}, function( name, original ) { - jQuery.fn[ name ] = function( selector ) { - var ret = [], - insert = jQuery( selector ), - parent = this.length === 1 && this[0].parentNode; - - if ( parent && parent.nodeType === 11 && parent.childNodes.length === 1 && insert.length === 1 ) { - insert[ original ]( this[0] ); - return this; - - } else { - for ( var i = 0, l = insert.length; i < l; i++ ) { - var elems = ( i > 0 ? this.clone(true) : this ).get(); - jQuery( insert[i] )[ original ]( elems ); - ret = ret.concat( elems ); - } - - return this.pushStack( ret, name, insert.selector ); - } - }; -}); - -function getAll( elem ) { - if ( typeof elem.getElementsByTagName !== "undefined" ) { - return elem.getElementsByTagName( "*" ); - - } else if ( typeof elem.querySelectorAll !== "undefined" ) { - return elem.querySelectorAll( "*" ); - - } else { - return []; - } -} - -// Used in clean, fixes the defaultChecked property -function fixDefaultChecked( elem ) { - if ( elem.type === "checkbox" || elem.type === "radio" ) { - elem.defaultChecked = elem.checked; - } -} -// Finds all inputs and passes them to fixDefaultChecked -function findInputs( elem ) { - var nodeName = ( elem.nodeName || "" ).toLowerCase(); - if ( nodeName === "input" ) { - fixDefaultChecked( elem ); - // Skip scripts, get other children - } else if ( nodeName !== "script" && typeof elem.getElementsByTagName !== "undefined" ) { - jQuery.grep( elem.getElementsByTagName("input"), fixDefaultChecked ); - } -} - -// Derived From: http://www.iecss.com/shimprove/javascript/shimprove.1-0-1.js -function shimCloneNode( elem ) { - var div = document.createElement( "div" ); - safeFragment.appendChild( div ); - - div.innerHTML = elem.outerHTML; - return div.firstChild; -} - -jQuery.extend({ - clone: function( elem, dataAndEvents, deepDataAndEvents ) { - var srcElements, - destElements, - i, - // IE<=8 does not properly clone detached, unknown element nodes - clone = jQuery.support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ? - elem.cloneNode( true ) : - shimCloneNode( elem ); - - if ( (!jQuery.support.noCloneEvent || !jQuery.support.noCloneChecked) && - (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) { - // IE copies events bound via attachEvent when using cloneNode. - // Calling detachEvent on the clone will also remove the events - // from the original. In order to get around this, we use some - // proprietary methods to clear the events. Thanks to MooTools - // guys for this hotness. - - cloneFixAttributes( elem, clone ); - - // Using Sizzle here is crazy slow, so we use getElementsByTagName instead - srcElements = getAll( elem ); - destElements = getAll( clone ); - - // Weird iteration because IE will replace the length property - // with an element if you are cloning the body and one of the - // elements on the page has a name or id of "length" - for ( i = 0; srcElements[i]; ++i ) { - // Ensure that the destination node is not null; Fixes #9587 - if ( destElements[i] ) { - cloneFixAttributes( srcElements[i], destElements[i] ); - } - } - } - - // Copy the events from the original to the clone - if ( dataAndEvents ) { - cloneCopyEvent( elem, clone ); - - if ( deepDataAndEvents ) { - srcElements = getAll( elem ); - destElements = getAll( clone ); - - for ( i = 0; srcElements[i]; ++i ) { - cloneCopyEvent( srcElements[i], destElements[i] ); - } - } - } - - srcElements = destElements = null; - - // Return the cloned set - return clone; - }, - - clean: function( elems, context, fragment, scripts ) { - var checkScriptType, script, j, - ret = []; - - context = context || document; - - // !context.createElement fails in IE with an error but returns typeof 'object' - if ( typeof context.createElement === "undefined" ) { - context = context.ownerDocument || context[0] && context[0].ownerDocument || document; - } - - for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) { - if ( typeof elem === "number" ) { - elem += ""; - } - - if ( !elem ) { - continue; - } - - // Convert html string into DOM nodes - if ( typeof elem === "string" ) { - if ( !rhtml.test( elem ) ) { - elem = context.createTextNode( elem ); - } else { - // Fix "XHTML"-style tags in all browsers - elem = elem.replace(rxhtmlTag, "<$1></$2>"); - - // Trim whitespace, otherwise indexOf won't work as expected - var tag = ( rtagName.exec( elem ) || ["", ""] )[1].toLowerCase(), - wrap = wrapMap[ tag ] || wrapMap._default, - depth = wrap[0], - div = context.createElement("div"), - safeChildNodes = safeFragment.childNodes, - remove; - - // Append wrapper element to unknown element safe doc fragment - if ( context === document ) { - // Use the fragment we've already created for this document - safeFragment.appendChild( div ); - } else { - // Use a fragment created with the owner document - createSafeFragment( context ).appendChild( div ); - } - - // Go to html and back, then peel off extra wrappers - div.innerHTML = wrap[1] + elem + wrap[2]; - - // Move to the right depth - while ( depth-- ) { - div = div.lastChild; - } - - // Remove IE's autoinserted <tbody> from table fragments - if ( !jQuery.support.tbody ) { - - // String was a <table>, *may* have spurious <tbody> - var hasBody = rtbody.test(elem), - tbody = tag === "table" && !hasBody ? - div.firstChild && div.firstChild.childNodes : - - // String was a bare <thead> or <tfoot> - wrap[1] === "<table>" && !hasBody ? - div.childNodes : - []; - - for ( j = tbody.length - 1; j >= 0 ; --j ) { - if ( jQuery.nodeName( tbody[ j ], "tbody" ) && !tbody[ j ].childNodes.length ) { - tbody[ j ].parentNode.removeChild( tbody[ j ] ); - } - } - } - - // IE completely kills leading whitespace when innerHTML is used - if ( !jQuery.support.leadingWhitespace && rleadingWhitespace.test( elem ) ) { - div.insertBefore( context.createTextNode( rleadingWhitespace.exec(elem)[0] ), div.firstChild ); - } - - elem = div.childNodes; - - // Clear elements from DocumentFragment (safeFragment or otherwise) - // to avoid hoarding elements. Fixes #11356 - if ( div ) { - div.parentNode.removeChild( div ); - - // Guard against -1 index exceptions in FF3.6 - if ( safeChildNodes.length > 0 ) { - remove = safeChildNodes[ safeChildNodes.length - 1 ]; - - if ( remove && remove.parentNode ) { - remove.parentNode.removeChild( remove ); - } - } - } - } - } - - // Resets defaultChecked for any radios and checkboxes - // about to be appended to the DOM in IE 6/7 (#8060) - var len; - if ( !jQuery.support.appendChecked ) { - if ( elem[0] && typeof (len = elem.length) === "number" ) { - for ( j = 0; j < len; j++ ) { - findInputs( elem[j] ); - } - } else { - findInputs( elem ); - } - } - - if ( elem.nodeType ) { - ret.push( elem ); - } else { - ret = jQuery.merge( ret, elem ); - } - } - - if ( fragment ) { - checkScriptType = function( elem ) { - return !elem.type || rscriptType.test( elem.type ); - }; - for ( i = 0; ret[i]; i++ ) { - script = ret[i]; - if ( scripts && jQuery.nodeName( script, "script" ) && (!script.type || rscriptType.test( script.type )) ) { - scripts.push( script.parentNode ? script.parentNode.removeChild( script ) : script ); - - } else { - if ( script.nodeType === 1 ) { - var jsTags = jQuery.grep( script.getElementsByTagName( "script" ), checkScriptType ); - - ret.splice.apply( ret, [i + 1, 0].concat( jsTags ) ); - } - fragment.appendChild( script ); - } - } - } - - return ret; - }, - - cleanData: function( elems ) { - var data, id, - cache = jQuery.cache, - special = jQuery.event.special, - deleteExpando = jQuery.support.deleteExpando; - - for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) { - if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) { - continue; - } - - id = elem[ jQuery.expando ]; - - if ( id ) { - data = cache[ id ]; - - if ( data && data.events ) { - for ( var type in data.events ) { - if ( special[ type ] ) { - jQuery.event.remove( elem, type ); - - // This is a shortcut to avoid jQuery.event.remove's overhead - } else { - jQuery.removeEvent( elem, type, data.handle ); - } - } - - // Null the DOM reference to avoid IE6/7/8 leak (#7054) - if ( data.handle ) { - data.handle.elem = null; - } - } - - if ( deleteExpando ) { - delete elem[ jQuery.expando ]; - - } else if ( elem.removeAttribute ) { - elem.removeAttribute( jQuery.expando ); - } - - delete cache[ id ]; - } - } - } -}); - - - - -var ralpha = /alpha\([^)]*\)/i, - ropacity = /opacity=([^)]*)/, - // fixed for IE9, see #8346 - rupper = /([A-Z]|^ms)/g, - rnum = /^[\-+]?(?:\d*\.)?\d+$/i, - rnumnonpx = /^-?(?:\d*\.)?\d+(?!px)[^\d\s]+$/i, - rrelNum = /^([\-+])=([\-+.\de]+)/, - rmargin = /^margin/, - - cssShow = { position: "absolute", visibility: "hidden", display: "block" }, - - // order is important! - cssExpand = [ "Top", "Right", "Bottom", "Left" ], - - curCSS, - - getComputedStyle, - currentStyle; - -jQuery.fn.css = function( name, value ) { - return jQuery.access( this, function( elem, name, value ) { - return value !== undefined ? - jQuery.style( elem, name, value ) : - jQuery.css( elem, name ); - }, name, value, arguments.length > 1 ); -}; - -jQuery.extend({ - // Add in style property hooks for overriding the default - // behavior of getting and setting a style property - cssHooks: { - opacity: { - get: function( elem, computed ) { - if ( computed ) { - // We should always get a number back from opacity - var ret = curCSS( elem, "opacity" ); - return ret === "" ? "1" : ret; - - } else { - return elem.style.opacity; - } - } - } - }, - - // Exclude the following css properties to add px - cssNumber: { - "fillOpacity": true, - "fontWeight": true, - "lineHeight": true, - "opacity": true, - "orphans": true, - "widows": true, - "zIndex": true, - "zoom": true - }, - - // Add in properties whose names you wish to fix before - // setting or getting the value - cssProps: { - // normalize float css property - "float": jQuery.support.cssFloat ? "cssFloat" : "styleFloat" - }, - - // Get and set the style property on a DOM Node - style: function( elem, name, value, extra ) { - // Don't set styles on text and comment nodes - if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { - return; - } - - // Make sure that we're working with the right name - var ret, type, origName = jQuery.camelCase( name ), - style = elem.style, hooks = jQuery.cssHooks[ origName ]; - - name = jQuery.cssProps[ origName ] || origName; - - // Check if we're setting a value - if ( value !== undefined ) { - type = typeof value; - - // convert relative number strings (+= or -=) to relative numbers. #7345 - if ( type === "string" && (ret = rrelNum.exec( value )) ) { - value = ( +( ret[1] + 1) * +ret[2] ) + parseFloat( jQuery.css( elem, name ) ); - // Fixes bug #9237 - type = "number"; - } - - // Make sure that NaN and null values aren't set. See: #7116 - if ( value == null || type === "number" && isNaN( value ) ) { - return; - } - - // If a number was passed in, add 'px' to the (except for certain CSS properties) - if ( type === "number" && !jQuery.cssNumber[ origName ] ) { - value += "px"; - } - - // If a hook was provided, use that value, otherwise just set the specified value - if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value )) !== undefined ) { - // Wrapped to prevent IE from throwing errors when 'invalid' values are provided - // Fixes bug #5509 - try { - style[ name ] = value; - } catch(e) {} - } - - } else { - // If a hook was provided get the non-computed value from there - if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) { - return ret; - } - - // Otherwise just get the value from the style object - return style[ name ]; - } - }, - - css: function( elem, name, extra ) { - var ret, hooks; - - // Make sure that we're working with the right name - name = jQuery.camelCase( name ); - hooks = jQuery.cssHooks[ name ]; - name = jQuery.cssProps[ name ] || name; - - // cssFloat needs a special treatment - if ( name === "cssFloat" ) { - name = "float"; - } - - // If a hook was provided get the computed value from there - if ( hooks && "get" in hooks && (ret = hooks.get( elem, true, extra )) !== undefined ) { - return ret; - - // Otherwise, if a way to get the computed value exists, use that - } else if ( curCSS ) { - return curCSS( elem, name ); - } - }, - - // A method for quickly swapping in/out CSS properties to get correct calculations - swap: function( elem, options, callback ) { - var old = {}, - ret, name; - - // Remember the old values, and insert the new ones - for ( name in options ) { - old[ name ] = elem.style[ name ]; - elem.style[ name ] = options[ name ]; - } - - ret = callback.call( elem ); - - // Revert the old values - for ( name in options ) { - elem.style[ name ] = old[ name ]; - } - - return ret; - } -}); - -// DEPRECATED in 1.3, Use jQuery.css() instead -jQuery.curCSS = jQuery.css; - -if ( document.defaultView && document.defaultView.getComputedStyle ) { - getComputedStyle = function( elem, name ) { - var ret, defaultView, computedStyle, width, - style = elem.style; - - name = name.replace( rupper, "-$1" ).toLowerCase(); - - if ( (defaultView = elem.ownerDocument.defaultView) && - (computedStyle = defaultView.getComputedStyle( elem, null )) ) { - - ret = computedStyle.getPropertyValue( name ); - if ( ret === "" && !jQuery.contains( elem.ownerDocument.documentElement, elem ) ) { - ret = jQuery.style( elem, name ); - } - } - - // A tribute to the "awesome hack by Dean Edwards" - // WebKit uses "computed value (percentage if specified)" instead of "used value" for margins - // which is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values - if ( !jQuery.support.pixelMargin && computedStyle && rmargin.test( name ) && rnumnonpx.test( ret ) ) { - width = style.width; - style.width = ret; - ret = computedStyle.width; - style.width = width; - } - - return ret; - }; -} - -if ( document.documentElement.currentStyle ) { - currentStyle = function( elem, name ) { - var left, rsLeft, uncomputed, - ret = elem.currentStyle && elem.currentStyle[ name ], - style = elem.style; - - // Avoid setting ret to empty string here - // so we don't default to auto - if ( ret == null && style && (uncomputed = style[ name ]) ) { - ret = uncomputed; - } - - // From the awesome hack by Dean Edwards - // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291 - - // If we're not dealing with a regular pixel number - // but a number that has a weird ending, we need to convert it to pixels - if ( rnumnonpx.test( ret ) ) { - - // Remember the original values - left = style.left; - rsLeft = elem.runtimeStyle && elem.runtimeStyle.left; - - // Put in the new values to get a computed value out - if ( rsLeft ) { - elem.runtimeStyle.left = elem.currentStyle.left; - } - style.left = name === "fontSize" ? "1em" : ret; - ret = style.pixelLeft + "px"; - - // Revert the changed values - style.left = left; - if ( rsLeft ) { - elem.runtimeStyle.left = rsLeft; - } - } - - return ret === "" ? "auto" : ret; - }; -} - -curCSS = getComputedStyle || currentStyle; - -function getWidthOrHeight( elem, name, extra ) { - - // Start with offset property - var val = name === "width" ? elem.offsetWidth : elem.offsetHeight, - i = name === "width" ? 1 : 0, - len = 4; - - if ( val > 0 ) { - if ( extra !== "border" ) { - for ( ; i < len; i += 2 ) { - if ( !extra ) { - val -= parseFloat( jQuery.css( elem, "padding" + cssExpand[ i ] ) ) || 0; - } - if ( extra === "margin" ) { - val += parseFloat( jQuery.css( elem, extra + cssExpand[ i ] ) ) || 0; - } else { - val -= parseFloat( jQuery.css( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0; - } - } - } - - return val + "px"; - } - - // Fall back to computed then uncomputed css if necessary - val = curCSS( elem, name ); - if ( val < 0 || val == null ) { - val = elem.style[ name ]; - } - - // Computed unit is not pixels. Stop here and return. - if ( rnumnonpx.test(val) ) { - return val; - } - - // Normalize "", auto, and prepare for extra - val = parseFloat( val ) || 0; - - // Add padding, border, margin - if ( extra ) { - for ( ; i < len; i += 2 ) { - val += parseFloat( jQuery.css( elem, "padding" + cssExpand[ i ] ) ) || 0; - if ( extra !== "padding" ) { - val += parseFloat( jQuery.css( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0; - } - if ( extra === "margin" ) { - val += parseFloat( jQuery.css( elem, extra + cssExpand[ i ]) ) || 0; - } - } - } - - return val + "px"; -} - -jQuery.each([ "height", "width" ], function( i, name ) { - jQuery.cssHooks[ name ] = { - get: function( elem, computed, extra ) { - if ( computed ) { - if ( elem.offsetWidth !== 0 ) { - return getWidthOrHeight( elem, name, extra ); - } else { - return jQuery.swap( elem, cssShow, function() { - return getWidthOrHeight( elem, name, extra ); - }); - } - } - }, - - set: function( elem, value ) { - return rnum.test( value ) ? - value + "px" : - value; - } - }; -}); - -if ( !jQuery.support.opacity ) { - jQuery.cssHooks.opacity = { - get: function( elem, computed ) { - // IE uses filters for opacity - return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ? - ( parseFloat( RegExp.$1 ) / 100 ) + "" : - computed ? "1" : ""; - }, - - set: function( elem, value ) { - var style = elem.style, - currentStyle = elem.currentStyle, - opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "", - filter = currentStyle && currentStyle.filter || style.filter || ""; - - // IE has trouble with opacity if it does not have layout - // Force it by setting the zoom level - style.zoom = 1; - - // if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652 - if ( value >= 1 && jQuery.trim( filter.replace( ralpha, "" ) ) === "" ) { - - // Setting style.filter to null, "" & " " still leave "filter:" in the cssText - // if "filter:" is present at all, clearType is disabled, we want to avoid this - // style.removeAttribute is IE Only, but so apparently is this code path... - style.removeAttribute( "filter" ); - - // if there there is no filter style applied in a css rule, we are done - if ( currentStyle && !currentStyle.filter ) { - return; - } - } - - // otherwise, set new filter values - style.filter = ralpha.test( filter ) ? - filter.replace( ralpha, opacity ) : - filter + " " + opacity; - } - }; -} - -jQuery(function() { - // This hook cannot be added until DOM ready because the support test - // for it is not run until after DOM ready - if ( !jQuery.support.reliableMarginRight ) { - jQuery.cssHooks.marginRight = { - get: function( elem, computed ) { - // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right - // Work around by temporarily setting element display to inline-block - return jQuery.swap( elem, { "display": "inline-block" }, function() { - if ( computed ) { - return curCSS( elem, "margin-right" ); - } else { - return elem.style.marginRight; - } - }); - } - }; - } -}); - -if ( jQuery.expr && jQuery.expr.filters ) { - jQuery.expr.filters.hidden = function( elem ) { - var width = elem.offsetWidth, - height = elem.offsetHeight; - - return ( width === 0 && height === 0 ) || (!jQuery.support.reliableHiddenOffsets && ((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none"); - }; - - jQuery.expr.filters.visible = function( elem ) { - return !jQuery.expr.filters.hidden( elem ); - }; -} - -// These hooks are used by animate to expand properties -jQuery.each({ - margin: "", - padding: "", - border: "Width" -}, function( prefix, suffix ) { - - jQuery.cssHooks[ prefix + suffix ] = { - expand: function( value ) { - var i, - - // assumes a single number if not a string - parts = typeof value === "string" ? value.split(" ") : [ value ], - expanded = {}; - - for ( i = 0; i < 4; i++ ) { - expanded[ prefix + cssExpand[ i ] + suffix ] = - parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; - } - - return expanded; - } - }; -}); - - - - -var r20 = /%20/g, - rbracket = /\[\]$/, - rCRLF = /\r?\n/g, - rhash = /#.*$/, - rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL - rinput = /^(?:color|date|datetime|datetime-local|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i, - // #7653, #8125, #8152: local protocol detection - rlocalProtocol = /^(?:about|app|app\-storage|.+\-extension|file|res|widget):$/, - rnoContent = /^(?:GET|HEAD)$/, - rprotocol = /^\/\//, - rquery = /\?/, - rscript = /<script\b[^<]*(?:(?!<\/script>)<[^<]*)*<\/script>/gi, - rselectTextarea = /^(?:select|textarea)/i, - rspacesAjax = /\s+/, - rts = /([?&])_=[^&]*/, - rurl = /^([\w\+\.\-]+:)(?:\/\/([^\/?#:]*)(?::(\d+))?)?/, - - // Keep a copy of the old load method - _load = jQuery.fn.load, - - /* Prefilters - * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) - * 2) These are called: - * - BEFORE asking for a transport - * - AFTER param serialization (s.data is a string if s.processData is true) - * 3) key is the dataType - * 4) the catchall symbol "*" can be used - * 5) execution will start with transport dataType and THEN continue down to "*" if needed - */ - prefilters = {}, - - /* Transports bindings - * 1) key is the dataType - * 2) the catchall symbol "*" can be used - * 3) selection will start with transport dataType and THEN go to "*" if needed - */ - transports = {}, - - // Document location - ajaxLocation, - - // Document location segments - ajaxLocParts, - - // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression - allTypes = ["*/"] + ["*"]; - -// #8138, IE may throw an exception when accessing -// a field from window.location if document.domain has been set -try { - ajaxLocation = location.href; -} catch( e ) { - // Use the href attribute of an A element - // since IE will modify it given document.location - ajaxLocation = document.createElement( "a" ); - ajaxLocation.href = ""; - ajaxLocation = ajaxLocation.href; -} - -// Segment location into parts -ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || []; - -// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport -function addToPrefiltersOrTransports( structure ) { - - // dataTypeExpression is optional and defaults to "*" - return function( dataTypeExpression, func ) { - - if ( typeof dataTypeExpression !== "string" ) { - func = dataTypeExpression; - dataTypeExpression = "*"; - } - - if ( jQuery.isFunction( func ) ) { - var dataTypes = dataTypeExpression.toLowerCase().split( rspacesAjax ), - i = 0, - length = dataTypes.length, - dataType, - list, - placeBefore; - - // For each dataType in the dataTypeExpression - for ( ; i < length; i++ ) { - dataType = dataTypes[ i ]; - // We control if we're asked to add before - // any existing element - placeBefore = /^\+/.test( dataType ); - if ( placeBefore ) { - dataType = dataType.substr( 1 ) || "*"; - } - list = structure[ dataType ] = structure[ dataType ] || []; - // then we add to the structure accordingly - list[ placeBefore ? "unshift" : "push" ]( func ); - } - } - }; -} - -// Base inspection function for prefilters and transports -function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR, - dataType /* internal */, inspected /* internal */ ) { - - dataType = dataType || options.dataTypes[ 0 ]; - inspected = inspected || {}; - - inspected[ dataType ] = true; - - var list = structure[ dataType ], - i = 0, - length = list ? list.length : 0, - executeOnly = ( structure === prefilters ), - selection; - - for ( ; i < length && ( executeOnly || !selection ); i++ ) { - selection = list[ i ]( options, originalOptions, jqXHR ); - // If we got redirected to another dataType - // we try there if executing only and not done already - if ( typeof selection === "string" ) { - if ( !executeOnly || inspected[ selection ] ) { - selection = undefined; - } else { - options.dataTypes.unshift( selection ); - selection = inspectPrefiltersOrTransports( - structure, options, originalOptions, jqXHR, selection, inspected ); - } - } - } - // If we're only executing or nothing was selected - // we try the catchall dataType if not done already - if ( ( executeOnly || !selection ) && !inspected[ "*" ] ) { - selection = inspectPrefiltersOrTransports( - structure, options, originalOptions, jqXHR, "*", inspected ); - } - // unnecessary when only executing (prefilters) - // but it'll be ignored by the caller in that case - return selection; -} - -// A special extend for ajax options -// that takes "flat" options (not to be deep extended) -// Fixes #9887 -function ajaxExtend( target, src ) { - var key, deep, - flatOptions = jQuery.ajaxSettings.flatOptions || {}; - for ( key in src ) { - if ( src[ key ] !== undefined ) { - ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; - } - } - if ( deep ) { - jQuery.extend( true, target, deep ); - } -} - -jQuery.fn.extend({ - load: function( url, params, callback ) { - if ( typeof url !== "string" && _load ) { - return _load.apply( this, arguments ); - - // Don't do a request if no elements are being requested - } else if ( !this.length ) { - return this; - } - - var off = url.indexOf( " " ); - if ( off >= 0 ) { - var selector = url.slice( off, url.length ); - url = url.slice( 0, off ); - } - - // Default to a GET request - var type = "GET"; - - // If the second parameter was provided - if ( params ) { - // If it's a function - if ( jQuery.isFunction( params ) ) { - // We assume that it's the callback - callback = params; - params = undefined; - - // Otherwise, build a param string - } else if ( typeof params === "object" ) { - params = jQuery.param( params, jQuery.ajaxSettings.traditional ); - type = "POST"; - } - } - - var self = this; - - // Request the remote document - jQuery.ajax({ - url: url, - type: type, - dataType: "html", - data: params, - // Complete callback (responseText is used internally) - complete: function( jqXHR, status, responseText ) { - // Store the response as specified by the jqXHR object - responseText = jqXHR.responseText; - // If successful, inject the HTML into all the matched elements - if ( jqXHR.isResolved() ) { - // #4825: Get the actual response in case - // a dataFilter is present in ajaxSettings - jqXHR.done(function( r ) { - responseText = r; - }); - // See if a selector was specified - self.html( selector ? - // Create a dummy div to hold the results - jQuery("<div>") - // inject the contents of the document in, removing the scripts - // to avoid any 'Permission Denied' errors in IE - .append(responseText.replace(rscript, "")) - - // Locate the specified elements - .find(selector) : - - // If not, just inject the full result - responseText ); - } - - if ( callback ) { - self.each( callback, [ responseText, status, jqXHR ] ); - } - } - }); - - return this; - }, - - serialize: function() { - return jQuery.param( this.serializeArray() ); - }, - - serializeArray: function() { - return this.map(function(){ - return this.elements ? jQuery.makeArray( this.elements ) : this; - }) - .filter(function(){ - return this.name && !this.disabled && - ( this.checked || rselectTextarea.test( this.nodeName ) || - rinput.test( this.type ) ); - }) - .map(function( i, elem ){ - var val = jQuery( this ).val(); - - return val == null ? - null : - jQuery.isArray( val ) ? - jQuery.map( val, function( val, i ){ - return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - }) : - { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; - }).get(); - } -}); - -// Attach a bunch of functions for handling common AJAX events -jQuery.each( "ajaxStart ajaxStop ajaxComplete ajaxError ajaxSuccess ajaxSend".split( " " ), function( i, o ){ - jQuery.fn[ o ] = function( f ){ - return this.on( o, f ); - }; -}); - -jQuery.each( [ "get", "post" ], function( i, method ) { - jQuery[ method ] = function( url, data, callback, type ) { - // shift arguments if data argument was omitted - if ( jQuery.isFunction( data ) ) { - type = type || callback; - callback = data; - data = undefined; - } - - return jQuery.ajax({ - type: method, - url: url, - data: data, - success: callback, - dataType: type - }); - }; -}); - -jQuery.extend({ - - getScript: function( url, callback ) { - return jQuery.get( url, undefined, callback, "script" ); - }, - - getJSON: function( url, data, callback ) { - return jQuery.get( url, data, callback, "json" ); - }, - - // Creates a full fledged settings object into target - // with both ajaxSettings and settings fields. - // If target is omitted, writes into ajaxSettings. - ajaxSetup: function( target, settings ) { - if ( settings ) { - // Building a settings object - ajaxExtend( target, jQuery.ajaxSettings ); - } else { - // Extending ajaxSettings - settings = target; - target = jQuery.ajaxSettings; - } - ajaxExtend( target, settings ); - return target; - }, - - ajaxSettings: { - url: ajaxLocation, - isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ), - global: true, - type: "GET", - contentType: "application/x-www-form-urlencoded; charset=UTF-8", - processData: true, - async: true, - /* - timeout: 0, - data: null, - dataType: null, - username: null, - password: null, - cache: null, - traditional: false, - headers: {}, - */ - - accepts: { - xml: "application/xml, text/xml", - html: "text/html", - text: "text/plain", - json: "application/json, text/javascript", - "*": allTypes - }, - - contents: { - xml: /xml/, - html: /html/, - json: /json/ - }, - - responseFields: { - xml: "responseXML", - text: "responseText" - }, - - // List of data converters - // 1) key format is "source_type destination_type" (a single space in-between) - // 2) the catchall symbol "*" can be used for source_type - converters: { - - // Convert anything to text - "* text": window.String, - - // Text to html (true = no transformation) - "text html": true, - - // Evaluate text as a json expression - "text json": jQuery.parseJSON, - - // Parse text as xml - "text xml": jQuery.parseXML - }, - - // For options that shouldn't be deep extended: - // you can add your own custom options here if - // and when you create one that shouldn't be - // deep extended (see ajaxExtend) - flatOptions: { - context: true, - url: true - } - }, - - ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), - ajaxTransport: addToPrefiltersOrTransports( transports ), - - // Main method - ajax: function( url, options ) { - - // If url is an object, simulate pre-1.5 signature - if ( typeof url === "object" ) { - options = url; - url = undefined; - } - - // Force options to be an object - options = options || {}; - - var // Create the final options object - s = jQuery.ajaxSetup( {}, options ), - // Callbacks context - callbackContext = s.context || s, - // Context for global events - // It's the callbackContext if one was provided in the options - // and if it's a DOM node or a jQuery collection - globalEventContext = callbackContext !== s && - ( callbackContext.nodeType || callbackContext instanceof jQuery ) ? - jQuery( callbackContext ) : jQuery.event, - // Deferreds - deferred = jQuery.Deferred(), - completeDeferred = jQuery.Callbacks( "once memory" ), - // Status-dependent callbacks - statusCode = s.statusCode || {}, - // ifModified key - ifModifiedKey, - // Headers (they are sent all at once) - requestHeaders = {}, - requestHeadersNames = {}, - // Response headers - responseHeadersString, - responseHeaders, - // transport - transport, - // timeout handle - timeoutTimer, - // Cross-domain detection vars - parts, - // The jqXHR state - state = 0, - // To know if global events are to be dispatched - fireGlobals, - // Loop variable - i, - // Fake xhr - jqXHR = { - - readyState: 0, - - // Caches the header - setRequestHeader: function( name, value ) { - if ( !state ) { - var lname = name.toLowerCase(); - name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name; - requestHeaders[ name ] = value; - } - return this; - }, - - // Raw string - getAllResponseHeaders: function() { - return state === 2 ? responseHeadersString : null; - }, - - // Builds headers hashtable if needed - getResponseHeader: function( key ) { - var match; - if ( state === 2 ) { - if ( !responseHeaders ) { - responseHeaders = {}; - while( ( match = rheaders.exec( responseHeadersString ) ) ) { - responseHeaders[ match[1].toLowerCase() ] = match[ 2 ]; - } - } - match = responseHeaders[ key.toLowerCase() ]; - } - return match === undefined ? null : match; - }, - - // Overrides response content-type header - overrideMimeType: function( type ) { - if ( !state ) { - s.mimeType = type; - } - return this; - }, - - // Cancel the request - abort: function( statusText ) { - statusText = statusText || "abort"; - if ( transport ) { - transport.abort( statusText ); - } - done( 0, statusText ); - return this; - } - }; - - // Callback for when everything is done - // It is defined here because jslint complains if it is declared - // at the end of the function (which would be more logical and readable) - function done( status, nativeStatusText, responses, headers ) { - - // Called once - if ( state === 2 ) { - return; - } - - // State is "done" now - state = 2; - - // Clear timeout if it exists - if ( timeoutTimer ) { - clearTimeout( timeoutTimer ); - } - - // Dereference transport for early garbage collection - // (no matter how long the jqXHR object will be used) - transport = undefined; - - // Cache response headers - responseHeadersString = headers || ""; - - // Set readyState - jqXHR.readyState = status > 0 ? 4 : 0; - - var isSuccess, - success, - error, - statusText = nativeStatusText, - response = responses ? ajaxHandleResponses( s, jqXHR, responses ) : undefined, - lastModified, - etag; - - // If successful, handle type chaining - if ( status >= 200 && status < 300 || status === 304 ) { - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - - if ( ( lastModified = jqXHR.getResponseHeader( "Last-Modified" ) ) ) { - jQuery.lastModified[ ifModifiedKey ] = lastModified; - } - if ( ( etag = jqXHR.getResponseHeader( "Etag" ) ) ) { - jQuery.etag[ ifModifiedKey ] = etag; - } - } - - // If not modified - if ( status === 304 ) { - - statusText = "notmodified"; - isSuccess = true; - - // If we have data - } else { - - try { - success = ajaxConvert( s, response ); - statusText = "success"; - isSuccess = true; - } catch(e) { - // We have a parsererror - statusText = "parsererror"; - error = e; - } - } - } else { - // We extract error from statusText - // then normalize statusText and status for non-aborts - error = statusText; - if ( !statusText || status ) { - statusText = "error"; - if ( status < 0 ) { - status = 0; - } - } - } - - // Set data for the fake xhr object - jqXHR.status = status; - jqXHR.statusText = "" + ( nativeStatusText || statusText ); - - // Success/Error - if ( isSuccess ) { - deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); - } else { - deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); - } - - // Status-dependent callbacks - jqXHR.statusCode( statusCode ); - statusCode = undefined; - - if ( fireGlobals ) { - globalEventContext.trigger( "ajax" + ( isSuccess ? "Success" : "Error" ), - [ jqXHR, s, isSuccess ? success : error ] ); - } - - // Complete - completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); - - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); - // Handle the global AJAX counter - if ( !( --jQuery.active ) ) { - jQuery.event.trigger( "ajaxStop" ); - } - } - } - - // Attach deferreds - deferred.promise( jqXHR ); - jqXHR.success = jqXHR.done; - jqXHR.error = jqXHR.fail; - jqXHR.complete = completeDeferred.add; - - // Status-dependent callbacks - jqXHR.statusCode = function( map ) { - if ( map ) { - var tmp; - if ( state < 2 ) { - for ( tmp in map ) { - statusCode[ tmp ] = [ statusCode[tmp], map[tmp] ]; - } - } else { - tmp = map[ jqXHR.status ]; - jqXHR.then( tmp, tmp ); - } - } - return this; - }; - - // Remove hash character (#7531: and string promotion) - // Add protocol if not provided (#5866: IE7 issue with protocol-less urls) - // We also use the url parameter if available - s.url = ( ( url || s.url ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" ); - - // Extract dataTypes list - s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax ); - - // Determine if a cross-domain request is in order - if ( s.crossDomain == null ) { - parts = rurl.exec( s.url.toLowerCase() ); - s.crossDomain = !!( parts && - ( parts[ 1 ] != ajaxLocParts[ 1 ] || parts[ 2 ] != ajaxLocParts[ 2 ] || - ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) != - ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? 80 : 443 ) ) ) - ); - } - - // Convert data if not already a string - if ( s.data && s.processData && typeof s.data !== "string" ) { - s.data = jQuery.param( s.data, s.traditional ); - } - - // Apply prefilters - inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); - - // If request was aborted inside a prefilter, stop there - if ( state === 2 ) { - return false; - } - - // We can fire global events as of now if asked to - fireGlobals = s.global; - - // Uppercase the type - s.type = s.type.toUpperCase(); - - // Determine if request has content - s.hasContent = !rnoContent.test( s.type ); - - // Watch for a new set of requests - if ( fireGlobals && jQuery.active++ === 0 ) { - jQuery.event.trigger( "ajaxStart" ); - } - - // More options handling for requests with no content - if ( !s.hasContent ) { - - // If data is available, append data to url - if ( s.data ) { - s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.data; - // #9682: remove data so that it's not used in an eventual retry - delete s.data; - } - - // Get ifModifiedKey before adding the anti-cache parameter - ifModifiedKey = s.url; - - // Add anti-cache in url if needed - if ( s.cache === false ) { - - var ts = jQuery.now(), - // try replacing _= if it is there - ret = s.url.replace( rts, "$1_=" + ts ); - - // if nothing was replaced, add timestamp to the end - s.url = ret + ( ( ret === s.url ) ? ( rquery.test( s.url ) ? "&" : "?" ) + "_=" + ts : "" ); - } - } - - // Set the correct header, if data is being sent - if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { - jqXHR.setRequestHeader( "Content-Type", s.contentType ); - } - - // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. - if ( s.ifModified ) { - ifModifiedKey = ifModifiedKey || s.url; - if ( jQuery.lastModified[ ifModifiedKey ] ) { - jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ ifModifiedKey ] ); - } - if ( jQuery.etag[ ifModifiedKey ] ) { - jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ ifModifiedKey ] ); - } - } - - // Set the Accepts header for the server, depending on the dataType - jqXHR.setRequestHeader( - "Accept", - s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ? - s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : - s.accepts[ "*" ] - ); - - // Check for headers option - for ( i in s.headers ) { - jqXHR.setRequestHeader( i, s.headers[ i ] ); - } - - // Allow custom headers/mimetypes and early abort - if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) { - // Abort if not done already - jqXHR.abort(); - return false; - - } - - // Install callbacks on deferreds - for ( i in { success: 1, error: 1, complete: 1 } ) { - jqXHR[ i ]( s[ i ] ); - } - - // Get transport - transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); - - // If no transport, we auto-abort - if ( !transport ) { - done( -1, "No Transport" ); - } else { - jqXHR.readyState = 1; - // Send global event - if ( fireGlobals ) { - globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); - } - // Timeout - if ( s.async && s.timeout > 0 ) { - timeoutTimer = setTimeout( function(){ - jqXHR.abort( "timeout" ); - }, s.timeout ); - } - - try { - state = 1; - transport.send( requestHeaders, done ); - } catch (e) { - // Propagate exception as error if not done - if ( state < 2 ) { - done( -1, e ); - // Simply rethrow otherwise - } else { - throw e; - } - } - } - - return jqXHR; - }, - - // Serialize an array of form elements or a set of - // key/values into a query string - param: function( a, traditional ) { - var s = [], - add = function( key, value ) { - // If value is a function, invoke it and return its value - value = jQuery.isFunction( value ) ? value() : value; - s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value ); - }; - - // Set traditional to true for jQuery <= 1.3.2 behavior. - if ( traditional === undefined ) { - traditional = jQuery.ajaxSettings.traditional; - } - - // If an array was passed in, assume that it is an array of form elements. - if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { - // Serialize the form elements - jQuery.each( a, function() { - add( this.name, this.value ); - }); - - } else { - // If traditional, encode the "old" way (the way 1.3.2 or older - // did it), otherwise encode params recursively. - for ( var prefix in a ) { - buildParams( prefix, a[ prefix ], traditional, add ); - } - } - - // Return the resulting serialization - return s.join( "&" ).replace( r20, "+" ); - } -}); - -function buildParams( prefix, obj, traditional, add ) { - if ( jQuery.isArray( obj ) ) { - // Serialize array item. - jQuery.each( obj, function( i, v ) { - if ( traditional || rbracket.test( prefix ) ) { - // Treat each array item as a scalar. - add( prefix, v ); - - } else { - // If array item is non-scalar (array or object), encode its - // numeric index to resolve deserialization ambiguity issues. - // Note that rack (as of 1.0.0) can't currently deserialize - // nested arrays properly, and attempting to do so may cause - // a server error. Possible fixes are to modify rack's - // deserialization algorithm or to provide an option or flag - // to force array serialization to be shallow. - buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add ); - } - }); - - } else if ( !traditional && jQuery.type( obj ) === "object" ) { - // Serialize object item. - for ( var name in obj ) { - buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); - } - - } else { - // Serialize scalar item. - add( prefix, obj ); - } -} - -// This is still on the jQuery object... for now -// Want to move this to jQuery.ajax some day -jQuery.extend({ - - // Counter for holding the number of active queries - active: 0, - - // Last-Modified header cache for next request - lastModified: {}, - etag: {} - -}); - -/* Handles responses to an ajax request: - * - sets all responseXXX fields accordingly - * - finds the right dataType (mediates between content-type and expected dataType) - * - returns the corresponding response - */ -function ajaxHandleResponses( s, jqXHR, responses ) { - - var contents = s.contents, - dataTypes = s.dataTypes, - responseFields = s.responseFields, - ct, - type, - finalDataType, - firstDataType; - - // Fill responseXXX fields - for ( type in responseFields ) { - if ( type in responses ) { - jqXHR[ responseFields[type] ] = responses[ type ]; - } - } - - // Remove auto dataType and get content-type in the process - while( dataTypes[ 0 ] === "*" ) { - dataTypes.shift(); - if ( ct === undefined ) { - ct = s.mimeType || jqXHR.getResponseHeader( "content-type" ); - } - } - - // Check if we're dealing with a known content-type - if ( ct ) { - for ( type in contents ) { - if ( contents[ type ] && contents[ type ].test( ct ) ) { - dataTypes.unshift( type ); - break; - } - } - } - - // Check to see if we have a response for the expected dataType - if ( dataTypes[ 0 ] in responses ) { - finalDataType = dataTypes[ 0 ]; - } else { - // Try convertible dataTypes - for ( type in responses ) { - if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) { - finalDataType = type; - break; - } - if ( !firstDataType ) { - firstDataType = type; - } - } - // Or just use first one - finalDataType = finalDataType || firstDataType; - } - - // If we found a dataType - // We add the dataType to the list if needed - // and return the corresponding response - if ( finalDataType ) { - if ( finalDataType !== dataTypes[ 0 ] ) { - dataTypes.unshift( finalDataType ); - } - return responses[ finalDataType ]; - } -} - -// Chain conversions given the request and the original response -function ajaxConvert( s, response ) { - - // Apply the dataFilter if provided - if ( s.dataFilter ) { - response = s.dataFilter( response, s.dataType ); - } - - var dataTypes = s.dataTypes, - converters = {}, - i, - key, - length = dataTypes.length, - tmp, - // Current and previous dataTypes - current = dataTypes[ 0 ], - prev, - // Conversion expression - conversion, - // Conversion function - conv, - // Conversion functions (transitive conversion) - conv1, - conv2; - - // For each dataType in the chain - for ( i = 1; i < length; i++ ) { - - // Create converters map - // with lowercased keys - if ( i === 1 ) { - for ( key in s.converters ) { - if ( typeof key === "string" ) { - converters[ key.toLowerCase() ] = s.converters[ key ]; - } - } - } - - // Get the dataTypes - prev = current; - current = dataTypes[ i ]; - - // If current is auto dataType, update it to prev - if ( current === "*" ) { - current = prev; - // If no auto and dataTypes are actually different - } else if ( prev !== "*" && prev !== current ) { - - // Get the converter - conversion = prev + " " + current; - conv = converters[ conversion ] || converters[ "* " + current ]; - - // If there is no direct converter, search transitively - if ( !conv ) { - conv2 = undefined; - for ( conv1 in converters ) { - tmp = conv1.split( " " ); - if ( tmp[ 0 ] === prev || tmp[ 0 ] === "*" ) { - conv2 = converters[ tmp[1] + " " + current ]; - if ( conv2 ) { - conv1 = converters[ conv1 ]; - if ( conv1 === true ) { - conv = conv2; - } else if ( conv2 === true ) { - conv = conv1; - } - break; - } - } - } - } - // If we found no converter, dispatch an error - if ( !( conv || conv2 ) ) { - jQuery.error( "No conversion from " + conversion.replace(" "," to ") ); - } - // If found converter is not an equivalence - if ( conv !== true ) { - // Convert with 1 or 2 converters accordingly - response = conv ? conv( response ) : conv2( conv1(response) ); - } - } - } - return response; -} - - - - -var jsc = jQuery.now(), - jsre = /(\=)\?(&|$)|\?\?/i; - -// Default jsonp settings -jQuery.ajaxSetup({ - jsonp: "callback", - jsonpCallback: function() { - return jQuery.expando + "_" + ( jsc++ ); - } -}); - -// Detect, normalize options and install callbacks for jsonp requests -jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) { - - var inspectData = ( typeof s.data === "string" ) && /^application\/x\-www\-form\-urlencoded/.test( s.contentType ); - - if ( s.dataTypes[ 0 ] === "jsonp" || - s.jsonp !== false && ( jsre.test( s.url ) || - inspectData && jsre.test( s.data ) ) ) { - - var responseContainer, - jsonpCallback = s.jsonpCallback = - jQuery.isFunction( s.jsonpCallback ) ? s.jsonpCallback() : s.jsonpCallback, - previous = window[ jsonpCallback ], - url = s.url, - data = s.data, - replace = "$1" + jsonpCallback + "$2"; - - if ( s.jsonp !== false ) { - url = url.replace( jsre, replace ); - if ( s.url === url ) { - if ( inspectData ) { - data = data.replace( jsre, replace ); - } - if ( s.data === data ) { - // Add callback manually - url += (/\?/.test( url ) ? "&" : "?") + s.jsonp + "=" + jsonpCallback; - } - } - } - - s.url = url; - s.data = data; - - // Install callback - window[ jsonpCallback ] = function( response ) { - responseContainer = [ response ]; - }; - - // Clean-up function - jqXHR.always(function() { - // Set callback back to previous value - window[ jsonpCallback ] = previous; - // Call if it was a function and we have a response - if ( responseContainer && jQuery.isFunction( previous ) ) { - window[ jsonpCallback ]( responseContainer[ 0 ] ); - } - }); - - // Use data converter to retrieve json after script execution - s.converters["script json"] = function() { - if ( !responseContainer ) { - jQuery.error( jsonpCallback + " was not called" ); - } - return responseContainer[ 0 ]; - }; - - // force json dataType - s.dataTypes[ 0 ] = "json"; - - // Delegate to script - return "script"; - } -}); - - - - -// Install script dataType -jQuery.ajaxSetup({ - accepts: { - script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript" - }, - contents: { - script: /javascript|ecmascript/ - }, - converters: { - "text script": function( text ) { - jQuery.globalEval( text ); - return text; - } - } -}); - -// Handle cache's special case and global -jQuery.ajaxPrefilter( "script", function( s ) { - if ( s.cache === undefined ) { - s.cache = false; - } - if ( s.crossDomain ) { - s.type = "GET"; - s.global = false; - } -}); - -// Bind script tag hack transport -jQuery.ajaxTransport( "script", function(s) { - - // This transport only deals with cross domain requests - if ( s.crossDomain ) { - - var script, - head = document.head || document.getElementsByTagName( "head" )[0] || document.documentElement; - - return { - - send: function( _, callback ) { - - script = document.createElement( "script" ); - - script.async = "async"; - - if ( s.scriptCharset ) { - script.charset = s.scriptCharset; - } - - script.src = s.url; - - // Attach handlers for all browsers - script.onload = script.onreadystatechange = function( _, isAbort ) { - - if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) { - - // Handle memory leak in IE - script.onload = script.onreadystatechange = null; - - // Remove the script - if ( head && script.parentNode ) { - head.removeChild( script ); - } - - // Dereference the script - script = undefined; - - // Callback if not abort - if ( !isAbort ) { - callback( 200, "success" ); - } - } - }; - // Use insertBefore instead of appendChild to circumvent an IE6 bug. - // This arises when a base node is used (#2709 and #4378). - head.insertBefore( script, head.firstChild ); - }, - - abort: function() { - if ( script ) { - script.onload( 0, 1 ); - } - } - }; - } -}); - - - - -var // #5280: Internet Explorer will keep connections alive if we don't abort on unload - xhrOnUnloadAbort = window.ActiveXObject ? function() { - // Abort all pending requests - for ( var key in xhrCallbacks ) { - xhrCallbacks[ key ]( 0, 1 ); - } - } : false, - xhrId = 0, - xhrCallbacks; - -// Functions to create xhrs -function createStandardXHR() { - try { - return new window.XMLHttpRequest(); - } catch( e ) {} -} - -function createActiveXHR() { - try { - return new window.ActiveXObject( "Microsoft.XMLHTTP" ); - } catch( e ) {} -} - -// Create the request object -// (This is still attached to ajaxSettings for backward compatibility) -jQuery.ajaxSettings.xhr = window.ActiveXObject ? - /* Microsoft failed to properly - * implement the XMLHttpRequest in IE7 (can't request local files), - * so we use the ActiveXObject when it is available - * Additionally XMLHttpRequest can be disabled in IE7/IE8 so - * we need a fallback. - */ - function() { - return !this.isLocal && createStandardXHR() || createActiveXHR(); - } : - // For all other browsers, use the standard XMLHttpRequest object - createStandardXHR; - -// Determine support properties -(function( xhr ) { - jQuery.extend( jQuery.support, { - ajax: !!xhr, - cors: !!xhr && ( "withCredentials" in xhr ) - }); -})( jQuery.ajaxSettings.xhr() ); - -// Create transport if the browser can provide an xhr -if ( jQuery.support.ajax ) { - - jQuery.ajaxTransport(function( s ) { - // Cross domain only allowed if supported through XMLHttpRequest - if ( !s.crossDomain || jQuery.support.cors ) { - - var callback; - - return { - send: function( headers, complete ) { - - // Get a new xhr - var xhr = s.xhr(), - handle, - i; - - // Open the socket - // Passing null username, generates a login popup on Opera (#2865) - if ( s.username ) { - xhr.open( s.type, s.url, s.async, s.username, s.password ); - } else { - xhr.open( s.type, s.url, s.async ); - } - - // Apply custom fields if provided - if ( s.xhrFields ) { - for ( i in s.xhrFields ) { - xhr[ i ] = s.xhrFields[ i ]; - } - } - - // Override mime type if needed - if ( s.mimeType && xhr.overrideMimeType ) { - xhr.overrideMimeType( s.mimeType ); - } - - // X-Requested-With header - // For cross-domain requests, seeing as conditions for a preflight are - // akin to a jigsaw puzzle, we simply never set it to be sure. - // (it can always be set on a per-request basis or even using ajaxSetup) - // For same-domain requests, won't change header if already provided. - if ( !s.crossDomain && !headers["X-Requested-With"] ) { - headers[ "X-Requested-With" ] = "XMLHttpRequest"; - } - - // Need an extra try/catch for cross domain requests in Firefox 3 - try { - for ( i in headers ) { - xhr.setRequestHeader( i, headers[ i ] ); - } - } catch( _ ) {} - - // Do send the request - // This may raise an exception which is actually - // handled in jQuery.ajax (so no try/catch here) - xhr.send( ( s.hasContent && s.data ) || null ); - - // Listener - callback = function( _, isAbort ) { - - var status, - statusText, - responseHeaders, - responses, - xml; - - // Firefox throws exceptions when accessing properties - // of an xhr when a network error occured - // http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0x80040111_(NS_ERROR_NOT_AVAILABLE) - try { - - // Was never called and is aborted or complete - if ( callback && ( isAbort || xhr.readyState === 4 ) ) { - - // Only called once - callback = undefined; - - // Do not keep as active anymore - if ( handle ) { - xhr.onreadystatechange = jQuery.noop; - if ( xhrOnUnloadAbort ) { - delete xhrCallbacks[ handle ]; - } - } - - // If it's an abort - if ( isAbort ) { - // Abort it manually if needed - if ( xhr.readyState !== 4 ) { - xhr.abort(); - } - } else { - status = xhr.status; - responseHeaders = xhr.getAllResponseHeaders(); - responses = {}; - xml = xhr.responseXML; - - // Construct response list - if ( xml && xml.documentElement /* #4958 */ ) { - responses.xml = xml; - } - - // When requesting binary data, IE6-9 will throw an exception - // on any attempt to access responseText (#11426) - try { - responses.text = xhr.responseText; - } catch( _ ) { - } - - // Firefox throws an exception when accessing - // statusText for faulty cross-domain requests - try { - statusText = xhr.statusText; - } catch( e ) { - // We normalize with Webkit giving an empty statusText - statusText = ""; - } - - // Filter status for non standard behaviors - - // If the request is local and we have data: assume a success - // (success with no data won't get notified, that's the best we - // can do given current implementations) - if ( !status && s.isLocal && !s.crossDomain ) { - status = responses.text ? 200 : 404; - // IE - #1450: sometimes returns 1223 when it should be 204 - } else if ( status === 1223 ) { - status = 204; - } - } - } - } catch( firefoxAccessException ) { - if ( !isAbort ) { - complete( -1, firefoxAccessException ); - } - } - - // Call complete if needed - if ( responses ) { - complete( status, statusText, responses, responseHeaders ); - } - }; - - // if we're in sync mode or it's in cache - // and has been retrieved directly (IE6 & IE7) - // we need to manually fire the callback - if ( !s.async || xhr.readyState === 4 ) { - callback(); - } else { - handle = ++xhrId; - if ( xhrOnUnloadAbort ) { - // Create the active xhrs callbacks list if needed - // and attach the unload handler - if ( !xhrCallbacks ) { - xhrCallbacks = {}; - jQuery( window ).unload( xhrOnUnloadAbort ); - } - // Add to list of active xhrs callbacks - xhrCallbacks[ handle ] = callback; - } - xhr.onreadystatechange = callback; - } - }, - - abort: function() { - if ( callback ) { - callback(0,1); - } - } - }; - } - }); -} - - - - -var elemdisplay = {}, - iframe, iframeDoc, - rfxtypes = /^(?:toggle|show|hide)$/, - rfxnum = /^([+\-]=)?([\d+.\-]+)([a-z%]*)$/i, - timerId, - fxAttrs = [ - // height animations - [ "height", "marginTop", "marginBottom", "paddingTop", "paddingBottom" ], - // width animations - [ "width", "marginLeft", "marginRight", "paddingLeft", "paddingRight" ], - // opacity animations - [ "opacity" ] - ], - fxNow; - -jQuery.fn.extend({ - show: function( speed, easing, callback ) { - var elem, display; - - if ( speed || speed === 0 ) { - return this.animate( genFx("show", 3), speed, easing, callback ); - - } else { - for ( var i = 0, j = this.length; i < j; i++ ) { - elem = this[ i ]; - - if ( elem.style ) { - display = elem.style.display; - - // Reset the inline display of this element to learn if it is - // being hidden by cascaded rules or not - if ( !jQuery._data(elem, "olddisplay") && display === "none" ) { - display = elem.style.display = ""; - } - - // Set elements which have been overridden with display: none - // in a stylesheet to whatever the default browser style is - // for such an element - if ( (display === "" && jQuery.css(elem, "display") === "none") || - !jQuery.contains( elem.ownerDocument.documentElement, elem ) ) { - jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) ); - } - } - } - - // Set the display of most of the elements in a second loop - // to avoid the constant reflow - for ( i = 0; i < j; i++ ) { - elem = this[ i ]; - - if ( elem.style ) { - display = elem.style.display; - - if ( display === "" || display === "none" ) { - elem.style.display = jQuery._data( elem, "olddisplay" ) || ""; - } - } - } - - return this; - } - }, - - hide: function( speed, easing, callback ) { - if ( speed || speed === 0 ) { - return this.animate( genFx("hide", 3), speed, easing, callback); - - } else { - var elem, display, - i = 0, - j = this.length; - - for ( ; i < j; i++ ) { - elem = this[i]; - if ( elem.style ) { - display = jQuery.css( elem, "display" ); - - if ( display !== "none" && !jQuery._data( elem, "olddisplay" ) ) { - jQuery._data( elem, "olddisplay", display ); - } - } - } - - // Set the display of the elements in a second loop - // to avoid the constant reflow - for ( i = 0; i < j; i++ ) { - if ( this[i].style ) { - this[i].style.display = "none"; - } - } - - return this; - } - }, - - // Save the old toggle function - _toggle: jQuery.fn.toggle, - - toggle: function( fn, fn2, callback ) { - var bool = typeof fn === "boolean"; - - if ( jQuery.isFunction(fn) && jQuery.isFunction(fn2) ) { - this._toggle.apply( this, arguments ); - - } else if ( fn == null || bool ) { - this.each(function() { - var state = bool ? fn : jQuery(this).is(":hidden"); - jQuery(this)[ state ? "show" : "hide" ](); - }); - - } else { - this.animate(genFx("toggle", 3), fn, fn2, callback); - } - - return this; - }, - - fadeTo: function( speed, to, easing, callback ) { - return this.filter(":hidden").css("opacity", 0).show().end() - .animate({opacity: to}, speed, easing, callback); - }, - - animate: function( prop, speed, easing, callback ) { - var optall = jQuery.speed( speed, easing, callback ); - - if ( jQuery.isEmptyObject( prop ) ) { - return this.each( optall.complete, [ false ] ); - } - - // Do not change referenced properties as per-property easing will be lost - prop = jQuery.extend( {}, prop ); - - function doAnimation() { - // XXX 'this' does not always have a nodeName when running the - // test suite - - if ( optall.queue === false ) { - jQuery._mark( this ); - } - - var opt = jQuery.extend( {}, optall ), - isElement = this.nodeType === 1, - hidden = isElement && jQuery(this).is(":hidden"), - name, val, p, e, hooks, replace, - parts, start, end, unit, - method; - - // will store per property easing and be used to determine when an animation is complete - opt.animatedProperties = {}; - - // first pass over propertys to expand / normalize - for ( p in prop ) { - name = jQuery.camelCase( p ); - if ( p !== name ) { - prop[ name ] = prop[ p ]; - delete prop[ p ]; - } - - if ( ( hooks = jQuery.cssHooks[ name ] ) && "expand" in hooks ) { - replace = hooks.expand( prop[ name ] ); - delete prop[ name ]; - - // not quite $.extend, this wont overwrite keys already present. - // also - reusing 'p' from above because we have the correct "name" - for ( p in replace ) { - if ( ! ( p in prop ) ) { - prop[ p ] = replace[ p ]; - } - } - } - } - - for ( name in prop ) { - val = prop[ name ]; - // easing resolution: per property > opt.specialEasing > opt.easing > 'swing' (default) - if ( jQuery.isArray( val ) ) { - opt.animatedProperties[ name ] = val[ 1 ]; - val = prop[ name ] = val[ 0 ]; - } else { - opt.animatedProperties[ name ] = opt.specialEasing && opt.specialEasing[ name ] || opt.easing || 'swing'; - } - - if ( val === "hide" && hidden || val === "show" && !hidden ) { - return opt.complete.call( this ); - } - - if ( isElement && ( name === "height" || name === "width" ) ) { - // Make sure that nothing sneaks out - // Record all 3 overflow attributes because IE does not - // change the overflow attribute when overflowX and - // overflowY are set to the same value - opt.overflow = [ this.style.overflow, this.style.overflowX, this.style.overflowY ]; - - // Set display property to inline-block for height/width - // animations on inline elements that are having width/height animated - if ( jQuery.css( this, "display" ) === "inline" && - jQuery.css( this, "float" ) === "none" ) { - - // inline-level elements accept inline-block; - // block-level elements need to be inline with layout - if ( !jQuery.support.inlineBlockNeedsLayout || defaultDisplay( this.nodeName ) === "inline" ) { - this.style.display = "inline-block"; - - } else { - this.style.zoom = 1; - } - } - } - } - - if ( opt.overflow != null ) { - this.style.overflow = "hidden"; - } - - for ( p in prop ) { - e = new jQuery.fx( this, opt, p ); - val = prop[ p ]; - - if ( rfxtypes.test( val ) ) { - - // Tracks whether to show or hide based on private - // data attached to the element - method = jQuery._data( this, "toggle" + p ) || ( val === "toggle" ? hidden ? "show" : "hide" : 0 ); - if ( method ) { - jQuery._data( this, "toggle" + p, method === "show" ? "hide" : "show" ); - e[ method ](); - } else { - e[ val ](); - } - - } else { - parts = rfxnum.exec( val ); - start = e.cur(); - - if ( parts ) { - end = parseFloat( parts[2] ); - unit = parts[3] || ( jQuery.cssNumber[ p ] ? "" : "px" ); - - // We need to compute starting value - if ( unit !== "px" ) { - jQuery.style( this, p, (end || 1) + unit); - start = ( (end || 1) / e.cur() ) * start; - jQuery.style( this, p, start + unit); - } - - // If a +=/-= token was provided, we're doing a relative animation - if ( parts[1] ) { - end = ( (parts[ 1 ] === "-=" ? -1 : 1) * end ) + start; - } - - e.custom( start, end, unit ); - - } else { - e.custom( start, val, "" ); - } - } - } - - // For JS strict compliance - return true; - } - - return optall.queue === false ? - this.each( doAnimation ) : - this.queue( optall.queue, doAnimation ); - }, - - stop: function( type, clearQueue, gotoEnd ) { - if ( typeof type !== "string" ) { - gotoEnd = clearQueue; - clearQueue = type; - type = undefined; - } - if ( clearQueue && type !== false ) { - this.queue( type || "fx", [] ); - } - - return this.each(function() { - var index, - hadTimers = false, - timers = jQuery.timers, - data = jQuery._data( this ); - - // clear marker counters if we know they won't be - if ( !gotoEnd ) { - jQuery._unmark( true, this ); - } - - function stopQueue( elem, data, index ) { - var hooks = data[ index ]; - jQuery.removeData( elem, index, true ); - hooks.stop( gotoEnd ); - } - - if ( type == null ) { - for ( index in data ) { - if ( data[ index ] && data[ index ].stop && index.indexOf(".run") === index.length - 4 ) { - stopQueue( this, data, index ); - } - } - } else if ( data[ index = type + ".run" ] && data[ index ].stop ){ - stopQueue( this, data, index ); - } - - for ( index = timers.length; index--; ) { - if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) { - if ( gotoEnd ) { - - // force the next step to be the last - timers[ index ]( true ); - } else { - timers[ index ].saveState(); - } - hadTimers = true; - timers.splice( index, 1 ); - } - } - - // start the next in the queue if the last step wasn't forced - // timers currently will call their complete callbacks, which will dequeue - // but only if they were gotoEnd - if ( !( gotoEnd && hadTimers ) ) { - jQuery.dequeue( this, type ); - } - }); - } - -}); - -// Animations created synchronously will run synchronously -function createFxNow() { - setTimeout( clearFxNow, 0 ); - return ( fxNow = jQuery.now() ); -} - -function clearFxNow() { - fxNow = undefined; -} - -// Generate parameters to create a standard animation -function genFx( type, num ) { - var obj = {}; - - jQuery.each( fxAttrs.concat.apply([], fxAttrs.slice( 0, num )), function() { - obj[ this ] = type; - }); - - return obj; -} - -// Generate shortcuts for custom animations -jQuery.each({ - slideDown: genFx( "show", 1 ), - slideUp: genFx( "hide", 1 ), - slideToggle: genFx( "toggle", 1 ), - fadeIn: { opacity: "show" }, - fadeOut: { opacity: "hide" }, - fadeToggle: { opacity: "toggle" } -}, function( name, props ) { - jQuery.fn[ name ] = function( speed, easing, callback ) { - return this.animate( props, speed, easing, callback ); - }; -}); - -jQuery.extend({ - speed: function( speed, easing, fn ) { - var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { - complete: fn || !fn && easing || - jQuery.isFunction( speed ) && speed, - duration: speed, - easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing - }; - - opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration : - opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default; - - // normalize opt.queue - true/undefined/null -> "fx" - if ( opt.queue == null || opt.queue === true ) { - opt.queue = "fx"; - } - - // Queueing - opt.old = opt.complete; - - opt.complete = function( noUnmark ) { - if ( jQuery.isFunction( opt.old ) ) { - opt.old.call( this ); - } - - if ( opt.queue ) { - jQuery.dequeue( this, opt.queue ); - } else if ( noUnmark !== false ) { - jQuery._unmark( this ); - } - }; - - return opt; - }, - - easing: { - linear: function( p ) { - return p; - }, - swing: function( p ) { - return ( -Math.cos( p*Math.PI ) / 2 ) + 0.5; - } - }, - - timers: [], - - fx: function( elem, options, prop ) { - this.options = options; - this.elem = elem; - this.prop = prop; - - options.orig = options.orig || {}; - } - -}); - -jQuery.fx.prototype = { - // Simple function for setting a style value - update: function() { - if ( this.options.step ) { - this.options.step.call( this.elem, this.now, this ); - } - - ( jQuery.fx.step[ this.prop ] || jQuery.fx.step._default )( this ); - }, - - // Get the current size - cur: function() { - if ( this.elem[ this.prop ] != null && (!this.elem.style || this.elem.style[ this.prop ] == null) ) { - return this.elem[ this.prop ]; - } - - var parsed, - r = jQuery.css( this.elem, this.prop ); - // Empty strings, null, undefined and "auto" are converted to 0, - // complex values such as "rotate(1rad)" are returned as is, - // simple values such as "10px" are parsed to Float. - return isNaN( parsed = parseFloat( r ) ) ? !r || r === "auto" ? 0 : r : parsed; - }, - - // Start an animation from one number to another - custom: function( from, to, unit ) { - var self = this, - fx = jQuery.fx; - - this.startTime = fxNow || createFxNow(); - this.end = to; - this.now = this.start = from; - this.pos = this.state = 0; - this.unit = unit || this.unit || ( jQuery.cssNumber[ this.prop ] ? "" : "px" ); - - function t( gotoEnd ) { - return self.step( gotoEnd ); - } - - t.queue = this.options.queue; - t.elem = this.elem; - t.saveState = function() { - if ( jQuery._data( self.elem, "fxshow" + self.prop ) === undefined ) { - if ( self.options.hide ) { - jQuery._data( self.elem, "fxshow" + self.prop, self.start ); - } else if ( self.options.show ) { - jQuery._data( self.elem, "fxshow" + self.prop, self.end ); - } - } - }; - - if ( t() && jQuery.timers.push(t) && !timerId ) { - timerId = setInterval( fx.tick, fx.interval ); - } - }, - - // Simple 'show' function - show: function() { - var dataShow = jQuery._data( this.elem, "fxshow" + this.prop ); - - // Remember where we started, so that we can go back to it later - this.options.orig[ this.prop ] = dataShow || jQuery.style( this.elem, this.prop ); - this.options.show = true; - - // Begin the animation - // Make sure that we start at a small width/height to avoid any flash of content - if ( dataShow !== undefined ) { - // This show is picking up where a previous hide or show left off - this.custom( this.cur(), dataShow ); - } else { - this.custom( this.prop === "width" || this.prop === "height" ? 1 : 0, this.cur() ); - } - - // Start by showing the element - jQuery( this.elem ).show(); - }, - - // Simple 'hide' function - hide: function() { - // Remember where we started, so that we can go back to it later - this.options.orig[ this.prop ] = jQuery._data( this.elem, "fxshow" + this.prop ) || jQuery.style( this.elem, this.prop ); - this.options.hide = true; - - // Begin the animation - this.custom( this.cur(), 0 ); - }, - - // Each step of an animation - step: function( gotoEnd ) { - var p, n, complete, - t = fxNow || createFxNow(), - done = true, - elem = this.elem, - options = this.options; - - if ( gotoEnd || t >= options.duration + this.startTime ) { - this.now = this.end; - this.pos = this.state = 1; - this.update(); - - options.animatedProperties[ this.prop ] = true; - - for ( p in options.animatedProperties ) { - if ( options.animatedProperties[ p ] !== true ) { - done = false; - } - } - - if ( done ) { - // Reset the overflow - if ( options.overflow != null && !jQuery.support.shrinkWrapBlocks ) { - - jQuery.each( [ "", "X", "Y" ], function( index, value ) { - elem.style[ "overflow" + value ] = options.overflow[ index ]; - }); - } - - // Hide the element if the "hide" operation was done - if ( options.hide ) { - jQuery( elem ).hide(); - } - - // Reset the properties, if the item has been hidden or shown - if ( options.hide || options.show ) { - for ( p in options.animatedProperties ) { - jQuery.style( elem, p, options.orig[ p ] ); - jQuery.removeData( elem, "fxshow" + p, true ); - // Toggle data is no longer needed - jQuery.removeData( elem, "toggle" + p, true ); - } - } - - // Execute the complete function - // in the event that the complete function throws an exception - // we must ensure it won't be called twice. #5684 - - complete = options.complete; - if ( complete ) { - - options.complete = false; - complete.call( elem ); - } - } - - return false; - - } else { - // classical easing cannot be used with an Infinity duration - if ( options.duration == Infinity ) { - this.now = t; - } else { - n = t - this.startTime; - this.state = n / options.duration; - - // Perform the easing function, defaults to swing - this.pos = jQuery.easing[ options.animatedProperties[this.prop] ]( this.state, n, 0, 1, options.duration ); - this.now = this.start + ( (this.end - this.start) * this.pos ); - } - // Perform the next step of the animation - this.update(); - } - - return true; - } -}; - -jQuery.extend( jQuery.fx, { - tick: function() { - var timer, - timers = jQuery.timers, - i = 0; - - for ( ; i < timers.length; i++ ) { - timer = timers[ i ]; - // Checks the timer has not already been removed - if ( !timer() && timers[ i ] === timer ) { - timers.splice( i--, 1 ); - } - } - - if ( !timers.length ) { - jQuery.fx.stop(); - } - }, - - interval: 13, - - stop: function() { - clearInterval( timerId ); - timerId = null; - }, - - speeds: { - slow: 600, - fast: 200, - // Default speed - _default: 400 - }, - - step: { - opacity: function( fx ) { - jQuery.style( fx.elem, "opacity", fx.now ); - }, - - _default: function( fx ) { - if ( fx.elem.style && fx.elem.style[ fx.prop ] != null ) { - fx.elem.style[ fx.prop ] = fx.now + fx.unit; - } else { - fx.elem[ fx.prop ] = fx.now; - } - } - } -}); - -// Ensure props that can't be negative don't go there on undershoot easing -jQuery.each( fxAttrs.concat.apply( [], fxAttrs ), function( i, prop ) { - // exclude marginTop, marginLeft, marginBottom and marginRight from this list - if ( prop.indexOf( "margin" ) ) { - jQuery.fx.step[ prop ] = function( fx ) { - jQuery.style( fx.elem, prop, Math.max(0, fx.now) + fx.unit ); - }; - } -}); - -if ( jQuery.expr && jQuery.expr.filters ) { - jQuery.expr.filters.animated = function( elem ) { - return jQuery.grep(jQuery.timers, function( fn ) { - return elem === fn.elem; - }).length; - }; -} - -// Try to restore the default display value of an element -function defaultDisplay( nodeName ) { - - if ( !elemdisplay[ nodeName ] ) { - - var body = document.body, - elem = jQuery( "<" + nodeName + ">" ).appendTo( body ), - display = elem.css( "display" ); - elem.remove(); - - // If the simple way fails, - // get element's real default display by attaching it to a temp iframe - if ( display === "none" || display === "" ) { - // No iframe to use yet, so create it - if ( !iframe ) { - iframe = document.createElement( "iframe" ); - iframe.frameBorder = iframe.width = iframe.height = 0; - } - - body.appendChild( iframe ); - - // Create a cacheable copy of the iframe document on first call. - // IE and Opera will allow us to reuse the iframeDoc without re-writing the fake HTML - // document to it; WebKit & Firefox won't allow reusing the iframe document. - if ( !iframeDoc || !iframe.createElement ) { - iframeDoc = ( iframe.contentWindow || iframe.contentDocument ).document; - iframeDoc.write( ( jQuery.support.boxModel ? "<!doctype html>" : "" ) + "<html><body>" ); - iframeDoc.close(); - } - - elem = iframeDoc.createElement( nodeName ); - - iframeDoc.body.appendChild( elem ); - - display = jQuery.css( elem, "display" ); - body.removeChild( iframe ); - } - - // Store the correct default display - elemdisplay[ nodeName ] = display; - } - - return elemdisplay[ nodeName ]; -} - - - - -var getOffset, - rtable = /^t(?:able|d|h)$/i, - rroot = /^(?:body|html)$/i; - -if ( "getBoundingClientRect" in document.documentElement ) { - getOffset = function( elem, doc, docElem, box ) { - try { - box = elem.getBoundingClientRect(); - } catch(e) {} - - // Make sure we're not dealing with a disconnected DOM node - if ( !box || !jQuery.contains( docElem, elem ) ) { - return box ? { top: box.top, left: box.left } : { top: 0, left: 0 }; - } - - var body = doc.body, - win = getWindow( doc ), - clientTop = docElem.clientTop || body.clientTop || 0, - clientLeft = docElem.clientLeft || body.clientLeft || 0, - scrollTop = win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop, - scrollLeft = win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft, - top = box.top + scrollTop - clientTop, - left = box.left + scrollLeft - clientLeft; - - return { top: top, left: left }; - }; - -} else { - getOffset = function( elem, doc, docElem ) { - var computedStyle, - offsetParent = elem.offsetParent, - prevOffsetParent = elem, - body = doc.body, - defaultView = doc.defaultView, - prevComputedStyle = defaultView ? defaultView.getComputedStyle( elem, null ) : elem.currentStyle, - top = elem.offsetTop, - left = elem.offsetLeft; - - while ( (elem = elem.parentNode) && elem !== body && elem !== docElem ) { - if ( jQuery.support.fixedPosition && prevComputedStyle.position === "fixed" ) { - break; - } - - computedStyle = defaultView ? defaultView.getComputedStyle(elem, null) : elem.currentStyle; - top -= elem.scrollTop; - left -= elem.scrollLeft; - - if ( elem === offsetParent ) { - top += elem.offsetTop; - left += elem.offsetLeft; - - if ( jQuery.support.doesNotAddBorder && !(jQuery.support.doesAddBorderForTableAndCells && rtable.test(elem.nodeName)) ) { - top += parseFloat( computedStyle.borderTopWidth ) || 0; - left += parseFloat( computedStyle.borderLeftWidth ) || 0; - } - - prevOffsetParent = offsetParent; - offsetParent = elem.offsetParent; - } - - if ( jQuery.support.subtractsBorderForOverflowNotVisible && computedStyle.overflow !== "visible" ) { - top += parseFloat( computedStyle.borderTopWidth ) || 0; - left += parseFloat( computedStyle.borderLeftWidth ) || 0; - } - - prevComputedStyle = computedStyle; - } - - if ( prevComputedStyle.position === "relative" || prevComputedStyle.position === "static" ) { - top += body.offsetTop; - left += body.offsetLeft; - } - - if ( jQuery.support.fixedPosition && prevComputedStyle.position === "fixed" ) { - top += Math.max( docElem.scrollTop, body.scrollTop ); - left += Math.max( docElem.scrollLeft, body.scrollLeft ); - } - - return { top: top, left: left }; - }; -} - -jQuery.fn.offset = function( options ) { - if ( arguments.length ) { - return options === undefined ? - this : - this.each(function( i ) { - jQuery.offset.setOffset( this, options, i ); - }); - } - - var elem = this[0], - doc = elem && elem.ownerDocument; - - if ( !doc ) { - return null; - } - - if ( elem === doc.body ) { - return jQuery.offset.bodyOffset( elem ); - } - - return getOffset( elem, doc, doc.documentElement ); -}; - -jQuery.offset = { - - bodyOffset: function( body ) { - var top = body.offsetTop, - left = body.offsetLeft; - - if ( jQuery.support.doesNotIncludeMarginInBodyOffset ) { - top += parseFloat( jQuery.css(body, "marginTop") ) || 0; - left += parseFloat( jQuery.css(body, "marginLeft") ) || 0; - } - - return { top: top, left: left }; - }, - - setOffset: function( elem, options, i ) { - var position = jQuery.css( elem, "position" ); - - // set position first, in-case top/left are set even on static elem - if ( position === "static" ) { - elem.style.position = "relative"; - } - - var curElem = jQuery( elem ), - curOffset = curElem.offset(), - curCSSTop = jQuery.css( elem, "top" ), - curCSSLeft = jQuery.css( elem, "left" ), - calculatePosition = ( position === "absolute" || position === "fixed" ) && jQuery.inArray("auto", [curCSSTop, curCSSLeft]) > -1, - props = {}, curPosition = {}, curTop, curLeft; - - // need to be able to calculate position if either top or left is auto and position is either absolute or fixed - if ( calculatePosition ) { - curPosition = curElem.position(); - curTop = curPosition.top; - curLeft = curPosition.left; - } else { - curTop = parseFloat( curCSSTop ) || 0; - curLeft = parseFloat( curCSSLeft ) || 0; - } - - if ( jQuery.isFunction( options ) ) { - options = options.call( elem, i, curOffset ); - } - - if ( options.top != null ) { - props.top = ( options.top - curOffset.top ) + curTop; - } - if ( options.left != null ) { - props.left = ( options.left - curOffset.left ) + curLeft; - } - - if ( "using" in options ) { - options.using.call( elem, props ); - } else { - curElem.css( props ); - } - } -}; - - -jQuery.fn.extend({ - - position: function() { - if ( !this[0] ) { - return null; - } - - var elem = this[0], - - // Get *real* offsetParent - offsetParent = this.offsetParent(), - - // Get correct offsets - offset = this.offset(), - parentOffset = rroot.test(offsetParent[0].nodeName) ? { top: 0, left: 0 } : offsetParent.offset(); - - // Subtract element margins - // note: when an element has margin: auto the offsetLeft and marginLeft - // are the same in Safari causing offset.left to incorrectly be 0 - offset.top -= parseFloat( jQuery.css(elem, "marginTop") ) || 0; - offset.left -= parseFloat( jQuery.css(elem, "marginLeft") ) || 0; - - // Add offsetParent borders - parentOffset.top += parseFloat( jQuery.css(offsetParent[0], "borderTopWidth") ) || 0; - parentOffset.left += parseFloat( jQuery.css(offsetParent[0], "borderLeftWidth") ) || 0; - - // Subtract the two offsets - return { - top: offset.top - parentOffset.top, - left: offset.left - parentOffset.left - }; - }, - - offsetParent: function() { - return this.map(function() { - var offsetParent = this.offsetParent || document.body; - while ( offsetParent && (!rroot.test(offsetParent.nodeName) && jQuery.css(offsetParent, "position") === "static") ) { - offsetParent = offsetParent.offsetParent; - } - return offsetParent; - }); - } -}); - - -// Create scrollLeft and scrollTop methods -jQuery.each( {scrollLeft: "pageXOffset", scrollTop: "pageYOffset"}, function( method, prop ) { - var top = /Y/.test( prop ); - - jQuery.fn[ method ] = function( val ) { - return jQuery.access( this, function( elem, method, val ) { - var win = getWindow( elem ); - - if ( val === undefined ) { - return win ? (prop in win) ? win[ prop ] : - jQuery.support.boxModel && win.document.documentElement[ method ] || - win.document.body[ method ] : - elem[ method ]; - } - - if ( win ) { - win.scrollTo( - !top ? val : jQuery( win ).scrollLeft(), - top ? val : jQuery( win ).scrollTop() - ); - - } else { - elem[ method ] = val; - } - }, method, val, arguments.length, null ); - }; -}); - -function getWindow( elem ) { - return jQuery.isWindow( elem ) ? - elem : - elem.nodeType === 9 ? - elem.defaultView || elem.parentWindow : - false; -} - - - - -// Create width, height, innerHeight, innerWidth, outerHeight and outerWidth methods -jQuery.each( { Height: "height", Width: "width" }, function( name, type ) { - var clientProp = "client" + name, - scrollProp = "scroll" + name, - offsetProp = "offset" + name; - - // innerHeight and innerWidth - jQuery.fn[ "inner" + name ] = function() { - var elem = this[0]; - return elem ? - elem.style ? - parseFloat( jQuery.css( elem, type, "padding" ) ) : - this[ type ]() : - null; - }; - - // outerHeight and outerWidth - jQuery.fn[ "outer" + name ] = function( margin ) { - var elem = this[0]; - return elem ? - elem.style ? - parseFloat( jQuery.css( elem, type, margin ? "margin" : "border" ) ) : - this[ type ]() : - null; - }; - - jQuery.fn[ type ] = function( value ) { - return jQuery.access( this, function( elem, type, value ) { - var doc, docElemProp, orig, ret; - - if ( jQuery.isWindow( elem ) ) { - // 3rd condition allows Nokia support, as it supports the docElem prop but not CSS1Compat - doc = elem.document; - docElemProp = doc.documentElement[ clientProp ]; - return jQuery.support.boxModel && docElemProp || - doc.body && doc.body[ clientProp ] || docElemProp; - } - - // Get document width or height - if ( elem.nodeType === 9 ) { - // Either scroll[Width/Height] or offset[Width/Height], whichever is greater - doc = elem.documentElement; - - // when a window > document, IE6 reports a offset[Width/Height] > client[Width/Height] - // so we can't use max, as it'll choose the incorrect offset[Width/Height] - // instead we use the correct client[Width/Height] - // support:IE6 - if ( doc[ clientProp ] >= doc[ scrollProp ] ) { - return doc[ clientProp ]; - } - - return Math.max( - elem.body[ scrollProp ], doc[ scrollProp ], - elem.body[ offsetProp ], doc[ offsetProp ] - ); - } - - // Get width or height on the element - if ( value === undefined ) { - orig = jQuery.css( elem, type ); - ret = parseFloat( orig ); - return jQuery.isNumeric( ret ) ? ret : orig; - } - - // Set the width or height on the element - jQuery( elem ).css( type, value ); - }, type, value, arguments.length, null ); - }; -}); - - - - -// Expose jQuery to the global object -window.jQuery = window.$ = jQuery; - -// Expose jQuery as an AMD module, but only for AMD loaders that -// understand the issues with loading multiple versions of jQuery -// in a page that all might call define(). The loader will indicate -// they have special allowances for multiple jQuery versions by -// specifying define.amd.jQuery = true. Register as a named module, -// since jQuery can be concatenated with other files that may use define, -// but not use a proper concatenation script that understands anonymous -// AMD modules. A named AMD is safest and most robust way to register. -// Lowercase jquery is used because AMD module names are derived from -// file names, and jQuery is normally delivered in a lowercase file name. -// Do this after creating the global so that if an AMD module wants to call -// noConflict to hide this version of jQuery, it will work. -if ( typeof define === "function" && define.amd && define.amd.jQuery ) { - define( "jquery", [], function () { return jQuery; } ); -} - - - -})( window ); diff --git a/docs/user/html/pymoose/_static/minus.png b/docs/user/html/pymoose/_static/minus.png deleted file mode 100644 index da1c5620d10c047525a467a425abe9ff5269cfc2..0000000000000000000000000000000000000000 Binary files a/docs/user/html/pymoose/_static/minus.png and /dev/null differ diff --git a/docs/user/html/pymoose/_static/plus.png b/docs/user/html/pymoose/_static/plus.png deleted file mode 100644 index b3cb37425ea68b39ffa7b2e5fb69161275a87541..0000000000000000000000000000000000000000 Binary files a/docs/user/html/pymoose/_static/plus.png and /dev/null differ diff --git a/docs/user/html/pymoose/_static/sidebar.js b/docs/user/html/pymoose/_static/sidebar.js deleted file mode 100644 index a45e1926addf0b96c1cf0180287763bbece82960..0000000000000000000000000000000000000000 --- a/docs/user/html/pymoose/_static/sidebar.js +++ /dev/null @@ -1,151 +0,0 @@ -/* - * sidebar.js - * ~~~~~~~~~~ - * - * This script makes the Sphinx sidebar collapsible. - * - * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds - * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton - * used to collapse and expand the sidebar. - * - * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden - * and the width of the sidebar and the margin-left of the document - * are decreased. When the sidebar is expanded the opposite happens. - * This script saves a per-browser/per-session cookie used to - * remember the position of the sidebar among the pages. - * Once the browser is closed the cookie is deleted and the position - * reset to the default (expanded). - * - * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -$(function() { - // global elements used by the functions. - // the 'sidebarbutton' element is defined as global after its - // creation, in the add_sidebar_button function - var bodywrapper = $('.bodywrapper'); - var sidebar = $('.sphinxsidebar'); - var sidebarwrapper = $('.sphinxsidebarwrapper'); - - // for some reason, the document has no sidebar; do not run into errors - if (!sidebar.length) return; - - // original margin-left of the bodywrapper and width of the sidebar - // with the sidebar expanded - var bw_margin_expanded = bodywrapper.css('margin-left'); - var ssb_width_expanded = sidebar.width(); - - // margin-left of the bodywrapper and width of the sidebar - // with the sidebar collapsed - var bw_margin_collapsed = '.8em'; - var ssb_width_collapsed = '.8em'; - - // colors used by the current theme - var dark_color = $('.related').css('background-color'); - var light_color = $('.document').css('background-color'); - - function sidebar_is_collapsed() { - return sidebarwrapper.is(':not(:visible)'); - } - - function toggle_sidebar() { - if (sidebar_is_collapsed()) - expand_sidebar(); - else - collapse_sidebar(); - } - - function collapse_sidebar() { - sidebarwrapper.hide(); - sidebar.css('width', ssb_width_collapsed); - bodywrapper.css('margin-left', bw_margin_collapsed); - sidebarbutton.css({ - 'margin-left': '0', - 'height': bodywrapper.height() - }); - sidebarbutton.find('span').text('»'); - sidebarbutton.attr('title', _('Expand sidebar')); - document.cookie = 'sidebar=collapsed'; - } - - function expand_sidebar() { - bodywrapper.css('margin-left', bw_margin_expanded); - sidebar.css('width', ssb_width_expanded); - sidebarwrapper.show(); - sidebarbutton.css({ - 'margin-left': ssb_width_expanded-12, - 'height': bodywrapper.height() - }); - sidebarbutton.find('span').text('«'); - sidebarbutton.attr('title', _('Collapse sidebar')); - document.cookie = 'sidebar=expanded'; - } - - function add_sidebar_button() { - sidebarwrapper.css({ - 'float': 'left', - 'margin-right': '0', - 'width': ssb_width_expanded - 28 - }); - // create the button - sidebar.append( - '<div id="sidebarbutton"><span>«</span></div>' - ); - var sidebarbutton = $('#sidebarbutton'); - light_color = sidebarbutton.css('background-color'); - // find the height of the viewport to center the '<<' in the page - var viewport_height; - if (window.innerHeight) - viewport_height = window.innerHeight; - else - viewport_height = $(window).height(); - sidebarbutton.find('span').css({ - 'display': 'block', - 'margin-top': (viewport_height - sidebar.position().top - 20) / 2 - }); - - sidebarbutton.click(toggle_sidebar); - sidebarbutton.attr('title', _('Collapse sidebar')); - sidebarbutton.css({ - 'color': '#FFFFFF', - 'border-left': '1px solid ' + dark_color, - 'font-size': '1.2em', - 'cursor': 'pointer', - 'height': bodywrapper.height(), - 'padding-top': '1px', - 'margin-left': ssb_width_expanded - 12 - }); - - sidebarbutton.hover( - function () { - $(this).css('background-color', dark_color); - }, - function () { - $(this).css('background-color', light_color); - } - ); - } - - function set_position_from_cookie() { - if (!document.cookie) - return; - var items = document.cookie.split(';'); - for(var k=0; k<items.length; k++) { - var key_val = items[k].split('='); - var key = key_val[0]; - if (key == 'sidebar') { - var value = key_val[1]; - if ((value == 'collapsed') && (!sidebar_is_collapsed())) - collapse_sidebar(); - else if ((value == 'expanded') && (sidebar_is_collapsed())) - expand_sidebar(); - } - } - } - - add_sidebar_button(); - var sidebarbutton = $('#sidebarbutton'); - set_position_from_cookie(); -}); diff --git a/docs/user/html/pymoose/_static/up-pressed.png b/docs/user/html/pymoose/_static/up-pressed.png deleted file mode 100644 index 8bd587afee2fe38989383ff82010147ea56b93dd..0000000000000000000000000000000000000000 Binary files a/docs/user/html/pymoose/_static/up-pressed.png and /dev/null differ diff --git a/docs/user/html/pymoose/_static/up.png b/docs/user/html/pymoose/_static/up.png deleted file mode 100644 index b94625680b4a4b9647c3a6f3f283776930696aa9..0000000000000000000000000000000000000000 Binary files a/docs/user/html/pymoose/_static/up.png and /dev/null differ diff --git a/docs/user/html/pymoose/genindex.html b/docs/user/html/pymoose/genindex.html deleted file mode 100644 index 6a097a5d93b81d78809177571f3b7329e5845dbe..0000000000000000000000000000000000000000 --- a/docs/user/html/pymoose/genindex.html +++ /dev/null @@ -1,8413 +0,0 @@ - - - - -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" - "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - - <title>Index — MOOSE 3.0 documentation</title> - - <link rel="stylesheet" href="_static/default.css" type="text/css" /> - <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> - - <script type="text/javascript"> - var DOCUMENTATION_OPTIONS = { - URL_ROOT: '', - VERSION: '3.0', - COLLAPSE_INDEX: false, - FILE_SUFFIX: '.html', - HAS_SOURCE: true - }; - </script> - <script type="text/javascript" src="_static/jquery.js"></script> - <script type="text/javascript" src="_static/underscore.js"></script> - <script type="text/javascript" src="_static/doctools.js"></script> - <link rel="top" title="MOOSE 3.0 documentation" href="index.html" /> - </head> - <body> - <div class="related"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="#" title="General Index" - accesskey="I">index</a></li> - <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> - - <li><a href="index.html">MOOSE 3.0 documentation</a> »</li> - - </ul> - </div> - - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body"> - - -<h1 id="index">Index</h1> - -<div class="genindex-jumpbox"> - <a href="#A"><strong>A</strong></a> - | <a href="#B"><strong>B</strong></a> - | <a href="#C"><strong>C</strong></a> - | <a href="#D"><strong>D</strong></a> - | <a href="#E"><strong>E</strong></a> - | <a href="#F"><strong>F</strong></a> - | <a href="#G"><strong>G</strong></a> - | <a href="#H"><strong>H</strong></a> - | <a href="#I"><strong>I</strong></a> - | <a href="#K"><strong>K</strong></a> - | <a href="#L"><strong>L</strong></a> - | <a href="#M"><strong>M</strong></a> - | <a href="#N"><strong>N</strong></a> - | <a href="#O"><strong>O</strong></a> - | <a href="#P"><strong>P</strong></a> - | <a href="#Q"><strong>Q</strong></a> - | <a href="#R"><strong>R</strong></a> - | <a href="#S"><strong>S</strong></a> - | <a href="#T"><strong>T</strong></a> - | <a href="#U"><strong>U</strong></a> - | <a href="#V"><strong>V</strong></a> - | <a href="#W"><strong>W</strong></a> - | <a href="#X"><strong>X</strong></a> - | <a href="#Y"><strong>Y</strong></a> - | <a href="#Z"><strong>Z</strong></a> - -</div> -<h2 id="A">A</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#HHGate.A">A (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.A">[1]</a>, <a href="moose_classes.html#HHGate.A">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.A">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.A">[1]</a>, <a href="moose_classes.html#HHGate2D.A">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.a">a (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.a">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.a">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.abs_refract">abs_refract (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.abs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.abs_refract">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.absoluteAccuracy">absoluteAccuracy (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.absoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.absoluteAccuracy">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.accommodating">accommodating (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.accommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.accommodating">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.activation">activation() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.activation">[1]</a>, <a href="moose_classes.html#SynChan.activation">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor">Adaptor (built-in class)</a>, <a href="moose_builtins.html#Adaptor">[1]</a>, <a href="moose_classes.html#Adaptor">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell.addMsg">addMsg() (Shell method)</a>, <a href="moose_builtins.html#Shell.addMsg">[1]</a>, <a href="moose_classes.html#Shell.addMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Synapse.addSpike">addSpike() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.addSpike">[1]</a>, <a href="moose_classes.html#Synapse.addSpike">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.aDest">aDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.aDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.aDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.adjacent">adjacent (Msg attribute)</a>, <a href="moose_builtins.html#Msg.adjacent">[1]</a>, <a href="moose_classes.html#Msg.adjacent">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.alpha">alpha (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.alpha">[1]</a>, <a href="moose_classes.html#HHGate.alpha">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.alpha">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.alpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.alpha">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.alphaParms">alphaParms (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.alphaParms">[1]</a>, <a href="moose_classes.html#HHGate.alphaParms">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CubeMesh.alwaysDiffuse">alwaysDiffuse (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.alwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.alwaysDiffuse">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator">Annotator (built-in class)</a>, <a href="moose_builtins.html#Annotator">[1]</a>, <a href="moose_classes.html#Annotator">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.anyValue">anyValue (Arith attribute)</a>, <a href="moose_builtins.html#Arith.anyValue">[1]</a>, <a href="moose_classes.html#Arith.anyValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.arg1">arg1() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg1">[1]</a>, <a href="moose_classes.html#Arith.arg1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.arg1">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg1">[1]</a>, <a href="moose_classes.html#MathFunc.arg1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Arith.arg1Value">arg1Value (Arith attribute)</a>, <a href="moose_builtins.html#Arith.arg1Value">[1]</a>, <a href="moose_classes.html#Arith.arg1Value">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.arg1x2">arg1x2() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg1x2">[1]</a>, <a href="moose_classes.html#Arith.arg1x2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.arg2">arg2() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg2">[1]</a>, <a href="moose_classes.html#Arith.arg2">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.arg2">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg2">[1]</a>, <a href="moose_classes.html#MathFunc.arg2">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Arith.arg3">arg3() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg3">[1]</a>, <a href="moose_classes.html#Arith.arg3">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.arg3">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg3">[1]</a>, <a href="moose_classes.html#MathFunc.arg3">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MathFunc.arg4">arg4() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg4">[1]</a>, <a href="moose_classes.html#MathFunc.arg4">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith">Arith (built-in class)</a>, <a href="moose_builtins.html#Arith">[1]</a>, <a href="moose_classes.html#Arith">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.axial">axial (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.axial">[1]</a>, <a href="moose_classes.html#CompartmentBase.axial">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.axialOut">axialOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.axialOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.axialOut">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="B">B</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CaConc.B">B (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.B">[1]</a>, <a href="moose_classes.html#CaConc.B">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate.B">(HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.B">[1]</a>, <a href="moose_classes.html#HHGate.B">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.B">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.B">[1]</a>, <a href="moose_classes.html#HHGate2D.B">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.b">b (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.b">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.b">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.B">B (ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.B">[1]</a>, <a href="moose_classes.html#ZombieCaConc.B">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.badStoichiometry">badStoichiometry (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.badStoichiometry">[1]</a>, <a href="moose_classes.html#SteadyState.badStoichiometry">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.basal">basal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.basal">[1]</a>, <a href="moose_classes.html#CaConc.basal">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.basal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.basal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.basal">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Cinfo.baseClass">baseClass (Cinfo attribute)</a>, <a href="moose_builtins.html#Cinfo.baseClass">[1]</a>, <a href="moose_classes.html#Cinfo.baseClass">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.baseLevel">baseLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.baseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.baseLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.bDest">bDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.bDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.bDest">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#HHGate.beta">beta (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.beta">[1]</a>, <a href="moose_classes.html#HHGate.beta">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.beta">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.beta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.beta">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#DifShell.buffer">buffer (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.buffer">[1]</a>, <a href="moose_classes.html#DifShell.buffer">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.bufferSize">bufferSize (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.bufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.bufferSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.bufferTime">bufferTime (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.bufferTime">[1]</a>, <a href="moose_classes.html#IntFire.bufferTime">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.bufferTime">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.bufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.bufferTime">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#BufPool">BufPool (built-in class)</a>, <a href="moose_builtins.html#BufPool">[1]</a>, <a href="moose_classes.html#BufPool">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.buildDefaultMesh">buildDefaultMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.buildDefaultMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.buildDefaultMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.buildNeuroMeshJunctions">buildNeuroMeshJunctions() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.buildNeuroMeshJunctions">[1]</a>, <a href="moose_classes.html#Dsolve.buildNeuroMeshJunctions">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="C">C</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#C">C</a>, <a href="moose_builtins.html#C">[1]</a>, <a href="moose_classes.html#C">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.c">c (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.c">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.c">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.C">C (RC attribute)</a>, <a href="moose_builtins.html#RC.C">[1]</a>, <a href="moose_classes.html#RC.C">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.Ca">Ca (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.Ca">[1]</a>, <a href="moose_classes.html#CaConc.Ca">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.Ca">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.Ca">[1]</a>, <a href="moose_classes.html#ZombieCaConc.Ca">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.Ca_base">Ca_base (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.Ca_base">[1]</a>, <a href="moose_classes.html#CaConc.Ca_base">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.Ca_base">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.Ca_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.Ca_base">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.caAdvance">caAdvance (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caAdvance">[1]</a>, <a href="moose_classes.html#HSolve.caAdvance">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.CaBasal">CaBasal (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.CaBasal">[1]</a>, <a href="moose_classes.html#CaConc.CaBasal">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.CaBasal">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.CaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.CaBasal">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.cable">cable() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.cable">[1]</a>, <a href="moose_classes.html#CompartmentBase.cable">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc">CaConc (built-in class)</a>, <a href="moose_builtins.html#CaConc">[1]</a>, <a href="moose_classes.html#CaConc">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.caDiv">caDiv (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caDiv">[1]</a>, <a href="moose_classes.html#HSolve.caDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.caMax">caMax (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caMax">[1]</a>, <a href="moose_classes.html#HSolve.caMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.caMin">caMin (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caMin">[1]</a>, <a href="moose_classes.html#HSolve.caMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.cDest">cDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.cDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.cDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.ceiling">ceiling (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.ceiling">[1]</a>, <a href="moose_classes.html#CaConc.ceiling">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.ceiling">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.ceiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.ceiling">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.cell">cell (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.cell">[1]</a>, <a href="moose_classes.html#NeuroMesh.cell">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.cellPortion">cellPortion() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.cellPortion">[1]</a>, <a href="moose_classes.html#NeuroMesh.cellPortion">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ceq">Ceq</a>, <a href="moose_builtins.html#Ceq">[1]</a>, <a href="moose_classes.html#Ceq">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase">ChanBase (built-in class)</a>, <a href="moose_builtins.html#ChanBase">[1]</a>, <a href="moose_classes.html#ChanBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.channel">channel (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.channel">[1]</a>, <a href="moose_classes.html#ChanBase.channel">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.channel">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.channel">[1]</a>, <a href="moose_classes.html#CompartmentBase.channel">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.channel">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.channel">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.channel">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.channel">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.channel">[1]</a>, <a href="moose_classes.html#MarkovRateTable.channel">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.channel">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.channel">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.channel">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.channel">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.channel">[1]</a>, <a href="moose_classes.html#SynChanBase.channel">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#GapJunction.channel1">channel1 (GapJunction attribute)</a>, <a href="moose_builtins.html#GapJunction.channel1">[1]</a>, <a href="moose_classes.html#GapJunction.channel1">[2]</a> - </dt> - - - <dt><a href="tmp.html#channel1Out">channel1Out</a>, <a href="moose_builtins.html#channel1Out">[1]</a>, <a href="moose_classes.html#channel1Out">[2]</a> - </dt> - - - <dt><a href="tmp.html#channel2">channel2</a>, <a href="moose_builtins.html#channel2">[1]</a>, <a href="moose_classes.html#channel2">[2]</a> - </dt> - - - <dt><a href="tmp.html#channel2Out">channel2Out</a>, <a href="moose_builtins.html#channel2Out">[1]</a>, <a href="moose_classes.html#channel2Out">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.channelOut">channelOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.channelOut">[1]</a>, <a href="moose_classes.html#ChanBase.channelOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.channelOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.channelOut">[1]</a>, <a href="moose_classes.html#SynChanBase.channelOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt">ChemCompt (built-in class)</a>, <a href="moose_builtins.html#ChemCompt">[1]</a>, <a href="moose_classes.html#ChemCompt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.childOut">childOut (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.childOut">[1]</a>, <a href="moose_classes.html#Neutral.childOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.children">children (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.children">[1]</a>, <a href="moose_classes.html#Neutral.children">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.ci">ci() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.ci">[1]</a>, <a href="moose_classes.html#Nernst.ci">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.Cin">Cin (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Cin">[1]</a>, <a href="moose_classes.html#Nernst.Cin">[2]</a> - </dt> - - - <dt><a href="tmp.html#Cinfo">Cinfo (built-in class)</a>, <a href="moose_builtins.html#Cinfo">[1]</a>, <a href="moose_classes.html#Cinfo">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.className">className (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.className">[1]</a>, <a href="moose_classes.html#Neutral.className">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.clear">clear() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.clear">[1]</a>, <a href="moose_classes.html#SparseMsg.clear">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.clearVec">clearVec() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.clearVec">[1]</a>, <a href="moose_classes.html#TableBase.clearVec">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock">Clock (built-in class)</a>, <a href="moose_builtins.html#Clock">[1]</a>, <a href="moose_classes.html#Clock">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.clockControl">clockControl (Clock attribute)</a>, <a href="moose_builtins.html#Clock.clockControl">[1]</a>, <a href="moose_classes.html#Clock.clockControl">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.Cm">Cm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Cm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Cm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.CMg">CMg (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.CMg">[1]</a>, <a href="moose_classes.html#MgBlock.CMg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.co">co() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.co">[1]</a>, <a href="moose_classes.html#Nernst.co">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Annotator.color">color (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.color">[1]</a>, <a href="moose_classes.html#Annotator.color">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.columnIndex">columnIndex (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.columnIndex">[1]</a>, <a href="moose_classes.html#Stoich.columnIndex">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.command">command (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.command">[1]</a>, <a href="moose_classes.html#PIDController.command">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.command">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.command">[1]</a>, <a href="moose_classes.html#VClamp.command">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.commandIn">commandIn() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.commandIn">[1]</a>, <a href="moose_classes.html#PIDController.commandIn">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.commandIn">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.commandIn">[1]</a>, <a href="moose_classes.html#VClamp.commandIn">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#TableBase.compareVec">compareVec() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.compareVec">[1]</a>, <a href="moose_classes.html#TableBase.compareVec">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.compareXplot">compareXplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.compareXplot">[1]</a>, <a href="moose_classes.html#TableBase.compareXplot">[2]</a> - </dt> - - - <dt><a href="tmp.html#Compartment">Compartment (built-in class)</a>, <a href="moose_builtins.html#Compartment">[1]</a>, <a href="moose_classes.html#Compartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.compartment">compartment (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.compartment">[1]</a>, <a href="moose_classes.html#Dsolve.compartment">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.compartment">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.compartment">[1]</a>, <a href="moose_classes.html#Ksolve.compartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.compartment">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.compartment">[1]</a>, <a href="moose_classes.html#Stoich.compartment">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase">CompartmentBase (built-in class)</a>, <a href="moose_builtins.html#CompartmentBase">[1]</a>, <a href="moose_classes.html#CompartmentBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.conc">conc (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.conc">[1]</a>, <a href="moose_classes.html#PoolBase.conc">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.concen">concen() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.concen">[1]</a>, <a href="moose_classes.html#HHChannel.concen">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.concen">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.concen">[1]</a>, <a href="moose_classes.html#HHChannel2D.concen">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.concen">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.concen">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.concen">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel2D.concen2">concen2() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.concen2">[1]</a>, <a href="moose_classes.html#HHChannel2D.concen2">[2]</a> - </dt> - - - <dt><a href="tmp.html#concentrationOut">concentrationOut</a>, <a href="moose_builtins.html#concentrationOut">[1]</a>, <a href="moose_classes.html#concentrationOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.concInit">concInit (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.concInit">[1]</a>, <a href="moose_classes.html#PoolBase.concInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.concK1">concK1 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.concK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.concK1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.concOut">concOut (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.concOut">[1]</a>, <a href="moose_classes.html#CaConc.concOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.concOut">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.concOut">[1]</a>, <a href="moose_classes.html#ZombieCaConc.concOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.convergenceCriterion">convergenceCriterion (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.convergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.convergenceCriterion">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.Coordinates">Coordinates (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.Coordinates">[1]</a>, <a href="moose_classes.html#MeshEntry.Coordinates">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.coords">coords (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.coords">[1]</a>, <a href="moose_classes.html#CubeMesh.coords">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.coords">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.coords">[1]</a>, <a href="moose_classes.html#CylMesh.coords">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Shell.copy">copy() (Shell method)</a>, <a href="moose_builtins.html#Shell.copy">[1]</a>, <a href="moose_classes.html#Shell.copy">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.count">count (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.count">[1]</a>, <a href="moose_classes.html#PulseGen.count">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.Cout">Cout (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Cout">[1]</a>, <a href="moose_classes.html#Nernst.Cout">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.cplx">cplx (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.cplx">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplx">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.cplxDest">cplxDest() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.cplxDest">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplxDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase">CplxEnzBase (built-in class)</a>, <a href="moose_builtins.html#CplxEnzBase">[1]</a>, <a href="moose_classes.html#CplxEnzBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.cplxOut">cplxOut (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.cplxOut">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplxOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell.create">create() (Shell method)</a>, <a href="moose_builtins.html#Shell.create">[1]</a>, <a href="moose_classes.html#Shell.create">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.createGate">createGate() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.createGate">[1]</a>, <a href="moose_classes.html#HHChannel.createGate">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieHHChannel.createGate">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.createGate">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.createGate">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh">CubeMesh (built-in class)</a>, <a href="moose_builtins.html#CubeMesh">[1]</a>, <a href="moose_classes.html#CubeMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.current">current (VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.current">[1]</a>, <a href="moose_classes.html#VClamp.current">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.current">current() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.current">[1]</a>, <a href="moose_classes.html#CaConc.current">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.current">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.current">[1]</a>, <a href="moose_classes.html#ZombieCaConc.current">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.currentFraction">currentFraction() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.currentFraction">[1]</a>, <a href="moose_classes.html#CaConc.currentFraction">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.currentFraction">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.currentFraction">[1]</a>, <a href="moose_classes.html#ZombieCaConc.currentFraction">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#VClamp.currentOut">currentOut (VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.currentOut">[1]</a>, <a href="moose_classes.html#VClamp.currentOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.currentStep">currentStep (Clock attribute)</a>, <a href="moose_builtins.html#Clock.currentStep">[1]</a>, <a href="moose_classes.html#Clock.currentStep">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.currentTime">currentTime (Clock attribute)</a>, <a href="moose_builtins.html#Clock.currentTime">[1]</a>, <a href="moose_classes.html#Clock.currentTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#cylinder">cylinder</a>, <a href="moose_builtins.html#cylinder">[1]</a>, <a href="moose_classes.html#cylinder">[2]</a> - </dt> - - - <dt><a href="tmp.html#cylinderOut">cylinderOut</a>, <a href="moose_builtins.html#cylinderOut">[1]</a>, <a href="moose_classes.html#cylinderOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh">CylMesh (built-in class)</a>, <a href="moose_builtins.html#CylMesh">[1]</a>, <a href="moose_classes.html#CylMesh">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="D">D</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#D">D</a>, <a href="moose_builtins.html#D">[1]</a>, <a href="moose_classes.html#D">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.d">d (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.d">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.d">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.dDest">dDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.dDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.dDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.decrease">decrease() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.decrease">[1]</a>, <a href="moose_classes.html#CaConc.decrease">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.decrease">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.decrease">[1]</a>, <a href="moose_classes.html#ZombieCaConc.decrease">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Pool.decrement">decrement() (Pool method)</a>, <a href="moose_builtins.html#Pool.decrement">[1]</a>, <a href="moose_classes.html#Pool.decrement">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.delay">delay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.delay">[1]</a>, <a href="moose_classes.html#PulseGen.delay">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Synapse.delay">(Synapse attribute)</a>, <a href="moose_builtins.html#Synapse.delay">[1]</a>, <a href="moose_classes.html#Synapse.delay">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.delayIn">delayIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.delayIn">[1]</a>, <a href="moose_classes.html#PulseGen.delayIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell.delete">delete() (Shell method)</a>, <a href="moose_builtins.html#Shell.delete">[1]</a>, <a href="moose_classes.html#Shell.delete">[2]</a> - </dt> - - - <dt><a href="tmp.html#derivative">derivative</a>, <a href="tmp.html#derivative">[1]</a>, <a href="moose_builtins.html#derivative">[2]</a>, <a href="moose_builtins.html#derivative">[3]</a>, <a href="moose_classes.html#derivative">[4]</a>, <a href="moose_classes.html#derivative">[5]</a> - </dt> - - - <dt><a href="tmp.html#derivativeOut">derivativeOut</a>, <a href="moose_builtins.html#derivativeOut">[1]</a>, <a href="moose_classes.html#derivativeOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.dest">dest (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.dest">[1]</a>, <a href="moose_classes.html#Finfo.dest">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.destFields">destFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.destFields">[1]</a>, <a href="moose_classes.html#Neutral.destFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.destFieldsOnE1">destFieldsOnE1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.destFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.destFieldsOnE1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.destFieldsOnE2">destFieldsOnE2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.destFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.destFieldsOnE2">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiagonalMsg">DiagonalMsg (built-in class)</a>, <a href="moose_builtins.html#DiagonalMsg">[1]</a>, <a href="moose_classes.html#DiagonalMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#diameter">diameter</a>, <a href="moose_builtins.html#diameter">[1]</a>, <a href="moose_classes.html#diameter">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.diameter">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.diameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.diameter">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#DiffAmp">DiffAmp (built-in class)</a>, <a href="moose_builtins.html#DiffAmp">[1]</a>, <a href="moose_classes.html#DiffAmp">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.diffConst">diffConst (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.diffConst">[1]</a>, <a href="moose_classes.html#PoolBase.diffConst">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CylMesh.diffLength">diffLength (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.diffLength">[1]</a>, <a href="moose_classes.html#CylMesh.diffLength">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#NeuroMesh.diffLength">(NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.diffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.diffLength">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MeshEntry.DiffusionArea">DiffusionArea (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.DiffusionArea">[1]</a>, <a href="moose_classes.html#MeshEntry.DiffusionArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.DiffusionScaling">DiffusionScaling (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.DiffusionScaling">[1]</a>, <a href="moose_classes.html#MeshEntry.DiffusionScaling">[2]</a> - </dt> - - - <dt><a href="tmp.html#DifShell">DifShell (built-in class)</a>, <a href="moose_builtins.html#DifShell">[1]</a>, <a href="moose_classes.html#DifShell">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.dimensions">dimensions (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.dimensions">[1]</a>, <a href="moose_classes.html#MeshEntry.dimensions">[2]</a> - </dt> - - - <dt><a href="tmp.html#distal">distal</a>, <a href="moose_builtins.html#distal">[1]</a>, <a href="moose_classes.html#distal">[2]</a> - </dt> - - - <dt><a href="tmp.html#distalOut">distalOut</a>, <a href="tmp.html#distalOut">[1]</a>, <a href="tmp.html#distalOut">[2]</a>, <a href="moose_builtins.html#distalOut">[3]</a>, <a href="moose_builtins.html#distalOut">[4]</a>, <a href="moose_builtins.html#distalOut">[5]</a>, <a href="moose_classes.html#distalOut">[6]</a>, <a href="moose_classes.html#distalOut">[7]</a>, <a href="moose_classes.html#distalOut">[8]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.divs">divs (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.divs">[1]</a>, <a href="moose_classes.html#HHGate.divs">[2]</a> - </dt> - - - <dt><a href="tmp.html#Cinfo.docs">docs (Cinfo attribute)</a>, <a href="moose_builtins.html#Cinfo.docs">[1]</a>, <a href="moose_classes.html#Cinfo.docs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Finfo.docs">(Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.docs">[1]</a>, <a href="moose_classes.html#Finfo.docs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#StimulusTable.doLoop">doLoop (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.doLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.doLoop">[2]</a> - </dt> - - - <dt><a href="tmp.html#Double">Double (built-in class)</a>, <a href="moose_builtins.html#Double">[1]</a>, <a href="moose_classes.html#Double">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve">Dsolve (built-in class)</a>, <a href="moose_builtins.html#Dsolve">[1]</a>, <a href="moose_classes.html#Dsolve">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.dsolve">dsolve (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.dsolve">[1]</a>, <a href="moose_classes.html#Ksolve.dsolve">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.dsolve">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.dsolve">[1]</a>, <a href="moose_classes.html#Stoich.dsolve">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.dt">dt (Clock attribute)</a>, <a href="moose_builtins.html#Clock.dt">[1]</a>, <a href="moose_classes.html#Clock.dt">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HSolve.dt">(HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.dt">[1]</a>, <a href="moose_classes.html#HSolve.dt">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.dts">dts (Clock attribute)</a>, <a href="moose_builtins.html#Clock.dts">[1]</a>, <a href="moose_classes.html#Clock.dts">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.dx">dx (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dx">[1]</a>, <a href="moose_classes.html#CubeMesh.dx">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.dx">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.dx">[1]</a>, <a href="moose_classes.html#Interpol2D.dx">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.dy">dy (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dy">[1]</a>, <a href="moose_classes.html#CubeMesh.dy">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.dy">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.dy">[1]</a>, <a href="moose_classes.html#Interpol2D.dy">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.dz">dz (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dz">[1]</a>, <a href="moose_classes.html#CubeMesh.dz">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="E">E</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Nernst.E">E (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.E">[1]</a>, <a href="moose_classes.html#Nernst.E">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.e1">e1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.e1">[1]</a>, <a href="moose_classes.html#Msg.e1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.e2">e2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.e2">[1]</a>, <a href="moose_classes.html#Msg.e2">[2]</a> - </dt> - - - <dt><a href="tmp.html#e_previous">e_previous</a>, <a href="moose_builtins.html#e_previous">[1]</a>, <a href="moose_classes.html#e_previous">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.edgeTriggered">edgeTriggered (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.edgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.edgeTriggered">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.eigenvalues">eigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.eigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.eigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.Ek">Ek (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Ek">[1]</a>, <a href="moose_classes.html#ChanBase.Ek">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.Ek">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Ek">[1]</a>, <a href="moose_classes.html#SynChanBase.Ek">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Ek">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ek">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ek">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.Em">Em (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Em">[1]</a>, <a href="moose_classes.html#CompartmentBase.Em">[2]</a> - </dt> - - - <dt><a href="tmp.html#Enz">Enz (built-in class)</a>, <a href="moose_builtins.html#Enz">[1]</a>, <a href="moose_classes.html#Enz">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.enz">enz (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.enz">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enz">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase">EnzBase (built-in class)</a>, <a href="moose_builtins.html#EnzBase">[1]</a>, <a href="moose_classes.html#EnzBase">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CplxEnzBase.enzDest">enzDest() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.enzDest">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enzDest">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#EnzBase.enzDest">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.enzDest">[1]</a>, <a href="moose_classes.html#EnzBase.enzDest">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CplxEnzBase.enzOut">enzOut (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.enzOut">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enzOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.Eout">Eout (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Eout">[1]</a>, <a href="moose_classes.html#Nernst.Eout">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.epsAbs">epsAbs (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.epsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.epsAbs">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.epsRel">epsRel (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.epsRel">[1]</a>, <a href="moose_classes.html#Ksolve.epsRel">[2]</a> - </dt> - - - <dt><a href="tmp.html#eqTauPump">eqTauPump()</a>, <a href="moose_builtins.html#eqTauPump">[1]</a>, <a href="moose_classes.html#eqTauPump">[2]</a> - </dt> - - - <dt><a href="tmp.html#error">error</a>, <a href="moose_builtins.html#error">[1]</a>, <a href="moose_classes.html#error">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.estimatedDt">estimatedDt (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.estimatedDt">[1]</a>, <a href="moose_classes.html#Stoich.estimatedDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.eventOut">eventOut (TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.eventOut">[1]</a>, <a href="moose_classes.html#TimeTable.eventOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#expr">expr</a>, <a href="moose_builtins.html#expr">[1]</a>, <a href="moose_classes.html#expr">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="F">F</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Finfo.fieldName">fieldName (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.fieldName">[1]</a>, <a href="moose_classes.html#Finfo.fieldName">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.filename">filename (TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.filename">[1]</a>, <a href="moose_classes.html#TimeTable.filename">[2]</a> - </dt> - - - <dt><a href="tmp.html#fInflux">fInflux()</a>, <a href="moose_builtins.html#fInflux">[1]</a>, <a href="moose_classes.html#fInflux">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo">Finfo (built-in class)</a>, <a href="moose_builtins.html#Finfo">[1]</a>, <a href="moose_classes.html#Finfo">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.finished">finished (Clock attribute)</a>, <a href="moose_builtins.html#Clock.finished">[1]</a>, <a href="moose_classes.html#Clock.finished">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.firstDelay">firstDelay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.firstDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.firstLevel">firstLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.firstLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.firstWidth">firstWidth (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.firstWidth">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CaConc.floor">floor (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.floor">[1]</a>, <a href="moose_classes.html#CaConc.floor">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.floor">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.floor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.floor">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#fluxFromIn">fluxFromIn()</a>, <a href="moose_builtins.html#fluxFromIn">[1]</a>, <a href="moose_classes.html#fluxFromIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#fluxFromOut">fluxFromOut()</a>, <a href="moose_builtins.html#fluxFromOut">[1]</a>, <a href="moose_classes.html#fluxFromOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#fOutflux">fOutflux()</a>, <a href="moose_builtins.html#fOutflux">[1]</a>, <a href="moose_classes.html#fOutflux">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func">Func (built-in class)</a>, <a href="moose_builtins.html#Func">[1]</a>, <a href="moose_classes.html#Func">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase">FuncBase (built-in class)</a>, <a href="moose_builtins.html#FuncBase">[1]</a>, <a href="moose_classes.html#FuncBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncPool">FuncPool (built-in class)</a>, <a href="moose_builtins.html#FuncPool">[1]</a>, <a href="moose_classes.html#FuncPool">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.function">function (Arith attribute)</a>, <a href="moose_builtins.html#Arith.function">[1]</a>, <a href="moose_classes.html#Arith.function">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.function">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.function">[1]</a>, <a href="moose_classes.html#MathFunc.function">[2]</a> - </dt> - - </dl></dd> - </dl></td> -</tr></table> - -<h2 id="G">G</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#gain">gain</a>, <a href="moose_builtins.html#gain">[1]</a>, <a href="moose_classes.html#gain">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#DiffAmp.gain">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.gain">[1]</a>, <a href="moose_classes.html#DiffAmp.gain">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.gain">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.gain">[1]</a>, <a href="moose_classes.html#PIDController.gain">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.gainDest">gainDest() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.gainDest">[1]</a>, <a href="moose_classes.html#PIDController.gainDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.gainIn">gainIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.gainIn">[1]</a>, <a href="moose_classes.html#DiffAmp.gainIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.gamma">gamma (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.gamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.gamma">[2]</a> - </dt> - - - <dt><a href="tmp.html#GapJunction">GapJunction (built-in class)</a>, <a href="moose_builtins.html#GapJunction">[1]</a>, <a href="moose_classes.html#GapJunction">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.Gbar">Gbar (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Gbar">[1]</a>, <a href="moose_classes.html#ChanBase.Gbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.gbar">gbar (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.gbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.gbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.Gbar">Gbar (SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Gbar">[1]</a>, <a href="moose_classes.html#SynChanBase.Gbar">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieHHChannel.Gbar">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Gbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Gbar">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.geometryPolicy">geometryPolicy (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.geometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.geometryPolicy">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getA">getA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getA">[1]</a>, <a href="moose_classes.html#HHGate.getA">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.getA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getA">[1]</a>, <a href="moose_classes.html#HHGate2D.getA">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getA">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getA">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getA">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SpikeGen.getAbs_refract">getAbs_refract() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getAbs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.getAbs_refract">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.getAbsoluteAccuracy">getAbsoluteAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getAbsoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getAbsoluteAccuracy">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getAccommodating">getAccommodating() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getAccommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getAccommodating">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getAdjacent">getAdjacent() (Msg method)</a>, <a href="moose_builtins.html#Msg.getAdjacent">[1]</a>, <a href="moose_classes.html#Msg.getAdjacent">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getAlpha">getAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getAlpha">[1]</a>, <a href="moose_classes.html#HHGate.getAlpha">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getAlpha">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getAlpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getAlpha">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.getAlphaParms">getAlphaParms() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getAlphaParms">[1]</a>, <a href="moose_classes.html#HHGate.getAlphaParms">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getAlwaysDiffuse">getAlwaysDiffuse() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getAlwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.getAlwaysDiffuse">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.getAnyValue">getAnyValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.getAnyValue">[1]</a>, <a href="moose_classes.html#Arith.getAnyValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.getArg1Value">getArg1Value() (Arith method)</a>, <a href="moose_builtins.html#Arith.getArg1Value">[1]</a>, <a href="moose_classes.html#Arith.getArg1Value">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getB">getB() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getB">[1]</a>, <a href="moose_classes.html#CaConc.getB">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate.getB">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.getB">[1]</a>, <a href="moose_classes.html#HHGate.getB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getB">[1]</a>, <a href="moose_classes.html#HHGate2D.getB">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getB">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getB">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getB">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.getB">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getB">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getB">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.getBadStoichiometry">getBadStoichiometry() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getBadStoichiometry">[1]</a>, <a href="moose_classes.html#SteadyState.getBadStoichiometry">[2]</a> - </dt> - - - <dt><a href="tmp.html#Cinfo.getBaseClass">getBaseClass() (Cinfo method)</a>, <a href="moose_builtins.html#Cinfo.getBaseClass">[1]</a>, <a href="moose_classes.html#Cinfo.getBaseClass">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getBaseLevel">getBaseLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getBaseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getBaseLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getBeta">getBeta() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getBeta">[1]</a>, <a href="moose_classes.html#HHGate.getBeta">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getBeta">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getBeta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getBeta">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PostMaster.getBufferSize">getBufferSize() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getBufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.getBufferSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.getBufferTime">getBufferTime() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getBufferTime">[1]</a>, <a href="moose_classes.html#IntFire.getBufferTime">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.getBufferTime">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getBufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.getBufferTime">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#getC">getC()</a>, <a href="moose_builtins.html#getC">[1]</a>, <a href="moose_classes.html#getC">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getC">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getC">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getC">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.getC">(RC method)</a>, <a href="moose_builtins.html#RC.getC">[1]</a>, <a href="moose_classes.html#RC.getC">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.getCa">getCa() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCa">[1]</a>, <a href="moose_classes.html#CaConc.getCa">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getCa">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCa">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCa">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.getCa_base">getCa_base() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCa_base">[1]</a>, <a href="moose_classes.html#CaConc.getCa_base">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getCa_base">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCa_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCa_base">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.getCaAdvance">getCaAdvance() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaAdvance">[1]</a>, <a href="moose_classes.html#HSolve.getCaAdvance">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getCaBasal">getCaBasal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCaBasal">[1]</a>, <a href="moose_classes.html#CaConc.getCaBasal">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getCaBasal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCaBasal">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.getCaDiv">getCaDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaDiv">[1]</a>, <a href="moose_classes.html#HSolve.getCaDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getCaMax">getCaMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaMax">[1]</a>, <a href="moose_classes.html#HSolve.getCaMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getCaMin">getCaMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaMin">[1]</a>, <a href="moose_classes.html#HSolve.getCaMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getCeiling">getCeiling() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCeiling">[1]</a>, <a href="moose_classes.html#CaConc.getCeiling">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getCeiling">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCeiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCeiling">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.getCell">getCell() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getCell">[1]</a>, <a href="moose_classes.html#NeuroMesh.getCell">[2]</a> - </dt> - - - <dt><a href="tmp.html#getCeq">getCeq()</a>, <a href="moose_builtins.html#getCeq">[1]</a>, <a href="moose_classes.html#getCeq">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getChildren">getChildren() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getChildren">[1]</a>, <a href="moose_classes.html#Neutral.getChildren">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.getCin">getCin() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getCin">[1]</a>, <a href="moose_classes.html#Nernst.getCin">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getClassName">getClassName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getClassName">[1]</a>, <a href="moose_classes.html#Neutral.getClassName">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.getCm">getCm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getCm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getCm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.getCMg">getCMg() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getCMg">[1]</a>, <a href="moose_classes.html#MgBlock.getCMg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.getColor">getColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getColor">[1]</a>, <a href="moose_classes.html#Annotator.getColor">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getColumnIndex">getColumnIndex() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getColumnIndex">[1]</a>, <a href="moose_classes.html#Stoich.getColumnIndex">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getCommand">getCommand() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getCommand">[1]</a>, <a href="moose_classes.html#PIDController.getCommand">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.getCommand">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getCommand">[1]</a>, <a href="moose_classes.html#VClamp.getCommand">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Dsolve.getCompartment">getCompartment() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getCompartment">[1]</a>, <a href="moose_classes.html#Dsolve.getCompartment">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.getCompartment">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getCompartment">[1]</a>, <a href="moose_classes.html#Ksolve.getCompartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getCompartment">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getCompartment">[1]</a>, <a href="moose_classes.html#Stoich.getCompartment">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.getConc">getConc() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getConc">[1]</a>, <a href="moose_classes.html#PoolBase.getConc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.getConcInit">getConcInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getConcInit">[1]</a>, <a href="moose_classes.html#PoolBase.getConcInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.getConcK1">getConcK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getConcK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getConcK1">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getConvergenceCriterion">getConvergenceCriterion() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getConvergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.getConvergenceCriterion">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getCoordinates">getCoordinates() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getCoordinates">[1]</a>, <a href="moose_classes.html#MeshEntry.getCoordinates">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getCoords">getCoords() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getCoords">[1]</a>, <a href="moose_classes.html#CubeMesh.getCoords">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.getCoords">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getCoords">[1]</a>, <a href="moose_classes.html#CylMesh.getCoords">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.getCount">getCount() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getCount">[1]</a>, <a href="moose_classes.html#PulseGen.getCount">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.getCout">getCout() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getCout">[1]</a>, <a href="moose_classes.html#Nernst.getCout">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.getCurrent">getCurrent() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getCurrent">[1]</a>, <a href="moose_classes.html#VClamp.getCurrent">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getCurrentStep">getCurrentStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.getCurrentStep">[1]</a>, <a href="moose_classes.html#Clock.getCurrentStep">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getCurrentTime">getCurrentTime() (Clock method)</a>, <a href="moose_builtins.html#Clock.getCurrentTime">[1]</a>, <a href="moose_classes.html#Clock.getCurrentTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#getD">getD()</a>, <a href="moose_builtins.html#getD">[1]</a>, <a href="moose_classes.html#getD">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getD">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getD">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getD">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.getDelay">getDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getDelay">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Synapse.getDelay">(Synapse method)</a>, <a href="moose_builtins.html#Synapse.getDelay">[1]</a>, <a href="moose_classes.html#Synapse.getDelay">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Func.getDerivative">getDerivative() (Func method)</a>, <a href="moose_builtins.html#Func.getDerivative">[1]</a>, <a href="moose_classes.html#Func.getDerivative">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.getDerivative">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getDerivative">[1]</a>, <a href="moose_classes.html#PIDController.getDerivative">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Finfo.getDest">getDest() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getDest">[1]</a>, <a href="moose_classes.html#Finfo.getDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getDestFields">getDestFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getDestFields">[1]</a>, <a href="moose_classes.html#Neutral.getDestFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getDestFieldsOnE1">getDestFieldsOnE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getDestFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.getDestFieldsOnE1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getDestFieldsOnE2">getDestFieldsOnE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getDestFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.getDestFieldsOnE2">[2]</a> - </dt> - - - <dt><a href="tmp.html#getDiameter">getDiameter()</a>, <a href="moose_builtins.html#getDiameter">[1]</a>, <a href="moose_classes.html#getDiameter">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.getDiameter">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getDiameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.getDiameter">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.getDiffConst">getDiffConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getDiffConst">[1]</a>, <a href="moose_classes.html#PoolBase.getDiffConst">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getDiffLength">getDiffLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getDiffLength">[1]</a>, <a href="moose_classes.html#CylMesh.getDiffLength">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#NeuroMesh.getDiffLength">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getDiffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.getDiffLength">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MeshEntry.getDiffusionArea">getDiffusionArea() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDiffusionArea">[1]</a>, <a href="moose_classes.html#MeshEntry.getDiffusionArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getDiffusionScaling">getDiffusionScaling() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDiffusionScaling">[1]</a>, <a href="moose_classes.html#MeshEntry.getDiffusionScaling">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getDimensions">getDimensions() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDimensions">[1]</a>, <a href="moose_classes.html#MeshEntry.getDimensions">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getDivs">getDivs() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getDivs">[1]</a>, <a href="moose_classes.html#HHGate.getDivs">[2]</a> - </dt> - - - <dt><a href="tmp.html#Cinfo.getDocs">getDocs() (Cinfo method)</a>, <a href="moose_builtins.html#Cinfo.getDocs">[1]</a>, <a href="moose_classes.html#Cinfo.getDocs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Finfo.getDocs">(Finfo method)</a>, <a href="moose_builtins.html#Finfo.getDocs">[1]</a>, <a href="moose_classes.html#Finfo.getDocs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#StimulusTable.getDoLoop">getDoLoop() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getDoLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.getDoLoop">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getDsolve">getDsolve() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getDsolve">[1]</a>, <a href="moose_classes.html#Ksolve.getDsolve">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.getDsolve">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getDsolve">[1]</a>, <a href="moose_classes.html#Stoich.getDsolve">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.getDt">getDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.getDt">[1]</a>, <a href="moose_classes.html#Clock.getDt">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HSolve.getDt">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.getDt">[1]</a>, <a href="moose_classes.html#HSolve.getDt">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.getDts">getDts() (Clock method)</a>, <a href="moose_builtins.html#Clock.getDts">[1]</a>, <a href="moose_classes.html#Clock.getDts">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getDx">getDx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDx">[1]</a>, <a href="moose_classes.html#CubeMesh.getDx">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.getDx">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getDx">[1]</a>, <a href="moose_classes.html#Interpol2D.getDx">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getDy">getDy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDy">[1]</a>, <a href="moose_classes.html#CubeMesh.getDy">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.getDy">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getDy">[1]</a>, <a href="moose_classes.html#Interpol2D.getDy">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getDz">getDz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDz">[1]</a>, <a href="moose_classes.html#CubeMesh.getDz">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.getE">getE() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getE">[1]</a>, <a href="moose_classes.html#Nernst.getE">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getE1">getE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getE1">[1]</a>, <a href="moose_classes.html#Msg.getE1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getE2">getE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getE2">[1]</a>, <a href="moose_classes.html#Msg.getE2">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getE_previous">getE_previous() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getE_previous">[1]</a>, <a href="moose_classes.html#PIDController.getE_previous">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.getEdgeTriggered">getEdgeTriggered() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getEdgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.getEdgeTriggered">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getEigenvalues">getEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getEigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.getEk">getEk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getEk">[1]</a>, <a href="moose_classes.html#ChanBase.getEk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.getEk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getEk">[1]</a>, <a href="moose_classes.html#SynChanBase.getEk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getEk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getEk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getEk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getEm">getEm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getEm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getEm">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getEpsAbs">getEpsAbs() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getEpsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.getEpsAbs">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getEpsRel">getEpsRel() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getEpsRel">[1]</a>, <a href="moose_classes.html#Ksolve.getEpsRel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getError">getError() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getError">[1]</a>, <a href="moose_classes.html#PIDController.getError">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getEstimatedDt">getEstimatedDt() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getEstimatedDt">[1]</a>, <a href="moose_classes.html#Stoich.getEstimatedDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getExpr">getExpr() (Func method)</a>, <a href="moose_builtins.html#Func.getExpr">[1]</a>, <a href="moose_classes.html#Func.getExpr">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.getFieldName">getFieldName() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getFieldName">[1]</a>, <a href="moose_classes.html#Finfo.getFieldName">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.getFilename">getFilename() (TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getFilename">[1]</a>, <a href="moose_classes.html#TimeTable.getFilename">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getFirstDelay">getFirstDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getFirstLevel">getFirstLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getFirstWidth">getFirstWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getFloor">getFloor() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getFloor">[1]</a>, <a href="moose_classes.html#CaConc.getFloor">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getFloor">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getFloor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getFloor">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Arith.getFunction">getFunction() (Arith method)</a>, <a href="moose_builtins.html#Arith.getFunction">[1]</a>, <a href="moose_classes.html#Arith.getFunction">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.getFunction">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getFunction">[1]</a>, <a href="moose_classes.html#MathFunc.getFunction">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#DiffAmp.getGain">getGain() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getGain">[1]</a>, <a href="moose_classes.html#DiffAmp.getGain">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.getGain">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getGain">[1]</a>, <a href="moose_classes.html#PIDController.getGain">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.getGain">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getGain">[1]</a>, <a href="moose_classes.html#VClamp.getGain">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.getGamma">getGamma() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getGamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getGamma">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.getGbar">getGbar() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getGbar">[1]</a>, <a href="moose_classes.html#ChanBase.getGbar">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovChannel.getGbar">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getGbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.getGbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.getGbar">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getGbar">[1]</a>, <a href="moose_classes.html#SynChanBase.getGbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getGbar">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getGbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getGbar">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.getGeometryPolicy">getGeometryPolicy() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getGeometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.getGeometryPolicy">[2]</a> - </dt> - - - <dt><a href="tmp.html#getGk">getGk()</a>, <a href="moose_builtins.html#getGk">[1]</a>, <a href="moose_classes.html#getGk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChanBase.getGk">(ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getGk">[1]</a>, <a href="moose_classes.html#ChanBase.getGk">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.getGk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getGk">[1]</a>, <a href="moose_classes.html#SynChanBase.getGk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getGk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getGk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getGk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SpikeGen.getHasFired">getHasFired() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getHasFired">[1]</a>, <a href="moose_classes.html#SpikeGen.getHasFired">[2]</a> - </dt> - - - <dt><a href="tmp.html#OneToAllMsg.getI1">getI1() (OneToAllMsg method)</a>, <a href="moose_builtins.html#OneToAllMsg.getI1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.getI1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SingleMsg.getI1">(SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.getI1">[1]</a>, <a href="moose_classes.html#SingleMsg.getI1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SingleMsg.getI2">getI2() (SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.getI2">[1]</a>, <a href="moose_classes.html#SingleMsg.getI2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.getIcon">getIcon() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getIcon">[1]</a>, <a href="moose_classes.html#Annotator.getIcon">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.getIk">getIk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getIk">[1]</a>, <a href="moose_classes.html#ChanBase.getIk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MgBlock.getIk">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getIk">[1]</a>, <a href="moose_classes.html#MgBlock.getIk">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.getIk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getIk">[1]</a>, <a href="moose_classes.html#SynChanBase.getIk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getIk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getIk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getIk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getIm">getIm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getIm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getIm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getIm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getIm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getIm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovChannel.getInitialState">getInitialState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getInitialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.getInitialState">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getInitialState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInitialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInitialState">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.getInitU">getInitU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInitU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInitU">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.getInitVm">getInitVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getInitVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getInitVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getInitVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInitVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInitVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getInject">getInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.getInject">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.getInject">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInject">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.getInject">(RC method)</a>, <a href="moose_builtins.html#RC.getInject">[1]</a>, <a href="moose_classes.html#RC.getInject">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#getInnerArea">getInnerArea()</a>, <a href="moose_builtins.html#getInnerArea">[1]</a>, <a href="moose_classes.html#getInnerArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.getInputOffset">getInputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getInputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.getInputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getInstant">getInstant() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getInstant">[1]</a>, <a href="moose_classes.html#HHChannel.getInstant">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getInstant">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getInstant">[1]</a>, <a href="moose_classes.html#HHChannel2D.getInstant">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getInstant">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getInstant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getInstant">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.getIntegral">getIntegral() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getIntegral">[1]</a>, <a href="moose_classes.html#PIDController.getIntegral">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.getInternalDt">getInternalDt() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getInternalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getInternalDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.getInvdx">getInvdx() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInvdx">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInvdx">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VectorTable.getInvdx">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getInvdx">[1]</a>, <a href="moose_classes.html#VectorTable.getInvdx">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovSolverBase.getInvdy">getInvdy() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInvdy">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInvdy">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.getIsInitialized">getIsInitialized() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getIsInitialized">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getIsInitialized">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SteadyState.getIsInitialized">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getIsInitialized">[1]</a>, <a href="moose_classes.html#SteadyState.getIsInitialized">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.getIsRunning">getIsRunning() (Clock method)</a>, <a href="moose_builtins.html#Clock.getIsRunning">[1]</a>, <a href="moose_classes.html#Clock.getIsRunning">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getIsToroid">getIsToroid() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getIsToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.getIsToroid">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.getK1">getK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.getK2">getK2() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK2">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.getK3">getK3() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK3">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.getKb">getKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getKb">[1]</a>, <a href="moose_classes.html#ReacBase.getKb">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.getKcat">getKcat() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getKcat">[1]</a>, <a href="moose_classes.html#EnzBase.getKcat">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.getKf">getKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getKf">[1]</a>, <a href="moose_classes.html#ReacBase.getKf">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.getKm">getKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getKm">[1]</a>, <a href="moose_classes.html#EnzBase.getKm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.getKMg_A">getKMg_A() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getKMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.getKMg_A">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.getKMg_B">getKMg_B() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getKMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.getKMg_B">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getKsolve">getKsolve() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getKsolve">[1]</a>, <a href="moose_classes.html#Stoich.getKsolve">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getLabels">getLabels() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getLabels">[1]</a>, <a href="moose_classes.html#MarkovChannel.getLabels">[2]</a> - </dt> - - - <dt><a href="tmp.html#getLeak">getLeak()</a>, <a href="moose_builtins.html#getLeak">[1]</a>, <a href="moose_classes.html#getLeak">[2]</a> - </dt> - - - <dt><a href="tmp.html#getLength">getLength()</a>, <a href="moose_builtins.html#getLength">[1]</a>, <a href="moose_classes.html#getLength">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.getLength">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getLength">[1]</a>, <a href="moose_classes.html#CompartmentBase.getLength">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.getLevel">getLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getLigandConc">getLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.getLigandConc">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovRateTable.getLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getLigandConc">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#VectorTable.getLookupindex">getLookupindex() (VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getLookupindex">[1]</a>, <a href="moose_classes.html#VectorTable.getLookupindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.getLookupvalue">getLookupvalue() (VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getLookupvalue">[1]</a>, <a href="moose_classes.html#VectorTable.getLookupvalue">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.getLoopTime">getLoopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getLoopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getLoopTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.getMathML">getMathML() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getMathML">[1]</a>, <a href="moose_classes.html#MathFunc.getMathML">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getMatrixEntry">getMatrixEntry() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getMatrixEntry">[1]</a>, <a href="moose_classes.html#Stoich.getMatrixEntry">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getMax">getMax() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMax">[1]</a>, <a href="moose_classes.html#HHGate.getMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getMaxIter">getMaxIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getMaxIter">[1]</a>, <a href="moose_classes.html#SteadyState.getMaxIter">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getMe">getMe() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMe">[1]</a>, <a href="moose_classes.html#Neutral.getMe">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.getMean">getMean() (Stats method)</a>, <a href="moose_builtins.html#Stats.getMean">[1]</a>, <a href="moose_classes.html#Stats.getMean">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getMeshToSpace">getMeshToSpace() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getMeshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.getMeshToSpace">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getMeshType">getMeshType() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getMeshType">[1]</a>, <a href="moose_classes.html#MeshEntry.getMeshType">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getMethod">getMethod() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getMethod">[1]</a>, <a href="moose_classes.html#Ksolve.getMethod">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovGslSolver.getMethod">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getMethod">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getMethod">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.getMethod">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getMethod">[1]</a>, <a href="moose_classes.html#TimeTable.getMethod">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.getMin">getMin() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMin">[1]</a>, <a href="moose_classes.html#HHGate.getMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.getMInfinity">getMInfinity() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMInfinity">[1]</a>, <a href="moose_classes.html#HHGate.getMInfinity">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getMode">getMode() (Func method)</a>, <a href="moose_builtins.html#Func.getMode">[1]</a>, <a href="moose_classes.html#Func.getMode">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.getMode">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getMode">[1]</a>, <a href="moose_classes.html#VClamp.getMode">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Species.getMolWt">getMolWt() (Species method)</a>, <a href="moose_builtins.html#Species.getMolWt">[1]</a>, <a href="moose_classes.html#Species.getMolWt">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.getMotorConst">getMotorConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getMotorConst">[1]</a>, <a href="moose_classes.html#PoolBase.getMotorConst">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getMsgDestFunctions">getMsgDestFunctions() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgDestFunctions">[1]</a>, <a href="moose_classes.html#Neutral.getMsgDestFunctions">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getMsgDests">getMsgDests() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgDests">[1]</a>, <a href="moose_classes.html#Neutral.getMsgDests">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getMsgIn">getMsgIn() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgIn">[1]</a>, <a href="moose_classes.html#Neutral.getMsgIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getMsgOut">getMsgOut() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgOut">[1]</a>, <a href="moose_classes.html#Neutral.getMsgOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.getMyNode">getMyNode() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getMyNode">[1]</a>, <a href="moose_classes.html#PostMaster.getMyNode">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.getN">getN() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getN">[1]</a>, <a href="moose_classes.html#PoolBase.getN">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getName">getName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getName">[1]</a>, <a href="moose_classes.html#Neutral.getName">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getNeighbors">getNeighbors() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getNeighbors">[1]</a>, <a href="moose_classes.html#MeshEntry.getNeighbors">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.getNeighbors">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNeighbors">[1]</a>, <a href="moose_classes.html#Neutral.getNeighbors">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.getNInit">getNInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getNInit">[1]</a>, <a href="moose_classes.html#PoolBase.getNInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getNIter">getNIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNIter">[1]</a>, <a href="moose_classes.html#SteadyState.getNIter">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getNNegEigenvalues">getNNegEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNNegEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getNNegEigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.getNormalizeWeights">getNormalizeWeights() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getNormalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.getNormalizeWeights">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.getNotes">getNotes() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getNotes">[1]</a>, <a href="moose_classes.html#Annotator.getNotes">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getNPosEigenvalues">getNPosEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNPosEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getNPosEigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getNsteps">getNsteps() (Clock method)</a>, <a href="moose_builtins.html#Clock.getNsteps">[1]</a>, <a href="moose_classes.html#Clock.getNsteps">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.getNum">getNum() (Stats method)</a>, <a href="moose_builtins.html#Stats.getNum">[1]</a>, <a href="moose_classes.html#Stats.getNum">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getNumAllPools">getNumAllPools() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumAllPools">[1]</a>, <a href="moose_classes.html#Stoich.getNumAllPools">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.getNumAllVoxels">getNumAllVoxels() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.getNumAllVoxels">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.getNumAllVoxels">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.getNumAllVoxels">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getNumAllVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.getNumAllVoxels">[2]</a> - </dt> - - </dl></dd> - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#SparseMsg.getNumColumns">getNumColumns() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumColumns">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumColumns">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getNumData">getNumData() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNumData">[1]</a>, <a href="moose_classes.html#Neutral.getNumData">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getNumDiffCompts">getNumDiffCompts() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getNumDiffCompts">[1]</a>, <a href="moose_classes.html#CylMesh.getNumDiffCompts">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#NeuroMesh.getNumDiffCompts">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getNumDiffCompts">[1]</a>, <a href="moose_classes.html#NeuroMesh.getNumDiffCompts">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.getNumDimensions">getNumDimensions() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getNumDimensions">[1]</a>, <a href="moose_classes.html#ChemCompt.getNumDimensions">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.getNumEntries">getNumEntries() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumEntries">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumEntries">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getNumField">getNumField() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNumField">[1]</a>, <a href="moose_classes.html#Neutral.getNumField">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getNumGateX">getNumGateX() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateX">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getNumGateX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateX">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getNumGateX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateX">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.getNumGateY">getNumGateY() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateY">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getNumGateY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateY">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getNumGateY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateY">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.getNumGateZ">getNumGateZ() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateZ">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getNumGateZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getNumGateZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateZ">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ReacBase.getNumKb">getNumKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumKb">[1]</a>, <a href="moose_classes.html#ReacBase.getNumKb">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.getNumKf">getNumKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumKf">[1]</a>, <a href="moose_classes.html#ReacBase.getNumKf">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.getNumKm">getNumKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getNumKm">[1]</a>, <a href="moose_classes.html#EnzBase.getNumKm">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.getNumLocalVoxels">getNumLocalVoxels() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumLocalVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.getNumLocalVoxels">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.getNumLocalVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumLocalVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.getNumLocalVoxels">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.getNumMesh">getNumMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getNumMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.getNumMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.getNumNodes">getNumNodes() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getNumNodes">[1]</a>, <a href="moose_classes.html#PostMaster.getNumNodes">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getNumOpenStates">getNumOpenStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getNumOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.getNumOpenStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.getNumPools">getNumPools() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumPools">[1]</a>, <a href="moose_classes.html#Dsolve.getNumPools">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.getNumPools">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumPools">[1]</a>, <a href="moose_classes.html#Gsolve.getNumPools">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getNumPools">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumPools">[1]</a>, <a href="moose_classes.html#Ksolve.getNumPools">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ReacBase.getNumProducts">getNumProducts() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumProducts">[1]</a>, <a href="moose_classes.html#ReacBase.getNumProducts">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getNumRates">getNumRates() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumRates">[1]</a>, <a href="moose_classes.html#Stoich.getNumRates">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.getNumRows">getNumRows() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumRows">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumRows">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.getNumSegments">getNumSegments() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getNumSegments">[1]</a>, <a href="moose_classes.html#NeuroMesh.getNumSegments">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getNumStates">getNumStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getNumStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.getNumStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.getNumSubstrates">getNumSubstrates() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getNumSubstrates">[1]</a>, <a href="moose_classes.html#EnzBase.getNumSubstrates">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.getNumSubstrates">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumSubstrates">[1]</a>, <a href="moose_classes.html#ReacBase.getNumSubstrates">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynHandler.getNumSynapse">getNumSynapse() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.getNumSynapse">[1]</a>, <a href="moose_classes.html#SynHandler.getNumSynapse">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynHandler.getNumSynapses">getNumSynapses() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.getNumSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.getNumSynapses">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getNumTicks">getNumTicks() (Clock method)</a>, <a href="moose_builtins.html#Clock.getNumTicks">[1]</a>, <a href="moose_classes.html#Clock.getNumTicks">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getNumVarPools">getNumVarPools() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNumVarPools">[1]</a>, <a href="moose_classes.html#SteadyState.getNumVarPools">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.getNumVarPools">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumVarPools">[1]</a>, <a href="moose_classes.html#Stoich.getNumVarPools">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Dsolve.getNumVoxels">getNumVoxels() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.getNumVoxels">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.getNVec">getNVec() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNVec">[1]</a>, <a href="moose_classes.html#Dsolve.getNVec">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.getNVec">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNVec">[1]</a>, <a href="moose_classes.html#Gsolve.getNVec">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getNVec">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNVec">[1]</a>, <a href="moose_classes.html#Ksolve.getNVec">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getNx">getNx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNx">[1]</a>, <a href="moose_classes.html#CubeMesh.getNx">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getNy">getNy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNy">[1]</a>, <a href="moose_classes.html#CubeMesh.getNy">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getNz">getNz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNz">[1]</a>, <a href="moose_classes.html#CubeMesh.getNz">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.getOneVoxelVolume">getOneVoxelVolume() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getOneVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getOneVoxelVolume">[2]</a> - </dt> - - - <dt><a href="tmp.html#getOuterArea">getOuterArea()</a>, <a href="moose_builtins.html#getOuterArea">[1]</a>, <a href="moose_classes.html#getOuterArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.getOutputOffset">getOutputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getOutputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.getOutputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.getOutputValue">getOutputValue() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getOutputValue">[1]</a>, <a href="moose_classes.html#Adaptor.getOutputValue">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Arith.getOutputValue">(Arith method)</a>, <a href="moose_builtins.html#Arith.getOutputValue">[1]</a>, <a href="moose_classes.html#Arith.getOutputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.getOutputValue">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getOutputValue">[1]</a>, <a href="moose_classes.html#DiffAmp.getOutputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getOutputValue">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getOutputValue">[1]</a>, <a href="moose_classes.html#PIDController.getOutputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getOutputValue">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getOutputValue">[1]</a>, <a href="moose_classes.html#PulseGen.getOutputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.getOutputValue">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getOutputValue">[1]</a>, <a href="moose_classes.html#TableBase.getOutputValue">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Neutral.getParent">getParent() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getParent">[1]</a>, <a href="moose_classes.html#Neutral.getParent">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.getParentVoxel">getParentVoxel() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getParentVoxel">[1]</a>, <a href="moose_classes.html#NeuroMesh.getParentVoxel">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SpineMesh.getParentVoxel">(SpineMesh method)</a>, <a href="moose_builtins.html#SpineMesh.getParentVoxel">[1]</a>, <a href="moose_classes.html#SpineMesh.getParentVoxel">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Dsolve.getPath">getPath() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getPath">[1]</a>, <a href="moose_classes.html#Dsolve.getPath">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.getPath">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getPath">[1]</a>, <a href="moose_classes.html#Neutral.getPath">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getPath">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getPath">[1]</a>, <a href="moose_classes.html#Stoich.getPath">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Stoich.getPoolIdMap">getPoolIdMap() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getPoolIdMap">[1]</a>, <a href="moose_classes.html#Stoich.getPoolIdMap">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getPreserveNumEntries">getPreserveNumEntries() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getPreserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.getPreserveNumEntries">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.getProbability">getProbability() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getProbability">[1]</a>, <a href="moose_classes.html#SparseMsg.getProbability">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.getQ">getQ() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getQ">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getQ">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getQ">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getQ">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getQ">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#RC.getR">getR() (RC method)</a>, <a href="moose_builtins.html#RC.getR">[1]</a>, <a href="moose_classes.html#RC.getR">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getR0">getR0() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getR0">[1]</a>, <a href="moose_classes.html#CylMesh.getR0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getR1">getR1() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getR1">[1]</a>, <a href="moose_classes.html#CylMesh.getR1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.getRa">getRa() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getRa">[1]</a>, <a href="moose_classes.html#CompartmentBase.getRa">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getRank">getRank() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getRank">[1]</a>, <a href="moose_classes.html#SteadyState.getRank">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.getRatio">getRatio() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getRatio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getRatio">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.getRefractoryPeriod">getRefractoryPeriod() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getRefractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.getRefractoryPeriod">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.getRefractT">getRefractT() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getRefractT">[1]</a>, <a href="moose_classes.html#SpikeGen.getRefractT">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.getRelativeAccuracy">getRelativeAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getRelativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getRelativeAccuracy">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.getResult">getResult() (FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.getResult">[1]</a>, <a href="moose_classes.html#FuncBase.getResult">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.getResult">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getResult">[1]</a>, <a href="moose_classes.html#MathFunc.getResult">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getRm">getRm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getRm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getRm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getRmByTau">getRmByTau() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getRmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getRmByTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.getRowStart">getRowStart() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getRowStart">[1]</a>, <a href="moose_classes.html#Stoich.getRowStart">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getRunTime">getRunTime() (Clock method)</a>, <a href="moose_builtins.html#Clock.getRunTime">[1]</a>, <a href="moose_classes.html#Clock.getRunTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.getSaturation">getSaturation() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getSaturation">[1]</a>, <a href="moose_classes.html#DiffAmp.getSaturation">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.getSaturation">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getSaturation">[1]</a>, <a href="moose_classes.html#PIDController.getSaturation">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Adaptor.getScale">getScale() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getScale">[1]</a>, <a href="moose_classes.html#Adaptor.getScale">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.getScale">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.getScale">[1]</a>, <a href="moose_classes.html#Nernst.getScale">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Stats.getSdev">getSdev() (Stats method)</a>, <a href="moose_builtins.html#Stats.getSdev">[1]</a>, <a href="moose_classes.html#Stats.getSdev">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getSecondDelay">getSecondDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getSecondLevel">getSecondLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getSecondWidth">getSecondWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getSeed">getSeed() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getSeed">[1]</a>, <a href="moose_classes.html#HSolve.getSeed">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SparseMsg.getSeed">(SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getSeed">[1]</a>, <a href="moose_classes.html#SparseMsg.getSeed">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.getSensed">getSensed() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getSensed">[1]</a>, <a href="moose_classes.html#PIDController.getSensed">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.getSensed">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getSensed">[1]</a>, <a href="moose_classes.html#VClamp.getSensed">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.getSeparateSpines">getSeparateSpines() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getSeparateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.getSeparateSpines">[2]</a> - </dt> - - - <dt><a href="tmp.html#getShapeMode">getShapeMode()</a>, <a href="moose_builtins.html#getShapeMode">[1]</a>, <a href="moose_classes.html#getShapeMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.getSize">getSize() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getSize">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getSize">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#TableBase.getSize">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getSize">[1]</a>, <a href="moose_classes.html#TableBase.getSize">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.getSolutionStatus">getSolutionStatus() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getSolutionStatus">[1]</a>, <a href="moose_classes.html#SteadyState.getSolutionStatus">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.getSourceFields">getSourceFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getSourceFields">[1]</a>, <a href="moose_classes.html#Neutral.getSourceFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getSpaceToMesh">getSpaceToMesh() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getSpaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.getSpaceToMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.getSpeciesId">getSpeciesId() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getSpeciesId">[1]</a>, <a href="moose_classes.html#PoolBase.getSpeciesId">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.getSrc">getSrc() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getSrc">[1]</a>, <a href="moose_classes.html#Finfo.getSrc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getSrcFieldsOnE1">getSrcFieldsOnE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getSrcFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.getSrcFieldsOnE1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.getSrcFieldsOnE2">getSrcFieldsOnE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getSrcFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.getSrcFieldsOnE2">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.getStartTime">getStartTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStartTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getStartTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getState">getState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getState">[1]</a>, <a href="moose_classes.html#MarkovChannel.getState">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getState">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.getState">(RC method)</a>, <a href="moose_builtins.html#RC.getState">[1]</a>, <a href="moose_classes.html#RC.getState">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.getState">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getState">[1]</a>, <a href="moose_classes.html#TimeTable.getState">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.getStateType">getStateType() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStateType">[1]</a>, <a href="moose_classes.html#SteadyState.getStateType">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getStatus">getStatus() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStatus">[1]</a>, <a href="moose_classes.html#SteadyState.getStatus">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.getStencilIndex">getStencilIndex() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getStencilIndex">[1]</a>, <a href="moose_classes.html#ChemCompt.getStencilIndex">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.getStencilRate">getStencilRate() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getStencilRate">[1]</a>, <a href="moose_classes.html#ChemCompt.getStencilRate">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.getStepPosition">getStepPosition() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.getStepPosition">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.getStepSize">getStepSize() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.getStepSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.getStoich">getStoich() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getStoich">[1]</a>, <a href="moose_classes.html#Dsolve.getStoich">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.getStoich">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getStoich">[1]</a>, <a href="moose_classes.html#Gsolve.getStoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.getStoich">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getStoich">[1]</a>, <a href="moose_classes.html#Ksolve.getStoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getStoich">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStoich">[1]</a>, <a href="moose_classes.html#SteadyState.getStoich">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#StimulusTable.getStopTime">getStopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getStopTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiagonalMsg.getStride">getStride() (DiagonalMsg method)</a>, <a href="moose_builtins.html#DiagonalMsg.getStride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.getStride">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.getSubTree">getSubTree() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getSubTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.getSubTree">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.getSum">getSum() (Stats method)</a>, <a href="moose_builtins.html#Stats.getSum">[1]</a>, <a href="moose_classes.html#Stats.getSum">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.getSurface">getSurface() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getSurface">[1]</a>, <a href="moose_classes.html#CubeMesh.getSurface">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.getTable">getTable() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getTable">[1]</a>, <a href="moose_classes.html#Interpol2D.getTable">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VectorTable.getTable">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getTable">[1]</a>, <a href="moose_classes.html#VectorTable.getTable">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.getTableA">getTableA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTableA">[1]</a>, <a href="moose_classes.html#HHGate.getTableA">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.getTableA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getTableA">[1]</a>, <a href="moose_classes.html#HHGate2D.getTableA">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.getTableB">getTableB() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTableB">[1]</a>, <a href="moose_classes.html#HHGate.getTableB">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.getTableB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getTableB">[1]</a>, <a href="moose_classes.html#HHGate2D.getTableB">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.getTableVector2D">getTableVector2D() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getTableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.getTableVector2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getTarget">getTarget() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getTarget">[1]</a>, <a href="moose_classes.html#HSolve.getTarget">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getTau">getTau() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getTau">[1]</a>, <a href="moose_classes.html#CaConc.getTau">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate.getTau">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTau">[1]</a>, <a href="moose_classes.html#HHGate.getTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.getTau">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.getTau">[1]</a>, <a href="moose_classes.html#IntFire.getTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.getTau">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTau">[1]</a>, <a href="moose_classes.html#VClamp.getTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.getTau">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getTau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getTau">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynChan.getTau1">getTau1() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getTau1">[1]</a>, <a href="moose_classes.html#SynChan.getTau1">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.getTau2">getTau2() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getTau2">[1]</a>, <a href="moose_classes.html#SynChan.getTau2">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getTauD">getTauD() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getTauD">[1]</a>, <a href="moose_classes.html#PIDController.getTauD">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.getTauI">getTauI() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getTauI">[1]</a>, <a href="moose_classes.html#PIDController.getTauI">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.getTd">getTd() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTd">[1]</a>, <a href="moose_classes.html#VClamp.getTd">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.getTemperature">getTemperature() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getTemperature">[1]</a>, <a href="moose_classes.html#Nernst.getTemperature">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.getTextColor">getTextColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getTextColor">[1]</a>, <a href="moose_classes.html#Annotator.getTextColor">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.getThick">getThick() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getThick">[1]</a>, <a href="moose_classes.html#CaConc.getThick">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.getThick">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getThick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getThick">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#getThickness">getThickness()</a>, <a href="moose_builtins.html#getThickness">[1]</a>, <a href="moose_classes.html#getThickness">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PsdMesh.getThickness">(PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.getThickness">[1]</a>, <a href="moose_classes.html#PsdMesh.getThickness">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Mstring.getThis">getThis() (Mstring method)</a>, <a href="moose_builtins.html#Mstring.getThis">[1]</a>, <a href="moose_classes.html#Mstring.getThis">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.getThis">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getThis">[1]</a>, <a href="moose_classes.html#Neutral.getThis">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IntFire.getThresh">getThresh() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getThresh">[1]</a>, <a href="moose_classes.html#IntFire.getThresh">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.getThreshold">getThreshold() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getThreshold">[1]</a>, <a href="moose_classes.html#SpikeGen.getThreshold">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Table.getThreshold">(Table method)</a>, <a href="moose_builtins.html#Table.getThreshold">[1]</a>, <a href="moose_classes.html#Table.getThreshold">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#VClamp.getTi">getTi() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTi">[1]</a>, <a href="moose_classes.html#VClamp.getTi">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getTickDt">getTickDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.getTickDt">[1]</a>, <a href="moose_classes.html#Clock.getTickDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.getTickStep">getTickStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.getTickStep">[1]</a>, <a href="moose_classes.html#Clock.getTickStep">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.getTotal">getTotal() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getTotal">[1]</a>, <a href="moose_classes.html#SteadyState.getTotal">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getTotLength">getTotLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getTotLength">[1]</a>, <a href="moose_classes.html#CylMesh.getTotLength">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getTrigMode">getTrigMode() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getTrigMode">[1]</a>, <a href="moose_classes.html#PulseGen.getTrigMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.getType">getType() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getType">[1]</a>, <a href="moose_classes.html#Finfo.getType">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getU">getU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getU">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getU0">getU0() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getU0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getU0">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getUseConcentration">getUseConcentration() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getUseConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.getUseConcentration">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieHHChannel.getUseConcentration">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getUseConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getUseConcentration">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.getUseInterpolation">getUseInterpolation() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getUseInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.getUseInterpolation">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.getUseRandInit">getUseRandInit() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getUseRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.getUseRandInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.getV0">getV0() (RC method)</a>, <a href="moose_builtins.html#RC.getV0">[1]</a>, <a href="moose_classes.html#RC.getV0">[2]</a> - </dt> - - - <dt><a href="tmp.html#getValence">getValence()</a>, <a href="moose_builtins.html#getValence">[1]</a>, <a href="moose_classes.html#getValence">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.getValence">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.getValence">[1]</a>, <a href="moose_classes.html#Nernst.getValence">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Double.getValue">getValue() (Double method)</a>, <a href="moose_builtins.html#Double.getValue">[1]</a>, <a href="moose_classes.html#Double.getValue">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Func.getValue">(Func method)</a>, <a href="moose_builtins.html#Func.getValue">[1]</a>, <a href="moose_classes.html#Func.getValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Long.getValue">(Long method)</a>, <a href="moose_builtins.html#Long.getValue">[1]</a>, <a href="moose_classes.html#Long.getValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Mstring.getValue">(Mstring method)</a>, <a href="moose_builtins.html#Mstring.getValue">[1]</a>, <a href="moose_classes.html#Mstring.getValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Unsigned.getValue">(Unsigned method)</a>, <a href="moose_builtins.html#Unsigned.getValue">[1]</a>, <a href="moose_classes.html#Unsigned.getValue">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Neutral.getValueFields">getValueFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getValueFields">[1]</a>, <a href="moose_classes.html#Neutral.getValueFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getVar">getVar() (Func method)</a>, <a href="moose_builtins.html#Func.getVar">[1]</a>, <a href="moose_classes.html#Func.getVar">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getVars">getVars() (Func method)</a>, <a href="moose_builtins.html#Func.getVars">[1]</a>, <a href="moose_classes.html#Func.getVars">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getVDiv">getVDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVDiv">[1]</a>, <a href="moose_classes.html#HSolve.getVDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.getVector">getVector() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.getVector">[1]</a>, <a href="moose_classes.html#TableBase.getVector">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.getVm">getVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IntFire.getVm">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.getVm">[1]</a>, <a href="moose_classes.html#IntFire.getVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.getVm">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getVm">[1]</a>, <a href="moose_classes.html#MarkovChannel.getVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.getVm">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.getVMax">getVMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVMax">[1]</a>, <a href="moose_classes.html#HSolve.getVMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.getVmax">getVmax() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getVmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getVmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.getVMin">getVMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVMin">[1]</a>, <a href="moose_classes.html#HSolve.getVMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#getVolume">getVolume()</a>, <a href="moose_builtins.html#getVolume">[1]</a>, <a href="moose_classes.html#getVolume">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChemCompt.getVolume">(ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getVolume">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.getVolume">(MeshEntry method)</a>, <a href="tmp.html#MeshEntry.getVolume">[1]</a>, <a href="moose_builtins.html#MeshEntry.getVolume">[2]</a>, <a href="moose_builtins.html#MeshEntry.getVolume">[3]</a>, <a href="moose_classes.html#MeshEntry.getVolume">[4]</a>, <a href="moose_classes.html#MeshEntry.getVolume">[5]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.getVolume">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getVolume">[1]</a>, <a href="moose_classes.html#PoolBase.getVolume">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.getVoxelVolume">getVoxelVolume() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getVoxelVolume">[2]</a> - </dt> - - - <dt><a href="tmp.html#Synapse.getWeight">getWeight() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.getWeight">[1]</a>, <a href="moose_classes.html#Synapse.getWeight">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.getWidth">getWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.getX">getX() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getX">[1]</a>, <a href="moose_classes.html#Annotator.getX">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.getX">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getX">[1]</a>, <a href="moose_classes.html#CompartmentBase.getX">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getX">(Func method)</a>, <a href="moose_builtins.html#Func.getX">[1]</a>, <a href="moose_classes.html#Func.getX">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getX">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getX">[1]</a>, <a href="moose_classes.html#HHChannel.getX">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.getX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getX">[1]</a>, <a href="moose_classes.html#HHChannel2D.getX">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getX">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getX0">getX0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getX0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getX0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.getX0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getX0">[1]</a>, <a href="moose_classes.html#CubeMesh.getX0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getX0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getX0">[1]</a>, <a href="moose_classes.html#CylMesh.getX0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getX1">getX1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getX1">[1]</a>, <a href="moose_classes.html#CubeMesh.getX1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.getX1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getX1">[1]</a>, <a href="moose_classes.html#CylMesh.getX1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.getXdivs">getXdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.getXdivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getXdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXdivs">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.getXdivs">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXdivs">[1]</a>, <a href="moose_classes.html#VectorTable.getXdivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getXdivsA">getXdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXdivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getXdivsB">getXdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXdivsB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.getXindex">getXindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getXindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getXindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.getXmax">getXmax() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.getXmax">[1]</a>, <a href="moose_classes.html#Interpol.getXmax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.getXmax">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXmax">[1]</a>, <a href="moose_classes.html#Interpol2D.getXmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.getXmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.getXmax">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXmax">[1]</a>, <a href="moose_classes.html#VectorTable.getXmax">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getXmaxA">getXmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXmaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getXmaxB">getXmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXmaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.getXmin">getXmin() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.getXmin">[1]</a>, <a href="moose_classes.html#Interpol.getXmin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.getXmin">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXmin">[1]</a>, <a href="moose_classes.html#Interpol2D.getXmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.getXmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.getXmin">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXmin">[1]</a>, <a href="moose_classes.html#VectorTable.getXmin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getXminA">getXminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXminA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getXminB">getXminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXminB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getXpower">getXpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getXpower">[1]</a>, <a href="moose_classes.html#HHChannel.getXpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getXpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getXpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getXpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getXpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getXpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getXpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Annotator.getY">getY() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getY">[1]</a>, <a href="moose_classes.html#Annotator.getY">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.getY">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getY">[1]</a>, <a href="moose_classes.html#CompartmentBase.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getY">(Func method)</a>, <a href="moose_builtins.html#Func.getY">[1]</a>, <a href="moose_classes.html#Func.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getY">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getY">[1]</a>, <a href="moose_classes.html#HHChannel.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.getY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getY">[1]</a>, <a href="moose_classes.html#HHChannel2D.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.getY">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.getY">[1]</a>, <a href="moose_classes.html#Interpol.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.getY">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getY">[1]</a>, <a href="moose_classes.html#TableBase.getY">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getY">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getY0">getY0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getY0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getY0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.getY0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getY0">[1]</a>, <a href="moose_classes.html#CubeMesh.getY0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getY0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getY0">[1]</a>, <a href="moose_classes.html#CylMesh.getY0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getY1">getY1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getY1">[1]</a>, <a href="moose_classes.html#CubeMesh.getY1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.getY1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getY1">[1]</a>, <a href="moose_classes.html#CylMesh.getY1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.getYdivs">getYdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.getYdivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getYdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYdivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getYdivsA">getYdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYdivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getYdivsB">getYdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYdivsB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.getYindex">getYindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getYindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getYindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.getYmax">getYmax() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYmax">[1]</a>, <a href="moose_classes.html#Interpol2D.getYmax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getYmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYmax">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getYmaxA">getYmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYmaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getYmaxB">getYmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYmaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.getYmin">getYmin() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYmin">[1]</a>, <a href="moose_classes.html#Interpol2D.getYmin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.getYmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYmin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.getYminA">getYminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYminA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.getYminB">getYminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYminB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getYpower">getYpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getYpower">[1]</a>, <a href="moose_classes.html#HHChannel.getYpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getYpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getYpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getYpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getYpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getYpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getYpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Annotator.getZ">getZ() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getZ">[1]</a>, <a href="moose_classes.html#Annotator.getZ">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.getZ">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getZ">[1]</a>, <a href="moose_classes.html#CompartmentBase.getZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.getZ">(Func method)</a>, <a href="moose_builtins.html#Func.getZ">[1]</a>, <a href="moose_classes.html#Func.getZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getZ">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getZ">[1]</a>, <a href="moose_classes.html#HHChannel.getZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.getZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.getZ">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getZ">[1]</a>, <a href="moose_classes.html#Interpol2D.getZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getZ">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.getZ0">getZ0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getZ0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getZ0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.getZ0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getZ0">[1]</a>, <a href="moose_classes.html#CubeMesh.getZ0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.getZ0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getZ0">[1]</a>, <a href="moose_classes.html#CylMesh.getZ0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.getZ1">getZ1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getZ1">[1]</a>, <a href="moose_classes.html#CubeMesh.getZ1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.getZ1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getZ1">[1]</a>, <a href="moose_classes.html#CylMesh.getZ1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel2D.getZindex">getZindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.getZk">getZk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getZk">[1]</a>, <a href="moose_classes.html#MgBlock.getZk">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.getZpower">getZpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getZpower">[1]</a>, <a href="moose_classes.html#HHChannel.getZpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.getZpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.getZpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getZpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getZpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChanBase.ghk">ghk (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.ghk">[1]</a>, <a href="moose_classes.html#ChanBase.ghk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.ghk">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.ghk">[1]</a>, <a href="moose_classes.html#SynChanBase.ghk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Gk">Gk</a>, <a href="moose_builtins.html#Gk">[1]</a>, <a href="moose_classes.html#Gk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChanBase.Gk">(ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Gk">[1]</a>, <a href="moose_classes.html#ChanBase.Gk">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.Gk">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Gk">[1]</a>, <a href="moose_classes.html#SynChanBase.Gk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Gk">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Gk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Gk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Group">Group (built-in class)</a>, <a href="moose_builtins.html#Group">[1]</a>, <a href="moose_classes.html#Group">[2]</a> - </dt> - - - <dt><a href="tmp.html#Group.group">group (Group attribute)</a>, <a href="moose_builtins.html#Group.group">[1]</a>, <a href="moose_classes.html#Group.group">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve">Gsolve (built-in class)</a>, <a href="moose_builtins.html#Gsolve">[1]</a>, <a href="moose_classes.html#Gsolve">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="H">H</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CompartmentBase.handleAxial">handleAxial() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleAxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleAxial">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.handleChannel">handleChannel() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleChannel">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleChannel">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.handleChannel">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.handleChannel">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.handleChannel">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovChannel.handleLigandConc">handleLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.handleLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.handleLigandConc">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovRateTable.handleLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.handleLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.handleLigandConc">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.handleMolWt">handleMolWt() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.handleMolWt">[1]</a>, <a href="moose_classes.html#PoolBase.handleMolWt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Species.handleMolWtRequest">handleMolWtRequest() (Species method)</a>, <a href="moose_builtins.html#Species.handleMolWtRequest">[1]</a>, <a href="moose_classes.html#Species.handleMolWtRequest">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.handleQ">handleQ() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.handleQ">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.handleQ">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.handleRaxial">handleRaxial() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleRaxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleRaxial">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.handleState">handleState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.handleState">[1]</a>, <a href="moose_classes.html#MarkovChannel.handleState">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#MarkovRateTable.handleVm">handleVm() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.handleVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.handleVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.handleVm">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.handleVm">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.handleVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SpikeGen.hasFired">hasFired (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.hasFired">[1]</a>, <a href="moose_classes.html#SpikeGen.hasFired">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel">HHChannel (built-in class)</a>, <a href="moose_builtins.html#HHChannel">[1]</a>, <a href="moose_classes.html#HHChannel">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D">HHChannel2D (built-in class)</a>, <a href="moose_builtins.html#HHChannel2D">[1]</a>, <a href="moose_classes.html#HHChannel2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate">HHGate (built-in class)</a>, <a href="moose_builtins.html#HHGate">[1]</a>, <a href="moose_classes.html#HHGate">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D">HHGate2D (built-in class)</a>, <a href="moose_builtins.html#HHGate2D">[1]</a>, <a href="moose_classes.html#HHGate2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#hillPump">hillPump()</a>, <a href="moose_builtins.html#hillPump">[1]</a>, <a href="moose_classes.html#hillPump">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve">HSolve (built-in class)</a>, <a href="moose_builtins.html#HSolve">[1]</a>, <a href="moose_classes.html#HSolve">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="I">I</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#OneToAllMsg.i1">i1 (OneToAllMsg attribute)</a>, <a href="moose_builtins.html#OneToAllMsg.i1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.i1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SingleMsg.i1">(SingleMsg attribute)</a>, <a href="moose_builtins.html#SingleMsg.i1">[1]</a>, <a href="moose_classes.html#SingleMsg.i1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SingleMsg.i2">i2 (SingleMsg attribute)</a>, <a href="moose_builtins.html#SingleMsg.i2">[1]</a>, <a href="moose_classes.html#SingleMsg.i2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.icon">icon (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.icon">[1]</a>, <a href="moose_classes.html#Annotator.icon">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.Ik">Ik (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Ik">[1]</a>, <a href="moose_classes.html#ChanBase.Ik">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MgBlock.Ik">(MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.Ik">[1]</a>, <a href="moose_classes.html#MgBlock.Ik">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.Ik">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Ik">[1]</a>, <a href="moose_classes.html#SynChanBase.Ik">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Ik">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ik">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ik">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChanBase.IkOut">IkOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.IkOut">[1]</a>, <a href="moose_classes.html#ChanBase.IkOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.IkOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.IkOut">[1]</a>, <a href="moose_classes.html#SynChanBase.IkOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.Im">Im (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Im">[1]</a>, <a href="moose_classes.html#CompartmentBase.Im">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.Im">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Im">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Im">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.increase">increase() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.increase">[1]</a>, <a href="moose_classes.html#CaConc.increase">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.increase">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.increase">[1]</a>, <a href="moose_classes.html#ZombieCaConc.increase">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Pool.increment">increment() (Pool method)</a>, <a href="moose_builtins.html#Pool.increment">[1]</a>, <a href="moose_classes.html#Pool.increment">[2]</a> - </dt> - - - <dt><a href="tmp.html#influx">influx()</a>, <a href="moose_builtins.html#influx">[1]</a>, <a href="moose_classes.html#influx">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.init">init (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.init">[1]</a>, <a href="moose_classes.html#CompartmentBase.init">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.init">init() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.init">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.init">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovRateTable.init">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.init">[1]</a>, <a href="moose_classes.html#MarkovRateTable.init">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.init">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.init">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.init">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovChannel.initialState">initialState (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.initialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.initialState">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.initialState">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.initialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.initialState">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.initProc">initProc() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.initProc">[1]</a>, <a href="moose_classes.html#CompartmentBase.initProc">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.initReinit">initReinit() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.initReinit">[1]</a>, <a href="moose_classes.html#CompartmentBase.initReinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.initU">initU (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.initU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.initU">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.initVm">initVm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.initVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.initVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.initVm">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.initVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.initVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.inject">inject (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.inject">[1]</a>, <a href="moose_classes.html#CompartmentBase.inject">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.inject">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.inject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.inject">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.inject">(RC attribute)</a>, <a href="moose_builtins.html#RC.inject">[1]</a>, <a href="moose_classes.html#RC.inject">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#RC.injectIn">injectIn() (RC method)</a>, <a href="moose_builtins.html#RC.injectIn">[1]</a>, <a href="moose_classes.html#RC.injectIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.injectMsg">injectMsg() (CompartmentBase method)</a>, <a href="tmp.html#CompartmentBase.injectMsg">[1]</a>, <a href="moose_builtins.html#CompartmentBase.injectMsg">[2]</a>, <a href="moose_builtins.html#CompartmentBase.injectMsg">[3]</a>, <a href="moose_classes.html#CompartmentBase.injectMsg">[4]</a>, <a href="moose_classes.html#CompartmentBase.injectMsg">[5]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.injectMsg">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.injectMsg">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.injectMsg">[2]</a> - </dt> - - </dl></dd> - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#innerArea">innerArea</a>, <a href="moose_builtins.html#innerArea">[1]</a>, <a href="moose_classes.html#innerArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#innerDif">innerDif</a>, <a href="moose_builtins.html#innerDif">[1]</a>, <a href="moose_classes.html#innerDif">[2]</a> - </dt> - - - <dt><a href="tmp.html#innerDifSourceOut">innerDifSourceOut</a>, <a href="moose_builtins.html#innerDifSourceOut">[1]</a>, <a href="moose_classes.html#innerDifSourceOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.input">input() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.input">[1]</a>, <a href="moose_classes.html#Adaptor.input">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#FuncBase.input">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.input">[1]</a>, <a href="moose_classes.html#FuncBase.input">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncPool.input">(FuncPool method)</a>, <a href="moose_builtins.html#FuncPool.input">[1]</a>, <a href="moose_classes.html#FuncPool.input">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.input">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.input">[1]</a>, <a href="moose_classes.html#Interpol.input">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.input">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.input">[1]</a>, <a href="moose_classes.html#PulseGen.input">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.input">(Table method)</a>, <a href="moose_builtins.html#Table.input">[1]</a>, <a href="moose_classes.html#Table.input">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieFuncPool.input">(ZombieFuncPool method)</a>, <a href="moose_builtins.html#ZombieFuncPool.input">[1]</a>, <a href="moose_classes.html#ZombieFuncPool.input">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Adaptor.inputOffset">inputOffset (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.inputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.inputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.instant">instant (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.instant">[1]</a>, <a href="moose_classes.html#HHChannel.instant">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.instant">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.instant">[1]</a>, <a href="moose_classes.html#HHChannel2D.instant">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.instant">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.instant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.instant">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovRateTable.instratesOut">instratesOut (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.instratesOut">[1]</a>, <a href="moose_classes.html#MarkovRateTable.instratesOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#integral">integral</a>, <a href="moose_builtins.html#integral">[1]</a>, <a href="moose_classes.html#integral">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.internalDt">internalDt (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.internalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.internalDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol">Interpol (built-in class)</a>, <a href="moose_builtins.html#Interpol">[1]</a>, <a href="moose_classes.html#Interpol">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D">Interpol2D (built-in class)</a>, <a href="moose_builtins.html#Interpol2D">[1]</a>, <a href="moose_classes.html#Interpol2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire">IntFire (built-in class)</a>, <a href="moose_builtins.html#IntFire">[1]</a>, <a href="moose_classes.html#IntFire">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.invdx">invdx (MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.invdx">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.invdx">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VectorTable.invdx">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.invdx">[1]</a>, <a href="moose_classes.html#VectorTable.invdx">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovSolverBase.invdy">invdy (MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.invdy">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.invdy">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.isInitialized">isInitialized (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.isInitialized">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.isInitialized">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SteadyState.isInitialized">(SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.isInitialized">[1]</a>, <a href="moose_classes.html#SteadyState.isInitialized">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.isRunning">isRunning (Clock attribute)</a>, <a href="moose_builtins.html#Clock.isRunning">[1]</a>, <a href="moose_classes.html#Clock.isRunning">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.isToroid">isToroid (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.isToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.isToroid">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn">IzhikevichNrn (built-in class)</a>, <a href="moose_builtins.html#IzhikevichNrn">[1]</a>, <a href="moose_classes.html#IzhikevichNrn">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="K">K</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CplxEnzBase.k1">k1 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.k2">k2 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k2">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.k3">k3 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k3">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.Kb">Kb (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.Kb">[1]</a>, <a href="moose_classes.html#ReacBase.Kb">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.kcat">kcat (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.kcat">[1]</a>, <a href="moose_classes.html#EnzBase.kcat">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.Kf">Kf (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.Kf">[1]</a>, <a href="moose_classes.html#ReacBase.Kf">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#EnzBase.Km">Km (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.Km">[1]</a>, <a href="moose_classes.html#EnzBase.Km">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.KMg_A">KMg_A (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.KMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.KMg_A">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.KMg_B">KMg_B (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.KMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.KMg_B">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve">Ksolve (built-in class)</a>, <a href="moose_builtins.html#Ksolve">[1]</a>, <a href="moose_classes.html#Ksolve">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.ksolve">ksolve (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.ksolve">[1]</a>, <a href="moose_classes.html#Stoich.ksolve">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="L">L</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#MarkovChannel.labels">labels (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.labels">[1]</a>, <a href="moose_classes.html#MarkovChannel.labels">[2]</a> - </dt> - - - <dt><a href="tmp.html#leak">leak</a>, <a href="moose_builtins.html#leak">[1]</a>, <a href="moose_classes.html#leak">[2]</a> - </dt> - - - <dt><a href="tmp.html#Leakage">Leakage (built-in class)</a>, <a href="moose_builtins.html#Leakage">[1]</a>, <a href="moose_classes.html#Leakage">[2]</a> - </dt> - - - <dt><a href="tmp.html#length">length</a>, <a href="moose_builtins.html#length">[1]</a>, <a href="moose_classes.html#length">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.length">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.length">[1]</a>, <a href="moose_classes.html#CompartmentBase.length">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.level">level (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.level">[1]</a>, <a href="moose_classes.html#PulseGen.level">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.levelIn">levelIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.levelIn">[1]</a>, <a href="moose_classes.html#PulseGen.levelIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.ligandConc">ligandConc (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.ligandConc">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovRateTable.ligandConc">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.ligandConc">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovSolverBase.ligandConc">ligandConc() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ligandConc">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.linearTransform">linearTransform() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.linearTransform">[1]</a>, <a href="moose_classes.html#TableBase.linearTransform">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.loadCSV">loadCSV() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadCSV">[1]</a>, <a href="moose_classes.html#TableBase.loadCSV">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#TableBase.loadXplot">loadXplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadXplot">[1]</a>, <a href="moose_classes.html#TableBase.loadXplot">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.loadXplotRange">loadXplotRange() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadXplotRange">[1]</a>, <a href="moose_classes.html#TableBase.loadXplotRange">[2]</a> - </dt> - - - <dt><a href="tmp.html#Long">Long (built-in class)</a>, <a href="moose_builtins.html#Long">[1]</a>, <a href="moose_classes.html#Long">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.lookup">lookup() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.lookup">[1]</a>, <a href="moose_classes.html#Interpol2D.lookup">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.lookupindex">lookupindex (VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.lookupindex">[1]</a>, <a href="moose_classes.html#VectorTable.lookupindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.lookupOut">lookupOut (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.lookupOut">[1]</a>, <a href="moose_classes.html#Interpol.lookupOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.lookupOut">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.lookupOut">[1]</a>, <a href="moose_classes.html#Interpol2D.lookupOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.lookupReturn2D">lookupReturn2D (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.lookupReturn2D">[1]</a>, <a href="moose_classes.html#Interpol2D.lookupReturn2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.lookupvalue">lookupvalue (VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.lookupvalue">[1]</a>, <a href="moose_classes.html#VectorTable.lookupvalue">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.loopTime">loopTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.loopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.loopTime">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="M">M</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#MarkovChannel">MarkovChannel (built-in class)</a>, <a href="moose_builtins.html#MarkovChannel">[1]</a>, <a href="moose_classes.html#MarkovChannel">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver">MarkovGslSolver (built-in class)</a>, <a href="moose_builtins.html#MarkovGslSolver">[1]</a>, <a href="moose_classes.html#MarkovGslSolver">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable">MarkovRateTable (built-in class)</a>, <a href="moose_builtins.html#MarkovRateTable">[1]</a>, <a href="moose_classes.html#MarkovRateTable">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolver">MarkovSolver (built-in class)</a>, <a href="moose_builtins.html#MarkovSolver">[1]</a>, <a href="moose_classes.html#MarkovSolver">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase">MarkovSolverBase (built-in class)</a>, <a href="moose_builtins.html#MarkovSolverBase">[1]</a>, <a href="moose_classes.html#MarkovSolverBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc">MathFunc (built-in class)</a>, <a href="moose_builtins.html#MathFunc">[1]</a>, <a href="moose_classes.html#MathFunc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.mathML">mathML (MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.mathML">[1]</a>, <a href="moose_classes.html#MathFunc.mathML">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.matrixEntry">matrixEntry (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.matrixEntry">[1]</a>, <a href="moose_classes.html#Stoich.matrixEntry">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.max">max (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.max">[1]</a>, <a href="moose_classes.html#HHGate.max">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.maxIter">maxIter (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.maxIter">[1]</a>, <a href="moose_classes.html#SteadyState.maxIter">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.me">me (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.me">[1]</a>, <a href="moose_classes.html#Neutral.me">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.mean">mean (Stats attribute)</a>, <a href="moose_builtins.html#Stats.mean">[1]</a>, <a href="moose_classes.html#Stats.mean">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.mesh">mesh (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.mesh">[1]</a>, <a href="moose_classes.html#MeshEntry.mesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry">MeshEntry (built-in class)</a>, <a href="moose_builtins.html#MeshEntry">[1]</a>, <a href="moose_classes.html#MeshEntry">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.meshToSpace">meshToSpace (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.meshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.meshToSpace">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.meshType">meshType (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.meshType">[1]</a>, <a href="moose_classes.html#MeshEntry.meshType">[2]</a> - </dt> - - - <dt><a href="tmp.html#method">method</a>, <a href="moose_builtins.html#method">[1]</a>, <a href="moose_classes.html#method">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.method">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.method">[1]</a>, <a href="moose_classes.html#Ksolve.method">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.method">(MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.method">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.method">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MgBlock">MgBlock (built-in class)</a>, <a href="moose_builtins.html#MgBlock">[1]</a>, <a href="moose_classes.html#MgBlock">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#HHGate.min">min (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.min">[1]</a>, <a href="moose_classes.html#HHGate.min">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.mInfinity">mInfinity (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.mInfinity">[1]</a>, <a href="moose_classes.html#HHGate.mInfinity">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.minusIn">minusIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.minusIn">[1]</a>, <a href="moose_classes.html#DiffAmp.minusIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#MMenz">MMenz (built-in class)</a>, <a href="moose_builtins.html#MMenz">[1]</a>, <a href="moose_classes.html#MMenz">[2]</a> - </dt> - - - <dt><a href="tmp.html#mmPump">mmPump()</a>, <a href="moose_builtins.html#mmPump">[1]</a>, <a href="moose_classes.html#mmPump">[2]</a> - </dt> - - - <dt><a href="tmp.html#mode">mode</a>, <a href="moose_builtins.html#mode">[1]</a>, <a href="moose_classes.html#mode">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.mode">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.mode">[1]</a>, <a href="moose_classes.html#VClamp.mode">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynChan.modulator">modulator() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.modulator">[1]</a>, <a href="moose_classes.html#SynChan.modulator">[2]</a> - </dt> - - - <dt><a href="tmp.html#Species.molWt">molWt (Species attribute)</a>, <a href="moose_builtins.html#Species.molWt">[1]</a>, <a href="moose_classes.html#Species.molWt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Species.molWtOut">molWtOut (Species attribute)</a>, <a href="moose_builtins.html#Species.molWtOut">[1]</a>, <a href="moose_classes.html#Species.molWtOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.motorConst">motorConst (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.motorConst">[1]</a>, <a href="moose_classes.html#PoolBase.motorConst">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell.move">move() (Shell method)</a>, <a href="moose_builtins.html#Shell.move">[1]</a>, <a href="moose_classes.html#Shell.move">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg">Msg (built-in class)</a>, <a href="moose_builtins.html#Msg">[1]</a>, <a href="moose_classes.html#Msg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.msgDestFunctions">msgDestFunctions (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgDestFunctions">[1]</a>, <a href="moose_classes.html#Neutral.msgDestFunctions">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.msgDests">msgDests (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgDests">[1]</a>, <a href="moose_classes.html#Neutral.msgDests">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.msgIn">msgIn (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgIn">[1]</a>, <a href="moose_classes.html#Neutral.msgIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.msgOut">msgOut (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgOut">[1]</a>, <a href="moose_classes.html#Neutral.msgOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Mstring">Mstring (built-in class)</a>, <a href="moose_builtins.html#Mstring">[1]</a>, <a href="moose_classes.html#Mstring">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.myNode">myNode (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.myNode">[1]</a>, <a href="moose_classes.html#PostMaster.myNode">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="N">N</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#PoolBase.n">n (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.n">[1]</a>, <a href="moose_classes.html#PoolBase.n">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.name">name (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.name">[1]</a>, <a href="moose_classes.html#Neutral.name">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.neighbors">neighbors (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.neighbors">[1]</a>, <a href="moose_classes.html#MeshEntry.neighbors">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.neighbors">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.neighbors">[1]</a>, <a href="moose_classes.html#Neutral.neighbors">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Nernst">Nernst (built-in class)</a>, <a href="moose_builtins.html#Nernst">[1]</a>, <a href="moose_classes.html#Nernst">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh">NeuroMesh (built-in class)</a>, <a href="moose_builtins.html#NeuroMesh">[1]</a>, <a href="moose_classes.html#NeuroMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neuron">Neuron (built-in class)</a>, <a href="moose_builtins.html#Neuron">[1]</a>, <a href="moose_classes.html#Neuron">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral">Neutral (built-in class)</a>, <a href="moose_builtins.html#Neutral">[1]</a>, <a href="moose_classes.html#Neutral">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.nInit">nInit (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.nInit">[1]</a>, <a href="moose_classes.html#PoolBase.nInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.nIter">nIter (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nIter">[1]</a>, <a href="moose_classes.html#SteadyState.nIter">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.nNegEigenvalues">nNegEigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nNegEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.nNegEigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.normalizeWeights">normalizeWeights (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.normalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.normalizeWeights">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.notes">notes (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.notes">[1]</a>, <a href="moose_classes.html#Annotator.notes">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.nOut">nOut (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.nOut">[1]</a>, <a href="moose_classes.html#PoolBase.nOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.nPosEigenvalues">nPosEigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nPosEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.nPosEigenvalues">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.nsteps">nsteps (Clock attribute)</a>, <a href="moose_builtins.html#Clock.nsteps">[1]</a>, <a href="moose_classes.html#Clock.nsteps">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.num">num (Stats attribute)</a>, <a href="moose_builtins.html#Stats.num">[1]</a>, <a href="moose_classes.html#Stats.num">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.numAllPools">numAllPools (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numAllPools">[1]</a>, <a href="moose_classes.html#Stoich.numAllPools">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.numAllVoxels">numAllVoxels (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.numAllVoxels">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.numAllVoxels">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.numAllVoxels">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.numAllVoxels">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.numAllVoxels">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SparseMsg.numColumns">numColumns (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numColumns">[1]</a>, <a href="moose_classes.html#SparseMsg.numColumns">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.numData">numData (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.numData">[1]</a>, <a href="moose_classes.html#Neutral.numData">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.numDiffCompts">numDiffCompts (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.numDiffCompts">[1]</a>, <a href="moose_classes.html#CylMesh.numDiffCompts">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#NeuroMesh.numDiffCompts">(NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.numDiffCompts">[1]</a>, <a href="moose_classes.html#NeuroMesh.numDiffCompts">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.numDimensions">numDimensions (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.numDimensions">[1]</a>, <a href="moose_classes.html#ChemCompt.numDimensions">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.numEntries">numEntries (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numEntries">[1]</a>, <a href="moose_classes.html#SparseMsg.numEntries">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Neutral.numField">numField (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.numField">[1]</a>, <a href="moose_classes.html#Neutral.numField">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.numKb">numKb (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numKb">[1]</a>, <a href="moose_classes.html#ReacBase.numKb">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.numKf">numKf (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numKf">[1]</a>, <a href="moose_classes.html#ReacBase.numKf">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.numKm">numKm (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.numKm">[1]</a>, <a href="moose_classes.html#EnzBase.numKm">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.numLocalVoxels">numLocalVoxels (Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numLocalVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.numLocalVoxels">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.numLocalVoxels">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numLocalVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.numLocalVoxels">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PostMaster.numNodes">numNodes (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.numNodes">[1]</a>, <a href="moose_classes.html#PostMaster.numNodes">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.numOpenStates">numOpenStates (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.numOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.numOpenStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.numPools">numPools (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numPools">[1]</a>, <a href="moose_classes.html#Dsolve.numPools">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.numPools">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numPools">[1]</a>, <a href="moose_classes.html#Gsolve.numPools">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.numPools">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numPools">[1]</a>, <a href="moose_classes.html#Ksolve.numPools">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ReacBase.numProducts">numProducts (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numProducts">[1]</a>, <a href="moose_classes.html#ReacBase.numProducts">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.numRates">numRates (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numRates">[1]</a>, <a href="moose_classes.html#Stoich.numRates">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.numRows">numRows (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numRows">[1]</a>, <a href="moose_classes.html#SparseMsg.numRows">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.numSegments">numSegments (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.numSegments">[1]</a>, <a href="moose_classes.html#NeuroMesh.numSegments">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.numStates">numStates (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.numStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.numStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.numSubstrates">numSubstrates (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.numSubstrates">[1]</a>, <a href="moose_classes.html#EnzBase.numSubstrates">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.numSubstrates">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numSubstrates">[1]</a>, <a href="moose_classes.html#ReacBase.numSubstrates">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynHandler.numSynapses">numSynapses (SynHandler attribute)</a>, <a href="moose_builtins.html#SynHandler.numSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.numSynapses">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.numTicks">numTicks (Clock attribute)</a>, <a href="moose_builtins.html#Clock.numTicks">[1]</a>, <a href="moose_classes.html#Clock.numTicks">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.numVarPools">numVarPools (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.numVarPools">[1]</a>, <a href="moose_classes.html#SteadyState.numVarPools">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.numVarPools">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numVarPools">[1]</a>, <a href="moose_classes.html#Stoich.numVarPools">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Dsolve.numVoxels">numVoxels (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.numVoxels">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.nVec">nVec (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.nVec">[1]</a>, <a href="moose_classes.html#Dsolve.nVec">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.nVec">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.nVec">[1]</a>, <a href="moose_classes.html#Gsolve.nVec">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.nVec">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.nVec">[1]</a>, <a href="moose_classes.html#Ksolve.nVec">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.nx">nx (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.nx">[1]</a>, <a href="moose_classes.html#CubeMesh.nx">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.ny">ny (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.ny">[1]</a>, <a href="moose_classes.html#CubeMesh.ny">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.nz">nz (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.nz">[1]</a>, <a href="moose_classes.html#CubeMesh.nz">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="O">O</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#OneToAllMsg">OneToAllMsg (built-in class)</a>, <a href="moose_builtins.html#OneToAllMsg">[1]</a>, <a href="moose_classes.html#OneToAllMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#OneToOneDataIndexMsg">OneToOneDataIndexMsg (built-in class)</a>, <a href="moose_builtins.html#OneToOneDataIndexMsg">[1]</a>, <a href="moose_classes.html#OneToOneDataIndexMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#OneToOneMsg">OneToOneMsg (built-in class)</a>, <a href="moose_builtins.html#OneToOneMsg">[1]</a>, <a href="moose_classes.html#OneToOneMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.oneVoxelVolume">oneVoxelVolume (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.oneVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.oneVoxelVolume">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.origChannel">origChannel() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.origChannel">[1]</a>, <a href="moose_classes.html#MgBlock.origChannel">[2]</a> - </dt> - - - <dt><a href="tmp.html#outerArea">outerArea</a>, <a href="moose_builtins.html#outerArea">[1]</a>, <a href="moose_classes.html#outerArea">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#outerDif">outerDif</a>, <a href="moose_builtins.html#outerDif">[1]</a>, <a href="moose_classes.html#outerDif">[2]</a> - </dt> - - - <dt><a href="tmp.html#outerDifSourceOut">outerDifSourceOut</a>, <a href="moose_builtins.html#outerDifSourceOut">[1]</a>, <a href="moose_classes.html#outerDifSourceOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#outflux">outflux()</a>, <a href="moose_builtins.html#outflux">[1]</a>, <a href="moose_classes.html#outflux">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.output">output (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.output">[1]</a>, <a href="moose_classes.html#Adaptor.output">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Arith.output">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.output">[1]</a>, <a href="moose_classes.html#Arith.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.output">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.output">[1]</a>, <a href="moose_classes.html#DiffAmp.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.output">(FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.output">[1]</a>, <a href="moose_classes.html#FuncBase.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.output">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.output">[1]</a>, <a href="moose_classes.html#MathFunc.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.output">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.output">[1]</a>, <a href="moose_classes.html#PIDController.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.output">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.output">[1]</a>, <a href="moose_classes.html#PulseGen.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.output">(RC attribute)</a>, <a href="moose_builtins.html#RC.output">[1]</a>, <a href="moose_classes.html#RC.output">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.output">(StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.output">[1]</a>, <a href="moose_classes.html#StimulusTable.output">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Adaptor.outputOffset">outputOffset (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.outputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.outputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.outputValue">outputValue (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.outputValue">[1]</a>, <a href="moose_classes.html#Adaptor.outputValue">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Arith.outputValue">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.outputValue">[1]</a>, <a href="moose_classes.html#Arith.outputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.outputValue">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.outputValue">[1]</a>, <a href="moose_classes.html#DiffAmp.outputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.outputValue">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.outputValue">[1]</a>, <a href="moose_classes.html#PIDController.outputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.outputValue">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.outputValue">[1]</a>, <a href="moose_classes.html#PulseGen.outputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.outputValue">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.outputValue">[1]</a>, <a href="moose_classes.html#TableBase.outputValue">[2]</a> - </dt> - - </dl></dd> - </dl></td> -</tr></table> - -<h2 id="P">P</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#SparseMsg.pairFill">pairFill() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.pairFill">[1]</a>, <a href="moose_classes.html#SparseMsg.pairFill">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.parent">parent (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.parent">[1]</a>, <a href="moose_classes.html#Neutral.parent">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.parentMsg">parentMsg() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.parentMsg">[1]</a>, <a href="moose_classes.html#Neutral.parentMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.parentVoxel">parentVoxel (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.parentVoxel">[1]</a>, <a href="moose_classes.html#NeuroMesh.parentVoxel">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SpineMesh.parentVoxel">(SpineMesh attribute)</a>, <a href="moose_builtins.html#SpineMesh.parentVoxel">[1]</a>, <a href="moose_classes.html#SpineMesh.parentVoxel">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Dsolve.path">path (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.path">[1]</a>, <a href="moose_classes.html#Dsolve.path">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.path">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.path">[1]</a>, <a href="moose_classes.html#Neutral.path">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.path">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.path">[1]</a>, <a href="moose_classes.html#Stoich.path">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChanBase.permeabilityOut">permeabilityOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.permeabilityOut">[1]</a>, <a href="moose_classes.html#ChanBase.permeabilityOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.permeabilityOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.permeabilityOut">[1]</a>, <a href="moose_classes.html#SynChanBase.permeabilityOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController">PIDController (built-in class)</a>, <a href="moose_builtins.html#PIDController">[1]</a>, <a href="moose_classes.html#PIDController">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.plainPlot">plainPlot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.plainPlot">[1]</a>, <a href="moose_classes.html#TableBase.plainPlot">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.plusIn">plusIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.plusIn">[1]</a>, <a href="moose_classes.html#DiffAmp.plusIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#Pool">Pool (built-in class)</a>, <a href="moose_builtins.html#Pool">[1]</a>, <a href="moose_classes.html#Pool">[2]</a> - </dt> - - - <dt><a href="tmp.html#Species.pool">pool (Species attribute)</a>, <a href="moose_builtins.html#Species.pool">[1]</a>, <a href="moose_classes.html#Species.pool">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase">PoolBase (built-in class)</a>, <a href="moose_builtins.html#PoolBase">[1]</a>, <a href="moose_classes.html#PoolBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.poolIdMap">poolIdMap (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.poolIdMap">[1]</a>, <a href="moose_classes.html#Stoich.poolIdMap">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster">PostMaster (built-in class)</a>, <a href="moose_builtins.html#PostMaster">[1]</a>, <a href="moose_classes.html#PostMaster">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.prd">prd (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.prd">[1]</a>, <a href="moose_classes.html#EnzBase.prd">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.prd">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.prd">[1]</a>, <a href="moose_classes.html#ReacBase.prd">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#EnzBase.prdDest">prdDest() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.prdDest">[1]</a>, <a href="moose_classes.html#EnzBase.prdDest">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.prdDest">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.prdDest">[1]</a>, <a href="moose_classes.html#ReacBase.prdDest">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#EnzBase.prdOut">prdOut (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.prdOut">[1]</a>, <a href="moose_classes.html#EnzBase.prdOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.prdOut">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.prdOut">[1]</a>, <a href="moose_classes.html#ReacBase.prdOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.preserveNumEntries">preserveNumEntries (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.preserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.preserveNumEntries">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.probability">probability (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.probability">[1]</a>, <a href="moose_classes.html#SparseMsg.probability">[2]</a> - </dt> - - - <dt><a href="tmp.html#proc">proc</a>, <a href="moose_builtins.html#proc">[1]</a>, <a href="moose_classes.html#proc">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Adaptor.proc">(Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.proc">[1]</a>, <a href="moose_classes.html#Adaptor.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.proc">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.proc">[1]</a>, <a href="moose_classes.html#Arith.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#BufPool.proc">(BufPool attribute)</a>, <a href="moose_builtins.html#BufPool.proc">[1]</a>, <a href="moose_classes.html#BufPool.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.proc">(CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.proc">[1]</a>, <a href="moose_classes.html#CaConc.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.proc">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.proc">[1]</a>, <a href="moose_classes.html#CompartmentBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.proc">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.proc">[1]</a>, <a href="moose_classes.html#DiffAmp.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.proc">(Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.proc">[1]</a>, <a href="moose_classes.html#Dsolve.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.proc">(EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.proc">[1]</a>, <a href="moose_classes.html#EnzBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.proc">(Func attribute)</a>, <a href="moose_builtins.html#Func.proc">[1]</a>, <a href="moose_classes.html#Func.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.proc">(FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.proc">[1]</a>, <a href="moose_classes.html#FuncBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.proc">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.proc">[1]</a>, <a href="moose_classes.html#Gsolve.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.proc">(HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.proc">[1]</a>, <a href="moose_classes.html#HHChannel.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.proc">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.proc">[1]</a>, <a href="moose_classes.html#HHChannel2D.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.proc">(HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.proc">[1]</a>, <a href="moose_classes.html#HSolve.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.proc">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.proc">[1]</a>, <a href="moose_classes.html#IntFire.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.proc">(Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.proc">[1]</a>, <a href="moose_classes.html#Interpol.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.proc">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.proc">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.proc">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.proc">[1]</a>, <a href="moose_classes.html#Ksolve.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Leakage.proc">(Leakage attribute)</a>, <a href="moose_builtins.html#Leakage.proc">[1]</a>, <a href="moose_classes.html#Leakage.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.proc">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.proc">[1]</a>, <a href="moose_classes.html#MarkovChannel.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.proc">(MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.proc">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.proc">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.proc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolver.proc">(MarkovSolver attribute)</a>, <a href="moose_builtins.html#MarkovSolver.proc">[1]</a>, <a href="moose_classes.html#MarkovSolver.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.proc">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.proc">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.proc">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.proc">[1]</a>, <a href="moose_classes.html#MathFunc.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.proc">(MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.proc">[1]</a>, <a href="moose_classes.html#MeshEntry.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.proc">(MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.proc">[1]</a>, <a href="moose_classes.html#MgBlock.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.proc">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.proc">[1]</a>, <a href="moose_classes.html#PIDController.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.proc">(PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.proc">[1]</a>, <a href="moose_classes.html#PoolBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.proc">(PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.proc">[1]</a>, <a href="moose_classes.html#PostMaster.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.proc">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.proc">[1]</a>, <a href="moose_classes.html#PulseGen.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.proc">(RC attribute)</a>, <a href="moose_builtins.html#RC.proc">[1]</a>, <a href="moose_classes.html#RC.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.proc">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.proc">[1]</a>, <a href="moose_classes.html#ReacBase.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.proc">(SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.proc">[1]</a>, <a href="moose_classes.html#SpikeGen.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.proc">(Stats attribute)</a>, <a href="moose_builtins.html#Stats.proc">[1]</a>, <a href="moose_classes.html#Stats.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.proc">(StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.proc">[1]</a>, <a href="moose_classes.html#StimulusTable.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.proc">(SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.proc">[1]</a>, <a href="moose_classes.html#SynChan.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.proc">(Table attribute)</a>, <a href="moose_builtins.html#Table.proc">[1]</a>, <a href="moose_classes.html#Table.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.proc">(TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.proc">[1]</a>, <a href="moose_classes.html#TimeTable.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.proc">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.proc">[1]</a>, <a href="moose_classes.html#VClamp.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.proc">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.proc">[1]</a>, <a href="moose_classes.html#ZombieCaConc.proc">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.proc">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.proc">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.proc">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.proc0">proc0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc0">[1]</a>, <a href="moose_classes.html#Clock.proc0">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc1">proc1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc1">[1]</a>, <a href="moose_classes.html#Clock.proc1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc2">proc2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc2">[1]</a>, <a href="moose_classes.html#Clock.proc2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc3">proc3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc3">[1]</a>, <a href="moose_classes.html#Clock.proc3">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc4">proc4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc4">[1]</a>, <a href="moose_classes.html#Clock.proc4">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Clock.proc5">proc5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc5">[1]</a>, <a href="moose_classes.html#Clock.proc5">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc6">proc6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc6">[1]</a>, <a href="moose_classes.html#Clock.proc6">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc7">proc7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc7">[1]</a>, <a href="moose_classes.html#Clock.proc7">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc8">proc8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc8">[1]</a>, <a href="moose_classes.html#Clock.proc8">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.proc9">proc9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc9">[1]</a>, <a href="moose_classes.html#Clock.proc9">[2]</a> - </dt> - - - <dt><a href="tmp.html#process">process()</a>, <a href="tmp.html#process">[1]</a>, <a href="tmp.html#process">[2]</a>, <a href="tmp.html#process">[3]</a>, <a href="tmp.html#process">[4]</a>, <a href="moose_builtins.html#process">[5]</a>, <a href="moose_builtins.html#process">[6]</a>, <a href="moose_builtins.html#process">[7]</a>, <a href="moose_builtins.html#process">[8]</a>, <a href="moose_builtins.html#process">[9]</a>, <a href="moose_classes.html#process">[10]</a>, <a href="moose_classes.html#process">[11]</a>, <a href="moose_classes.html#process">[12]</a>, <a href="moose_classes.html#process">[13]</a>, <a href="moose_classes.html#process">[14]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Adaptor.process">(Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.process">[1]</a>, <a href="moose_classes.html#Adaptor.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.process">(Arith method)</a>, <a href="moose_builtins.html#Arith.process">[1]</a>, <a href="moose_classes.html#Arith.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#BufPool.process">(BufPool method)</a>, <a href="moose_builtins.html#BufPool.process">[1]</a>, <a href="moose_classes.html#BufPool.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.process">(CaConc method)</a>, <a href="moose_builtins.html#CaConc.process">[1]</a>, <a href="moose_classes.html#CaConc.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.process">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.process">[1]</a>, <a href="moose_classes.html#CompartmentBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.process">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.process">[1]</a>, <a href="moose_classes.html#DiffAmp.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.process">(Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.process">[1]</a>, <a href="moose_classes.html#Dsolve.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.process">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.process">[1]</a>, <a href="moose_classes.html#EnzBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.process">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.process">[1]</a>, <a href="moose_classes.html#FuncBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.process">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.process">[1]</a>, <a href="moose_classes.html#Gsolve.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.process">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.process">[1]</a>, <a href="moose_classes.html#HHChannel.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.process">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.process">[1]</a>, <a href="moose_classes.html#HHChannel2D.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.process">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.process">[1]</a>, <a href="moose_classes.html#HSolve.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.process">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.process">[1]</a>, <a href="moose_classes.html#IntFire.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.process">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.process">[1]</a>, <a href="moose_classes.html#Interpol.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.process">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.process">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.process">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.process">[1]</a>, <a href="moose_classes.html#Ksolve.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.process">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.process">[1]</a>, <a href="moose_classes.html#MarkovChannel.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.process">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.process">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.process">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.process">[1]</a>, <a href="moose_classes.html#MarkovRateTable.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolver.process">(MarkovSolver method)</a>, <a href="moose_builtins.html#MarkovSolver.process">[1]</a>, <a href="moose_classes.html#MarkovSolver.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.process">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.process">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.process">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.process">[1]</a>, <a href="moose_classes.html#MathFunc.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.process">(MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.process">[1]</a>, <a href="moose_classes.html#MeshEntry.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.process">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.process">[1]</a>, <a href="moose_classes.html#MgBlock.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.process">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.process">[1]</a>, <a href="moose_classes.html#PIDController.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.process">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.process">[1]</a>, <a href="moose_classes.html#PoolBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.process">(PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.process">[1]</a>, <a href="moose_classes.html#PostMaster.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.process">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.process">[1]</a>, <a href="moose_classes.html#PulseGen.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.process">(RC method)</a>, <a href="moose_builtins.html#RC.process">[1]</a>, <a href="moose_classes.html#RC.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.process">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.process">[1]</a>, <a href="moose_classes.html#ReacBase.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.process">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.process">[1]</a>, <a href="moose_classes.html#SpikeGen.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.process">(Stats method)</a>, <a href="tmp.html#Stats.process">[1]</a>, <a href="moose_builtins.html#Stats.process">[2]</a>, <a href="moose_builtins.html#Stats.process">[3]</a>, <a href="moose_classes.html#Stats.process">[4]</a>, <a href="moose_classes.html#Stats.process">[5]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.process">(StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.process">[1]</a>, <a href="moose_classes.html#StimulusTable.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.process">(SynChan method)</a>, <a href="moose_builtins.html#SynChan.process">[1]</a>, <a href="moose_classes.html#SynChan.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.process">(Table method)</a>, <a href="moose_builtins.html#Table.process">[1]</a>, <a href="moose_classes.html#Table.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.process">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.process">[1]</a>, <a href="moose_classes.html#TimeTable.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.process">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.process">[1]</a>, <a href="moose_classes.html#VClamp.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.process">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.process">[1]</a>, <a href="moose_classes.html#ZombieCaConc.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.process">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.process">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.process">[2]</a> - </dt> - - - <dt><a href="tmp.html#testSched.process">(testSched method)</a>, <a href="moose_builtins.html#testSched.process">[1]</a>, <a href="moose_classes.html#testSched.process">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.process0">process0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process0">[1]</a>, <a href="moose_classes.html#Clock.process0">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process1">process1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process1">[1]</a>, <a href="moose_classes.html#Clock.process1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process2">process2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process2">[1]</a>, <a href="moose_classes.html#Clock.process2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process3">process3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process3">[1]</a>, <a href="moose_classes.html#Clock.process3">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process4">process4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process4">[1]</a>, <a href="moose_classes.html#Clock.process4">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process5">process5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process5">[1]</a>, <a href="moose_classes.html#Clock.process5">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process6">process6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process6">[1]</a>, <a href="moose_classes.html#Clock.process6">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process7">process7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process7">[1]</a>, <a href="moose_classes.html#Clock.process7">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process8">process8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process8">[1]</a>, <a href="moose_classes.html#Clock.process8">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.process9">process9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process9">[1]</a>, <a href="moose_classes.html#Clock.process9">[2]</a> - </dt> - - - <dt><a href="tmp.html#DifShell.process_0">process_0 (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.process_0">[1]</a>, <a href="moose_classes.html#DifShell.process_0">[2]</a> - </dt> - - - <dt><a href="tmp.html#DifShell.process_1">process_1 (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.process_1">[1]</a>, <a href="moose_classes.html#DifShell.process_1">[2]</a> - </dt> - - - <dt><a href="tmp.html#SymCompartment.proximal">proximal (SymCompartment attribute)</a>, <a href="moose_builtins.html#SymCompartment.proximal">[1]</a>, <a href="moose_classes.html#SymCompartment.proximal">[2]</a> - </dt> - - - <dt><a href="tmp.html#proximalOnly">proximalOnly</a>, <a href="moose_builtins.html#proximalOnly">[1]</a>, <a href="moose_classes.html#proximalOnly">[2]</a> - </dt> - - - <dt><a href="tmp.html#proximalOut">proximalOut</a>, <a href="tmp.html#proximalOut">[1]</a>, <a href="moose_builtins.html#proximalOut">[2]</a>, <a href="moose_builtins.html#proximalOut">[3]</a>, <a href="moose_classes.html#proximalOut">[4]</a>, <a href="moose_classes.html#proximalOut">[5]</a> - </dt> - - - <dt><a href="tmp.html#PsdMesh.psdList">psdList() (PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.psdList">[1]</a>, <a href="moose_classes.html#PsdMesh.psdList">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.psdListOut">psdListOut (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.psdListOut">[1]</a>, <a href="moose_classes.html#NeuroMesh.psdListOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#PsdMesh">PsdMesh (built-in class)</a>, <a href="moose_builtins.html#PsdMesh">[1]</a>, <a href="moose_classes.html#PsdMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen">PulseGen (built-in class)</a>, <a href="moose_builtins.html#PulseGen">[1]</a>, <a href="moose_classes.html#PulseGen">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="Q">Q</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#MarkovRateTable.Q">Q (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.Q">[1]</a>, <a href="moose_classes.html#MarkovRateTable.Q">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.Q">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.Q">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.Q">[2]</a> - </dt> - - </dl></dd> - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Shell.quit">quit() (Shell method)</a>, <a href="moose_builtins.html#Shell.quit">[1]</a>, <a href="moose_classes.html#Shell.quit">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="R">R</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#RC.R">R (RC attribute)</a>, <a href="moose_builtins.html#RC.R">[1]</a>, <a href="moose_classes.html#RC.R">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.r0">r0 (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.r0">[1]</a>, <a href="moose_classes.html#CylMesh.r0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.r1">r1 (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.r1">[1]</a>, <a href="moose_classes.html#CylMesh.r1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.Ra">Ra (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Ra">[1]</a>, <a href="moose_classes.html#CompartmentBase.Ra">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.randInject">randInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.randInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.randInject">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.randomInit">randomInit() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.randomInit">[1]</a>, <a href="moose_classes.html#SteadyState.randomInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.rank">rank (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.rank">[1]</a>, <a href="moose_classes.html#SteadyState.rank">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.ratio">ratio (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.ratio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.ratio">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.raxial">raxial (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.raxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.raxial">[2]</a> - </dt> - - - <dt><a href="tmp.html#raxialCylinder">raxialCylinder()</a>, <a href="moose_builtins.html#raxialCylinder">[1]</a>, <a href="moose_classes.html#raxialCylinder">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.raxialOut">raxialOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.raxialOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.raxialOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#raxialSphere">raxialSphere()</a>, <a href="tmp.html#raxialSphere">[1]</a>, <a href="moose_builtins.html#raxialSphere">[2]</a>, <a href="moose_builtins.html#raxialSphere">[3]</a>, <a href="moose_classes.html#raxialSphere">[4]</a>, <a href="moose_classes.html#raxialSphere">[5]</a> - </dt> - - - <dt><a href="tmp.html#raxialSym">raxialSym()</a>, <a href="tmp.html#raxialSym">[1]</a>, <a href="tmp.html#raxialSym">[2]</a>, <a href="moose_builtins.html#raxialSym">[3]</a>, <a href="moose_builtins.html#raxialSym">[4]</a>, <a href="moose_builtins.html#raxialSym">[5]</a>, <a href="moose_classes.html#raxialSym">[6]</a>, <a href="moose_classes.html#raxialSym">[7]</a>, <a href="moose_classes.html#raxialSym">[8]</a> - </dt> - - - <dt><a href="tmp.html#RC">RC (built-in class)</a>, <a href="moose_builtins.html#RC">[1]</a>, <a href="moose_classes.html#RC">[2]</a> - </dt> - - - <dt><a href="tmp.html#Reac">Reac (built-in class)</a>, <a href="moose_builtins.html#Reac">[1]</a>, <a href="moose_classes.html#Reac">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.reac">reac (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.reac">[1]</a>, <a href="moose_classes.html#PoolBase.reac">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase">ReacBase (built-in class)</a>, <a href="moose_builtins.html#ReacBase">[1]</a>, <a href="moose_classes.html#ReacBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.reacDest">reacDest() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.reacDest">[1]</a>, <a href="moose_classes.html#PoolBase.reacDest">[2]</a> - </dt> - - - <dt><a href="tmp.html#reaction">reaction()</a>, <a href="moose_builtins.html#reaction">[1]</a>, <a href="moose_classes.html#reaction">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.refractoryPeriod">refractoryPeriod (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.refractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.refractoryPeriod">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.refractT">refractT (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.refractT">[1]</a>, <a href="moose_classes.html#SpikeGen.refractT">[2]</a> - </dt> - - - <dt><a href="tmp.html#reinit">reinit()</a>, <a href="tmp.html#reinit">[1]</a>, <a href="tmp.html#reinit">[2]</a>, <a href="tmp.html#reinit">[3]</a>, <a href="tmp.html#reinit">[4]</a>, <a href="moose_builtins.html#reinit">[5]</a>, <a href="moose_builtins.html#reinit">[6]</a>, <a href="moose_builtins.html#reinit">[7]</a>, <a href="moose_builtins.html#reinit">[8]</a>, <a href="moose_builtins.html#reinit">[9]</a>, <a href="moose_classes.html#reinit">[10]</a>, <a href="moose_classes.html#reinit">[11]</a>, <a href="moose_classes.html#reinit">[12]</a>, <a href="moose_classes.html#reinit">[13]</a>, <a href="moose_classes.html#reinit">[14]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Adaptor.reinit">(Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.reinit">[1]</a>, <a href="moose_classes.html#Adaptor.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.reinit">(Arith method)</a>, <a href="moose_builtins.html#Arith.reinit">[1]</a>, <a href="moose_classes.html#Arith.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#BufPool.reinit">(BufPool method)</a>, <a href="moose_builtins.html#BufPool.reinit">[1]</a>, <a href="moose_classes.html#BufPool.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.reinit">(CaConc method)</a>, <a href="moose_builtins.html#CaConc.reinit">[1]</a>, <a href="moose_classes.html#CaConc.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit">(Clock method)</a>, <a href="moose_builtins.html#Clock.reinit">[1]</a>, <a href="moose_classes.html#Clock.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.reinit">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.reinit">[1]</a>, <a href="moose_classes.html#CompartmentBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.reinit">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.reinit">[1]</a>, <a href="moose_classes.html#DiffAmp.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.reinit">(Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.reinit">[1]</a>, <a href="moose_classes.html#Dsolve.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.reinit">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.reinit">[1]</a>, <a href="moose_classes.html#EnzBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.reinit">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.reinit">[1]</a>, <a href="moose_classes.html#FuncBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.reinit">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.reinit">[1]</a>, <a href="moose_classes.html#Gsolve.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.reinit">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.reinit">[1]</a>, <a href="moose_classes.html#HHChannel.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.reinit">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.reinit">[1]</a>, <a href="moose_classes.html#HHChannel2D.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.reinit">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.reinit">[1]</a>, <a href="moose_classes.html#HSolve.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.reinit">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.reinit">[1]</a>, <a href="moose_classes.html#IntFire.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.reinit">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.reinit">[1]</a>, <a href="moose_classes.html#Interpol.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.reinit">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.reinit">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.reinit">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.reinit">[1]</a>, <a href="moose_classes.html#Ksolve.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.reinit">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.reinit">[1]</a>, <a href="moose_classes.html#MarkovChannel.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.reinit">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.reinit">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.reinit">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.reinit">[1]</a>, <a href="moose_classes.html#MarkovRateTable.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolver.reinit">(MarkovSolver method)</a>, <a href="moose_builtins.html#MarkovSolver.reinit">[1]</a>, <a href="moose_classes.html#MarkovSolver.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.reinit">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.reinit">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.reinit">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.reinit">[1]</a>, <a href="moose_classes.html#MathFunc.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.reinit">(MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.reinit">[1]</a>, <a href="moose_classes.html#MeshEntry.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.reinit">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.reinit">[1]</a>, <a href="moose_classes.html#MgBlock.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.reinit">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.reinit">[1]</a>, <a href="moose_classes.html#PIDController.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.reinit">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.reinit">[1]</a>, <a href="moose_classes.html#PoolBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#PostMaster.reinit">(PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.reinit">[1]</a>, <a href="moose_classes.html#PostMaster.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.reinit">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.reinit">[1]</a>, <a href="moose_classes.html#PulseGen.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.reinit">(RC method)</a>, <a href="moose_builtins.html#RC.reinit">[1]</a>, <a href="moose_classes.html#RC.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.reinit">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.reinit">[1]</a>, <a href="moose_classes.html#ReacBase.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.reinit">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.reinit">[1]</a>, <a href="moose_classes.html#SpikeGen.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.reinit">(Stats method)</a>, <a href="tmp.html#Stats.reinit">[1]</a>, <a href="moose_builtins.html#Stats.reinit">[2]</a>, <a href="moose_builtins.html#Stats.reinit">[3]</a>, <a href="moose_classes.html#Stats.reinit">[4]</a>, <a href="moose_classes.html#Stats.reinit">[5]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.reinit">(StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.reinit">[1]</a>, <a href="moose_classes.html#StimulusTable.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.reinit">(SynChan method)</a>, <a href="moose_builtins.html#SynChan.reinit">[1]</a>, <a href="moose_classes.html#SynChan.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.reinit">(Table method)</a>, <a href="moose_builtins.html#Table.reinit">[1]</a>, <a href="moose_classes.html#Table.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.reinit">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.reinit">[1]</a>, <a href="moose_classes.html#TimeTable.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.reinit">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.reinit">[1]</a>, <a href="moose_classes.html#VClamp.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.reinit">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.reinit">[1]</a>, <a href="moose_classes.html#ZombieCaConc.reinit">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.reinit">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.reinit">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.reinit">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.reinit0">reinit0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit0">[1]</a>, <a href="moose_classes.html#Clock.reinit0">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit1">reinit1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit1">[1]</a>, <a href="moose_classes.html#Clock.reinit1">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Clock.reinit2">reinit2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit2">[1]</a>, <a href="moose_classes.html#Clock.reinit2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit3">reinit3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit3">[1]</a>, <a href="moose_classes.html#Clock.reinit3">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit4">reinit4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit4">[1]</a>, <a href="moose_classes.html#Clock.reinit4">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit5">reinit5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit5">[1]</a>, <a href="moose_classes.html#Clock.reinit5">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit6">reinit6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit6">[1]</a>, <a href="moose_classes.html#Clock.reinit6">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit7">reinit7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit7">[1]</a>, <a href="moose_classes.html#Clock.reinit7">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit8">reinit8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit8">[1]</a>, <a href="moose_classes.html#Clock.reinit8">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.reinit9">reinit9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit9">[1]</a>, <a href="moose_classes.html#Clock.reinit9">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.relativeAccuracy">relativeAccuracy (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.relativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.relativeAccuracy">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.remesh">remesh() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.remesh">[1]</a>, <a href="moose_classes.html#EnzBase.remesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.remeshOut">remeshOut (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.remeshOut">[1]</a>, <a href="moose_classes.html#MeshEntry.remeshOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.remeshReacsOut">remeshReacsOut (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.remeshReacsOut">[1]</a>, <a href="moose_classes.html#MeshEntry.remeshReacsOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.requestField">requestField (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.requestField">[1]</a>, <a href="moose_classes.html#Adaptor.requestField">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.requestInput">requestInput (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.requestInput">[1]</a>, <a href="moose_classes.html#Adaptor.requestInput">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.requestMolWt">requestMolWt (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.requestMolWt">[1]</a>, <a href="moose_classes.html#PoolBase.requestMolWt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.requestOut">requestOut (Table attribute)</a>, <a href="moose_builtins.html#Table.requestOut">[1]</a>, <a href="moose_classes.html#Table.requestOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.resetStencil">resetStencil() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.resetStencil">[1]</a>, <a href="moose_classes.html#ChemCompt.resetStencil">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.resettle">resettle() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.resettle">[1]</a>, <a href="moose_classes.html#SteadyState.resettle">[2]</a> - </dt> - - - <dt><a href="tmp.html#FuncBase.result">result (FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.result">[1]</a>, <a href="moose_classes.html#FuncBase.result">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.result">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.result">[1]</a>, <a href="moose_classes.html#MathFunc.result">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.Rm">Rm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Rm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Rm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.RmByTau">RmByTau (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.RmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.RmByTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.rowStart">rowStart (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.rowStart">[1]</a>, <a href="moose_classes.html#Stoich.rowStart">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.runTime">runTime (Clock attribute)</a>, <a href="moose_builtins.html#Clock.runTime">[1]</a>, <a href="moose_classes.html#Clock.runTime">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="S">S</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#DiffAmp.saturation">saturation (DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.saturation">[1]</a>, <a href="moose_classes.html#DiffAmp.saturation">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.saturation">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.saturation">[1]</a>, <a href="moose_classes.html#PIDController.saturation">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Adaptor.scale">scale (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.scale">[1]</a>, <a href="moose_classes.html#Adaptor.scale">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.scale">(Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.scale">[1]</a>, <a href="moose_classes.html#Nernst.scale">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Stats.sdev">sdev (Stats attribute)</a>, <a href="moose_builtins.html#Stats.sdev">[1]</a>, <a href="moose_classes.html#Stats.sdev">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.secondDelay">secondDelay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.secondDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.secondLevel">secondLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.secondLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.secondWidth">secondWidth (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.secondWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.seed">seed (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.seed">[1]</a>, <a href="moose_classes.html#HSolve.seed">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SparseMsg.seed">(SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.seed">[1]</a>, <a href="moose_classes.html#SparseMsg.seed">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.sensed">sensed (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.sensed">[1]</a>, <a href="moose_classes.html#PIDController.sensed">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.sensed">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.sensed">[1]</a>, <a href="moose_classes.html#VClamp.sensed">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PIDController.sensedIn">sensedIn() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.sensedIn">[1]</a>, <a href="moose_classes.html#PIDController.sensedIn">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.sensedIn">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.sensedIn">[1]</a>, <a href="moose_classes.html#VClamp.sensedIn">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.separateSpines">separateSpines (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.separateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.separateSpines">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.set1d">set1d() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.set1d">[1]</a>, <a href="moose_classes.html#MarkovRateTable.set1d">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.set2d">set2d() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.set2d">[1]</a>, <a href="moose_classes.html#MarkovRateTable.set2d">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setA">setA() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setA">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setA">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.setAbs_refract">setAbs_refract() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setAbs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.setAbs_refract">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.setAbsoluteAccuracy">setAbsoluteAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setAbsoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setAbsoluteAccuracy">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setAccommodating">setAccommodating() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setAccommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setAccommodating">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setAlpha">setAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setAlpha">[1]</a>, <a href="moose_classes.html#HHGate.setAlpha">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setAlpha">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setAlpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setAlpha">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setAlphaParms">setAlphaParms() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setAlphaParms">[1]</a>, <a href="moose_classes.html#HHGate.setAlphaParms">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setAlwaysDiffuse">setAlwaysDiffuse() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setAlwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.setAlwaysDiffuse">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.setAnyValue">setAnyValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.setAnyValue">[1]</a>, <a href="moose_classes.html#Arith.setAnyValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setB">setB() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setB">[1]</a>, <a href="moose_classes.html#CaConc.setB">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setB">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setB">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setB">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.setB">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setB">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setB">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.setBaseLevel">setBaseLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setBaseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setBaseLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setBeta">setBeta() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setBeta">[1]</a>, <a href="moose_classes.html#HHGate.setBeta">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setBeta">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setBeta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setBeta">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PostMaster.setBufferSize">setBufferSize() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.setBufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.setBufferSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.setBufferTime">setBufferTime() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setBufferTime">[1]</a>, <a href="moose_classes.html#IntFire.setBufferTime">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.setBufferTime">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setBufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.setBufferTime">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.setC">setC() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setC">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setC">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#RC.setC">(RC method)</a>, <a href="moose_builtins.html#RC.setC">[1]</a>, <a href="moose_classes.html#RC.setC">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.setCa">setCa() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCa">[1]</a>, <a href="moose_classes.html#CaConc.setCa">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setCa">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCa">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCa">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CaConc.setCa_base">setCa_base() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCa_base">[1]</a>, <a href="moose_classes.html#CaConc.setCa_base">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setCa_base">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCa_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCa_base">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.setCaAdvance">setCaAdvance() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaAdvance">[1]</a>, <a href="moose_classes.html#HSolve.setCaAdvance">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setCaBasal">setCaBasal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCaBasal">[1]</a>, <a href="moose_classes.html#CaConc.setCaBasal">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setCaBasal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCaBasal">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.setCaDiv">setCaDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaDiv">[1]</a>, <a href="moose_classes.html#HSolve.setCaDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setCaMax">setCaMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaMax">[1]</a>, <a href="moose_classes.html#HSolve.setCaMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setCaMin">setCaMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaMin">[1]</a>, <a href="moose_classes.html#HSolve.setCaMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setCeiling">setCeiling() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCeiling">[1]</a>, <a href="moose_classes.html#CaConc.setCeiling">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setCeiling">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCeiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCeiling">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.setCell">setCell() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setCell">[1]</a>, <a href="moose_classes.html#NeuroMesh.setCell">[2]</a> - </dt> - - - <dt><a href="tmp.html#setCeq">setCeq()</a>, <a href="moose_builtins.html#setCeq">[1]</a>, <a href="moose_classes.html#setCeq">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.setCin">setCin() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setCin">[1]</a>, <a href="moose_classes.html#Nernst.setCin">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell.setclock">setclock() (Shell method)</a>, <a href="moose_builtins.html#Shell.setclock">[1]</a>, <a href="moose_classes.html#Shell.setclock">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.setCm">setCm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setCm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setCm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.setCMg">setCMg() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setCMg">[1]</a>, <a href="moose_classes.html#MgBlock.setCMg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.setColor">setColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setColor">[1]</a>, <a href="moose_classes.html#Annotator.setColor">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.setCommand">setCommand() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setCommand">[1]</a>, <a href="moose_classes.html#PIDController.setCommand">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.setCompartment">setCompartment() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setCompartment">[1]</a>, <a href="moose_classes.html#Dsolve.setCompartment">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.setCompartment">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setCompartment">[1]</a>, <a href="moose_classes.html#Ksolve.setCompartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.setCompartment">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setCompartment">[1]</a>, <a href="moose_classes.html#Stoich.setCompartment">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.setConc">setConc() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setConc">[1]</a>, <a href="moose_classes.html#PoolBase.setConc">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setConcInit">setConcInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setConcInit">[1]</a>, <a href="moose_classes.html#PoolBase.setConcInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.setConcK1">setConcK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setConcK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setConcK1">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.setconst">setconst() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setconst">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setconst">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.setConvergenceCriterion">setConvergenceCriterion() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setConvergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.setConvergenceCriterion">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setCoords">setCoords() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setCoords">[1]</a>, <a href="moose_classes.html#CubeMesh.setCoords">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.setCoords">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setCoords">[1]</a>, <a href="moose_classes.html#CylMesh.setCoords">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.setCount">setCount() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setCount">[1]</a>, <a href="moose_classes.html#PulseGen.setCount">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.setCout">setCout() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setCout">[1]</a>, <a href="moose_classes.html#Nernst.setCout">[2]</a> - </dt> - - - <dt><a href="tmp.html#setD">setD()</a>, <a href="moose_builtins.html#setD">[1]</a>, <a href="moose_classes.html#setD">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setD">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setD">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setD">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.setDelay">setDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setDelay">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Synapse.setDelay">(Synapse method)</a>, <a href="moose_builtins.html#Synapse.setDelay">[1]</a>, <a href="moose_classes.html#Synapse.setDelay">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#setDiameter">setDiameter()</a>, <a href="moose_builtins.html#setDiameter">[1]</a>, <a href="moose_classes.html#setDiameter">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.setDiameter">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setDiameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.setDiameter">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PoolBase.setDiffConst">setDiffConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setDiffConst">[1]</a>, <a href="moose_classes.html#PoolBase.setDiffConst">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setDiffLength">setDiffLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setDiffLength">[1]</a>, <a href="moose_classes.html#CylMesh.setDiffLength">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#NeuroMesh.setDiffLength">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setDiffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.setDiffLength">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setDivs">setDivs() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setDivs">[1]</a>, <a href="moose_classes.html#HHGate.setDivs">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.setDoLoop">setDoLoop() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setDoLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.setDoLoop">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setDsolve">setDsolve() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setDsolve">[1]</a>, <a href="moose_classes.html#Ksolve.setDsolve">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.setDsolve">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setDsolve">[1]</a>, <a href="moose_classes.html#Stoich.setDsolve">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.setDt">setDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.setDt">[1]</a>, <a href="moose_classes.html#Clock.setDt">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HSolve.setDt">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.setDt">[1]</a>, <a href="moose_classes.html#HSolve.setDt">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setDx">setDx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDx">[1]</a>, <a href="moose_classes.html#CubeMesh.setDx">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.setDx">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setDx">[1]</a>, <a href="moose_classes.html#Interpol2D.setDx">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setDy">setDy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDy">[1]</a>, <a href="moose_classes.html#CubeMesh.setDy">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.setDy">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setDy">[1]</a>, <a href="moose_classes.html#Interpol2D.setDy">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setDz">setDz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDz">[1]</a>, <a href="moose_classes.html#CubeMesh.setDz">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.setEdgeTriggered">setEdgeTriggered() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setEdgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.setEdgeTriggered">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.setEk">setEk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setEk">[1]</a>, <a href="moose_classes.html#ChanBase.setEk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SynChanBase.setEk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setEk">[1]</a>, <a href="moose_classes.html#SynChanBase.setEk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setEk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setEk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setEk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.setEm">setEm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setEm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setEm">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.setEntry">setEntry() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setEntry">[1]</a>, <a href="moose_classes.html#SparseMsg.setEntry">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setEpsAbs">setEpsAbs() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setEpsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.setEpsAbs">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setEpsRel">setEpsRel() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setEpsRel">[1]</a>, <a href="moose_classes.html#Ksolve.setEpsRel">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.setExpr">setExpr() (Func method)</a>, <a href="moose_builtins.html#Func.setExpr">[1]</a>, <a href="moose_classes.html#Func.setExpr">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.setFilename">setFilename() (TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.setFilename">[1]</a>, <a href="moose_classes.html#TimeTable.setFilename">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setFirstDelay">setFirstDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setFirstLevel">setFirstLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setFirstWidth">setFirstWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setFloor">setFloor() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setFloor">[1]</a>, <a href="moose_classes.html#CaConc.setFloor">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setFloor">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setFloor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setFloor">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Arith.setFunction">setFunction() (Arith method)</a>, <a href="moose_builtins.html#Arith.setFunction">[1]</a>, <a href="moose_classes.html#Arith.setFunction">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MathFunc.setFunction">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.setFunction">[1]</a>, <a href="moose_classes.html#MathFunc.setFunction">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#DiffAmp.setGain">setGain() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.setGain">[1]</a>, <a href="moose_classes.html#DiffAmp.setGain">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.setGain">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.setGain">[1]</a>, <a href="moose_classes.html#PIDController.setGain">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.setGain">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setGain">[1]</a>, <a href="moose_classes.html#VClamp.setGain">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.setGamma">setGamma() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setGamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setGamma">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChanBase.setGbar">setGbar() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setGbar">[1]</a>, <a href="moose_classes.html#ChanBase.setGbar">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovChannel.setGbar">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setGbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.setGbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.setGbar">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setGbar">[1]</a>, <a href="moose_classes.html#SynChanBase.setGbar">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setGbar">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setGbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setGbar">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.setGeometryPolicy">setGeometryPolicy() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setGeometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.setGeometryPolicy">[2]</a> - </dt> - - - <dt><a href="tmp.html#setGk">setGk()</a>, <a href="moose_builtins.html#setGk">[1]</a>, <a href="moose_classes.html#setGk">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChanBase.setGk">(ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setGk">[1]</a>, <a href="moose_classes.html#ChanBase.setGk">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.setGk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setGk">[1]</a>, <a href="moose_classes.html#SynChanBase.setGk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setGk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setGk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setGk">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#OneToAllMsg.setI1">setI1() (OneToAllMsg method)</a>, <a href="moose_builtins.html#OneToAllMsg.setI1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.setI1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SingleMsg.setI1">(SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.setI1">[1]</a>, <a href="moose_classes.html#SingleMsg.setI1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SingleMsg.setI2">setI2() (SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.setI2">[1]</a>, <a href="moose_classes.html#SingleMsg.setI2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.setIcon">setIcon() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setIcon">[1]</a>, <a href="moose_classes.html#Annotator.setIcon">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.setIk">setIk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setIk">[1]</a>, <a href="moose_classes.html#MgBlock.setIk">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.setInitialState">setInitialState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setInitialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.setInitialState">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.setInitialState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setInitialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setInitialState">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IzhikevichNrn.setInitU">setInitU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInitU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInitU">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.setInitVm">setInitVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setInitVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setInitVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setInitVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInitVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInitVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.setInject">setInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.setInject">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.setInject">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInject">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.setInject">(RC method)</a>, <a href="moose_builtins.html#RC.setInject">[1]</a>, <a href="moose_classes.html#RC.setInject">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#setInnerArea">setInnerArea()</a>, <a href="moose_builtins.html#setInnerArea">[1]</a>, <a href="moose_classes.html#setInnerArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.setInputOffset">setInputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setInputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.setInputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setInstant">setInstant() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setInstant">[1]</a>, <a href="moose_classes.html#HHChannel.setInstant">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setInstant">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setInstant">[1]</a>, <a href="moose_classes.html#HHChannel2D.setInstant">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setInstant">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setInstant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setInstant">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovGslSolver.setInternalDt">setInternalDt() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setInternalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setInternalDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setIsToroid">setIsToroid() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setIsToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.setIsToroid">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.setK1">setK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.setK2">setK2() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK2">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.setK3">setK3() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK3">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.setKb">setKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setKb">[1]</a>, <a href="moose_classes.html#ReacBase.setKb">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.setKcat">setKcat() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setKcat">[1]</a>, <a href="moose_classes.html#EnzBase.setKcat">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.setKf">setKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setKf">[1]</a>, <a href="moose_classes.html#ReacBase.setKf">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.setKm">setKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setKm">[1]</a>, <a href="moose_classes.html#EnzBase.setKm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.setKMg_A">setKMg_A() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setKMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.setKMg_A">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.setKMg_B">setKMg_B() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setKMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.setKMg_B">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.setKsolve">setKsolve() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.setKsolve">[1]</a>, <a href="moose_classes.html#Stoich.setKsolve">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.setLabels">setLabels() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setLabels">[1]</a>, <a href="moose_classes.html#MarkovChannel.setLabels">[2]</a> - </dt> - - - <dt><a href="tmp.html#setLeak">setLeak()</a>, <a href="moose_builtins.html#setLeak">[1]</a>, <a href="moose_classes.html#setLeak">[2]</a> - </dt> - - - <dt><a href="tmp.html#setLength">setLength()</a>, <a href="moose_builtins.html#setLength">[1]</a>, <a href="moose_classes.html#setLength">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.setLength">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setLength">[1]</a>, <a href="moose_classes.html#CompartmentBase.setLength">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.setLevel">setLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.setLigandConc">setLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.setLigandConc">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovRateTable.setLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setLigandConc">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#StimulusTable.setLoopTime">setLoopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setLoopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setLoopTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#MathFunc.setMathML">setMathML() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.setMathML">[1]</a>, <a href="moose_classes.html#MathFunc.setMathML">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setMax">setMax() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMax">[1]</a>, <a href="moose_classes.html#HHGate.setMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.setMaxIter">setMaxIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setMaxIter">[1]</a>, <a href="moose_classes.html#SteadyState.setMaxIter">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setMeshToSpace">setMeshToSpace() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setMeshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.setMeshToSpace">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setMethod">setMethod() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setMethod">[1]</a>, <a href="moose_classes.html#Ksolve.setMethod">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovGslSolver.setMethod">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setMethod">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setMethod">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable.setMethod">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.setMethod">[1]</a>, <a href="moose_classes.html#TimeTable.setMethod">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setMin">setMin() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMin">[1]</a>, <a href="moose_classes.html#HHGate.setMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setMInfinity">setMInfinity() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMInfinity">[1]</a>, <a href="moose_classes.html#HHGate.setMInfinity">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.setMode">setMode() (Func method)</a>, <a href="moose_builtins.html#Func.setMode">[1]</a>, <a href="moose_classes.html#Func.setMode">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VClamp.setMode">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setMode">[1]</a>, <a href="moose_classes.html#VClamp.setMode">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Species.setMolWt">setMolWt() (Species method)</a>, <a href="moose_builtins.html#Species.setMolWt">[1]</a>, <a href="moose_classes.html#Species.setMolWt">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setMotorConst">setMotorConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setMotorConst">[1]</a>, <a href="moose_classes.html#PoolBase.setMotorConst">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setN">setN() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setN">[1]</a>, <a href="moose_classes.html#PoolBase.setN">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.setName">setName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setName">[1]</a>, <a href="moose_classes.html#Neutral.setName">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setNInit">setNInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setNInit">[1]</a>, <a href="moose_classes.html#PoolBase.setNInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.setNormalizeWeights">setNormalizeWeights() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setNormalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.setNormalizeWeights">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.setNotes">setNotes() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setNotes">[1]</a>, <a href="moose_classes.html#Annotator.setNotes">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.setNumAllVoxels">setNumAllVoxels() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNumAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.setNumAllVoxels">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Ksolve.setNumAllVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNumAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.setNumAllVoxels">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Neutral.setNumData">setNumData() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setNumData">[1]</a>, <a href="moose_classes.html#Neutral.setNumData">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.setNumField">setNumField() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setNumField">[1]</a>, <a href="moose_classes.html#Neutral.setNumField">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setNumGateX">setNumGateX() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateX">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setNumGateX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateX">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setNumGateX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateX">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.setNumGateY">setNumGateY() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateY">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setNumGateY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateY">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setNumGateY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateY">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.setNumGateZ">setNumGateZ() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateZ">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setNumGateZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setNumGateZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateZ">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ReacBase.setNumKb">setNumKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setNumKb">[1]</a>, <a href="moose_classes.html#ReacBase.setNumKb">[2]</a> - </dt> - - - <dt><a href="tmp.html#ReacBase.setNumKf">setNumKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setNumKf">[1]</a>, <a href="moose_classes.html#ReacBase.setNumKf">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.setNumKm">setNumKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setNumKm">[1]</a>, <a href="moose_classes.html#EnzBase.setNumKm">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.setNumMesh">setNumMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setNumMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.setNumMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.setNumOpenStates">setNumOpenStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setNumOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.setNumOpenStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.setNumPools">setNumPools() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setNumPools">[1]</a>, <a href="moose_classes.html#Dsolve.setNumPools">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.setNumPools">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNumPools">[1]</a>, <a href="moose_classes.html#Gsolve.setNumPools">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setNumPools">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNumPools">[1]</a>, <a href="moose_classes.html#Ksolve.setNumPools">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovChannel.setNumStates">setNumStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setNumStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.setNumStates">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynHandler.setNumSynapse">setNumSynapse() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.setNumSynapse">[1]</a>, <a href="moose_classes.html#SynHandler.setNumSynapse">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynHandler.setNumSynapses">setNumSynapses() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.setNumSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.setNumSynapses">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.setNVec">setNVec() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setNVec">[1]</a>, <a href="moose_classes.html#Dsolve.setNVec">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.setNVec">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNVec">[1]</a>, <a href="moose_classes.html#Gsolve.setNVec">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setNVec">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNVec">[1]</a>, <a href="moose_classes.html#Ksolve.setNVec">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setNx">setNx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNx">[1]</a>, <a href="moose_classes.html#CubeMesh.setNx">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setNy">setNy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNy">[1]</a>, <a href="moose_classes.html#CubeMesh.setNy">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setNz">setNz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNz">[1]</a>, <a href="moose_classes.html#CubeMesh.setNz">[2]</a> - </dt> - - - <dt><a href="tmp.html#setOuterArea">setOuterArea()</a>, <a href="moose_builtins.html#setOuterArea">[1]</a>, <a href="moose_classes.html#setOuterArea">[2]</a> - </dt> - - - <dt><a href="tmp.html#Adaptor.setOutputOffset">setOutputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setOutputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.setOutputOffset">[2]</a> - </dt> - - - <dt><a href="tmp.html#Arith.setOutputValue">setOutputValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.setOutputValue">[1]</a>, <a href="moose_classes.html#Arith.setOutputValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.setPath">setPath() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setPath">[1]</a>, <a href="moose_classes.html#Dsolve.setPath">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Stoich.setPath">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setPath">[1]</a>, <a href="moose_classes.html#Stoich.setPath">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setPreserveNumEntries">setPreserveNumEntries() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setPreserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.setPreserveNumEntries">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.setProbability">setProbability() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setProbability">[1]</a>, <a href="moose_classes.html#SparseMsg.setProbability">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.setR">setR() (RC method)</a>, <a href="moose_builtins.html#RC.setR">[1]</a>, <a href="moose_classes.html#RC.setR">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setR0">setR0() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setR0">[1]</a>, <a href="moose_classes.html#CylMesh.setR0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setR1">setR1() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setR1">[1]</a>, <a href="moose_classes.html#CylMesh.setR1">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.setRa">setRa() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setRa">[1]</a>, <a href="moose_classes.html#CompartmentBase.setRa">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.setRandomConnectivity">setRandomConnectivity() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setRandomConnectivity">[1]</a>, <a href="moose_classes.html#SparseMsg.setRandomConnectivity">[2]</a> - </dt> - - - <dt><a href="tmp.html#CplxEnzBase.setRatio">setRatio() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setRatio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setRatio">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.setRefractoryPeriod">setRefractoryPeriod() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setRefractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.setRefractoryPeriod">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.setRefractT">setRefractT() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setRefractT">[1]</a>, <a href="moose_classes.html#SpikeGen.setRefractT">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovGslSolver.setRelativeAccuracy">setRelativeAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setRelativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setRelativeAccuracy">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CompartmentBase.setRm">setRm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setRm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setRm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setRmByTau">setRmByTau() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setRmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setRmByTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiffAmp.setSaturation">setSaturation() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.setSaturation">[1]</a>, <a href="moose_classes.html#DiffAmp.setSaturation">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PIDController.setSaturation">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.setSaturation">[1]</a>, <a href="moose_classes.html#PIDController.setSaturation">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Adaptor.setScale">setScale() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setScale">[1]</a>, <a href="moose_classes.html#Adaptor.setScale">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.setScale">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.setScale">[1]</a>, <a href="moose_classes.html#Nernst.setScale">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#PulseGen.setSecondDelay">setSecondDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondDelay">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setSecondLevel">setSecondLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondLevel">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setSecondWidth">setSecondWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setSeed">setSeed() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setSeed">[1]</a>, <a href="moose_classes.html#HSolve.setSeed">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SparseMsg.setSeed">(SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setSeed">[1]</a>, <a href="moose_classes.html#SparseMsg.setSeed">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.setSeparateSpines">setSeparateSpines() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setSeparateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.setSeparateSpines">[2]</a> - </dt> - - - <dt><a href="tmp.html#setShapeMode">setShapeMode()</a>, <a href="moose_builtins.html#setShapeMode">[1]</a>, <a href="moose_classes.html#setShapeMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setSpaceToMesh">setSpaceToMesh() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setSpaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.setSpaceToMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setSpeciesId">setSpeciesId() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setSpeciesId">[1]</a>, <a href="moose_classes.html#PoolBase.setSpeciesId">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.setStartTime">setStartTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStartTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setStartTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.setStepPosition">setStepPosition() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.setStepPosition">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.setStepSize">setStepSize() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.setStepSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.setStoich">setStoich() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setStoich">[1]</a>, <a href="moose_classes.html#Dsolve.setStoich">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.setStoich">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setStoich">[1]</a>, <a href="moose_classes.html#Gsolve.setStoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.setStoich">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setStoich">[1]</a>, <a href="moose_classes.html#Ksolve.setStoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.setStoich">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setStoich">[1]</a>, <a href="moose_classes.html#SteadyState.setStoich">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#StimulusTable.setStopTime">setStopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setStopTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiagonalMsg.setStride">setStride() (DiagonalMsg method)</a>, <a href="moose_builtins.html#DiagonalMsg.setStride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.setStride">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.setSubTree">setSubTree() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setSubTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.setSubTree">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.setSurface">setSurface() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setSurface">[1]</a>, <a href="moose_classes.html#CubeMesh.setSurface">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.setTable">setTable() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setTable">[1]</a>, <a href="moose_classes.html#Interpol2D.setTable">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VectorTable.setTable">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setTable">[1]</a>, <a href="moose_classes.html#VectorTable.setTable">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setTableA">setTableA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTableA">[1]</a>, <a href="moose_classes.html#HHGate.setTableA">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.setTableA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setTableA">[1]</a>, <a href="moose_classes.html#HHGate2D.setTableA">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setTableB">setTableB() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTableB">[1]</a>, <a href="moose_classes.html#HHGate.setTableB">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.setTableB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setTableB">[1]</a>, <a href="moose_classes.html#HHGate2D.setTableB">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.setTableVector2D">setTableVector2D() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setTableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.setTableVector2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setTarget">setTarget() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setTarget">[1]</a>, <a href="moose_classes.html#HSolve.setTarget">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setTau">setTau() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setTau">[1]</a>, <a href="moose_classes.html#CaConc.setTau">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate.setTau">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTau">[1]</a>, <a href="moose_classes.html#HHGate.setTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.setTau">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.setTau">[1]</a>, <a href="moose_classes.html#IntFire.setTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.setTau">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTau">[1]</a>, <a href="moose_classes.html#VClamp.setTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.setTau">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setTau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setTau">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynChan.setTau1">setTau1() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setTau1">[1]</a>, <a href="moose_classes.html#SynChan.setTau1">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.setTau2">setTau2() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setTau2">[1]</a>, <a href="moose_classes.html#SynChan.setTau2">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.setTauD">setTauD() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setTauD">[1]</a>, <a href="moose_classes.html#PIDController.setTauD">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.setTauI">setTauI() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setTauI">[1]</a>, <a href="moose_classes.html#PIDController.setTauI">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp.setTd">setTd() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTd">[1]</a>, <a href="moose_classes.html#VClamp.setTd">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.setTemperature">setTemperature() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setTemperature">[1]</a>, <a href="moose_classes.html#Nernst.setTemperature">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.setTextColor">setTextColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setTextColor">[1]</a>, <a href="moose_classes.html#Annotator.setTextColor">[2]</a> - </dt> - - - <dt><a href="tmp.html#CaConc.setThick">setThick() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setThick">[1]</a>, <a href="moose_classes.html#CaConc.setThick">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.setThick">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setThick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setThick">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#setThickness">setThickness()</a>, <a href="moose_builtins.html#setThickness">[1]</a>, <a href="moose_classes.html#setThickness">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PsdMesh.setThickness">(PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.setThickness">[1]</a>, <a href="moose_classes.html#PsdMesh.setThickness">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Mstring.setThis">setThis() (Mstring method)</a>, <a href="moose_builtins.html#Mstring.setThis">[1]</a>, <a href="moose_classes.html#Mstring.setThis">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.setThis">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.setThis">[1]</a>, <a href="moose_classes.html#Neutral.setThis">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IntFire.setThresh">setThresh() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setThresh">[1]</a>, <a href="moose_classes.html#IntFire.setThresh">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.setThreshold">setThreshold() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setThreshold">[1]</a>, <a href="moose_classes.html#SpikeGen.setThreshold">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Table.setThreshold">(Table method)</a>, <a href="moose_builtins.html#Table.setThreshold">[1]</a>, <a href="moose_classes.html#Table.setThreshold">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#VClamp.setTi">setTi() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTi">[1]</a>, <a href="moose_classes.html#VClamp.setTi">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.setTickDt">setTickDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.setTickDt">[1]</a>, <a href="moose_classes.html#Clock.setTickDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.setTickStep">setTickStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.setTickStep">[1]</a>, <a href="moose_classes.html#Clock.setTickStep">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.settle">settle() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.settle">[1]</a>, <a href="moose_classes.html#SteadyState.settle">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.setTotal">setTotal() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setTotal">[1]</a>, <a href="moose_classes.html#SteadyState.setTotal">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setTrigMode">setTrigMode() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setTrigMode">[1]</a>, <a href="moose_classes.html#PulseGen.setTrigMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setU0">setU0() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setU0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setU0">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setupAlpha">setupAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupAlpha">[1]</a>, <a href="moose_classes.html#HHGate.setupAlpha">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setupGate">setupGate() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupGate">[1]</a>, <a href="moose_classes.html#HHGate.setupGate">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.setupMatrix">setupMatrix() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setupMatrix">[1]</a>, <a href="moose_classes.html#SteadyState.setupMatrix">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.setupTau">setupTau() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupTau">[1]</a>, <a href="moose_classes.html#HHGate.setupTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setUseConcentration">setUseConcentration() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setUseConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.setUseConcentration">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieHHChannel.setUseConcentration">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setUseConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setUseConcentration">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.setUseInterpolation">setUseInterpolation() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setUseInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.setUseInterpolation">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.setUseRandInit">setUseRandInit() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setUseRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.setUseRandInit">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.setV0">setV0() (RC method)</a>, <a href="moose_builtins.html#RC.setV0">[1]</a>, <a href="moose_classes.html#RC.setV0">[2]</a> - </dt> - - - <dt><a href="tmp.html#setValence">setValence()</a>, <a href="moose_builtins.html#setValence">[1]</a>, <a href="moose_classes.html#setValence">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.setValence">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.setValence">[1]</a>, <a href="moose_classes.html#Nernst.setValence">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Double.setValue">setValue() (Double method)</a>, <a href="moose_builtins.html#Double.setValue">[1]</a>, <a href="moose_classes.html#Double.setValue">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Long.setValue">(Long method)</a>, <a href="moose_builtins.html#Long.setValue">[1]</a>, <a href="moose_classes.html#Long.setValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Mstring.setValue">(Mstring method)</a>, <a href="moose_builtins.html#Mstring.setValue">[1]</a>, <a href="moose_classes.html#Mstring.setValue">[2]</a> - </dt> - - - <dt><a href="tmp.html#Unsigned.setValue">(Unsigned method)</a>, <a href="moose_builtins.html#Unsigned.setValue">[1]</a>, <a href="moose_classes.html#Unsigned.setValue">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Func.setVar">setVar() (Func method)</a>, <a href="moose_builtins.html#Func.setVar">[1]</a>, <a href="moose_classes.html#Func.setVar">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setVDiv">setVDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVDiv">[1]</a>, <a href="moose_classes.html#HSolve.setVDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.setVector">setVector() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.setVector">[1]</a>, <a href="moose_classes.html#TableBase.setVector">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.setVm">setVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setVm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IntFire.setVm">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.setVm">[1]</a>, <a href="moose_classes.html#IntFire.setVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.setVm">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setVm">[1]</a>, <a href="moose_classes.html#MarkovChannel.setVm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.setVm">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setVm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HSolve.setVMax">setVMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVMax">[1]</a>, <a href="moose_classes.html#HSolve.setVMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.setVmax">setVmax() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setVmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setVmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.setVMin">setVMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVMin">[1]</a>, <a href="moose_classes.html#HSolve.setVMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#setVolume">setVolume()</a>, <a href="moose_builtins.html#setVolume">[1]</a>, <a href="moose_classes.html#setVolume">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChemCompt.setVolume">(ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.setVolume">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.setVolume">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setVolume">[1]</a>, <a href="moose_classes.html#PoolBase.setVolume">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.setVolumeNotRates">setVolumeNotRates() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setVolumeNotRates">[1]</a>, <a href="moose_classes.html#ChemCompt.setVolumeNotRates">[2]</a> - </dt> - - - <dt><a href="tmp.html#Synapse.setWeight">setWeight() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.setWeight">[1]</a>, <a href="moose_classes.html#Synapse.setWeight">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.setWidth">setWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setWidth">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.setX">setX() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setX">[1]</a>, <a href="moose_classes.html#Annotator.setX">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.setX">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setX">[1]</a>, <a href="moose_classes.html#CompartmentBase.setX">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.setX">(Func method)</a>, <a href="moose_builtins.html#Func.setX">[1]</a>, <a href="moose_classes.html#Func.setX">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setX">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setX">[1]</a>, <a href="moose_classes.html#HHChannel.setX">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.setX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setX">[1]</a>, <a href="moose_classes.html#HHChannel2D.setX">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setX">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.setX0">setX0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setX0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setX0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.setX0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setX0">[1]</a>, <a href="moose_classes.html#CubeMesh.setX0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setX0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setX0">[1]</a>, <a href="moose_classes.html#CylMesh.setX0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setX1">setX1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setX1">[1]</a>, <a href="moose_classes.html#CubeMesh.setX1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.setX1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setX1">[1]</a>, <a href="moose_classes.html#CylMesh.setX1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.setXdivs">setXdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.setXdivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.setXdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXdivs">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.setXdivs">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXdivs">[1]</a>, <a href="moose_classes.html#VectorTable.setXdivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setXdivsA">setXdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXdivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setXdivsB">setXdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXdivsB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.setXindex">setXindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setXindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setXindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.setXmax">setXmax() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.setXmax">[1]</a>, <a href="moose_classes.html#Interpol.setXmax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.setXmax">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXmax">[1]</a>, <a href="moose_classes.html#Interpol2D.setXmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.setXmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.setXmax">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXmax">[1]</a>, <a href="moose_classes.html#VectorTable.setXmax">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setXmaxA">setXmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXmaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setXmaxB">setXmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXmaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.setXmin">setXmin() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.setXmin">[1]</a>, <a href="moose_classes.html#Interpol.setXmin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.setXmin">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXmin">[1]</a>, <a href="moose_classes.html#Interpol2D.setXmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.setXmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.setXmin">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXmin">[1]</a>, <a href="moose_classes.html#VectorTable.setXmin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setXminA">setXminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXminA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setXminB">setXminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXminB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setXpower">setXpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setXpower">[1]</a>, <a href="moose_classes.html#HHChannel.setXpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setXpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setXpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setXpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setXpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setXpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setXpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Annotator.setY">setY() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setY">[1]</a>, <a href="moose_classes.html#Annotator.setY">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.setY">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setY">[1]</a>, <a href="moose_classes.html#CompartmentBase.setY">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.setY">(Func method)</a>, <a href="moose_builtins.html#Func.setY">[1]</a>, <a href="moose_classes.html#Func.setY">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setY">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setY">[1]</a>, <a href="moose_classes.html#HHChannel.setY">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.setY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setY">[1]</a>, <a href="moose_classes.html#HHChannel2D.setY">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setY">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.setY0">setY0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setY0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setY0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.setY0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setY0">[1]</a>, <a href="moose_classes.html#CubeMesh.setY0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setY0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setY0">[1]</a>, <a href="moose_classes.html#CylMesh.setY0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setY1">setY1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setY1">[1]</a>, <a href="moose_classes.html#CubeMesh.setY1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.setY1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setY1">[1]</a>, <a href="moose_classes.html#CylMesh.setY1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.setYdivs">setYdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.setYdivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.setYdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYdivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setYdivsA">setYdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYdivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setYdivsB">setYdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYdivsB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.setYindex">setYindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setYindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setYindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.setYmax">setYmax() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYmax">[1]</a>, <a href="moose_classes.html#Interpol2D.setYmax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.setYmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYmax">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setYmaxA">setYmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYmaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setYmaxB">setYmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYmaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.setYmin">setYmin() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYmin">[1]</a>, <a href="moose_classes.html#Interpol2D.setYmin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.setYmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYmin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.setYminA">setYminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYminA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.setYminB">setYminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYminB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setYpower">setYpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setYpower">[1]</a>, <a href="moose_classes.html#HHChannel.setYpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setYpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setYpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setYpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setYpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setYpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setYpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Annotator.setZ">setZ() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setZ">[1]</a>, <a href="moose_classes.html#Annotator.setZ">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CompartmentBase.setZ">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setZ">[1]</a>, <a href="moose_classes.html#CompartmentBase.setZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.setZ">(Func method)</a>, <a href="moose_builtins.html#Func.setZ">[1]</a>, <a href="moose_classes.html#Func.setZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setZ">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setZ">[1]</a>, <a href="moose_classes.html#HHChannel.setZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.setZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZ">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setZ">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.setZ0">setZ0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setZ0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setZ0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.setZ0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setZ0">[1]</a>, <a href="moose_classes.html#CubeMesh.setZ0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.setZ0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setZ0">[1]</a>, <a href="moose_classes.html#CylMesh.setZ0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.setZ1">setZ1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setZ1">[1]</a>, <a href="moose_classes.html#CubeMesh.setZ1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.setZ1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setZ1">[1]</a>, <a href="moose_classes.html#CylMesh.setZ1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel2D.setZindex">setZindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.setZk">setZk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setZk">[1]</a>, <a href="moose_classes.html#MgBlock.setZk">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.setZpower">setZpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setZpower">[1]</a>, <a href="moose_classes.html#HHChannel.setZpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.setZpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.setZpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setZpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setZpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#shapeMode">shapeMode</a>, <a href="moose_builtins.html#shapeMode">[1]</a>, <a href="moose_classes.html#shapeMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#Shell">Shell (built-in class)</a>, <a href="moose_builtins.html#Shell">[1]</a>, <a href="moose_classes.html#Shell">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.showMatrices">showMatrices() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.showMatrices">[1]</a>, <a href="moose_classes.html#SteadyState.showMatrices">[2]</a> - </dt> - - - <dt><a href="tmp.html#sibling">sibling</a>, <a href="moose_builtins.html#sibling">[1]</a>, <a href="moose_classes.html#sibling">[2]</a> - </dt> - - - <dt><a href="tmp.html#SingleMsg">SingleMsg (built-in class)</a>, <a href="moose_builtins.html#SingleMsg">[1]</a>, <a href="moose_classes.html#SingleMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.size">size (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.size">[1]</a>, <a href="moose_classes.html#MarkovRateTable.size">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#TableBase.size">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.size">[1]</a>, <a href="moose_classes.html#TableBase.size">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.solutionStatus">solutionStatus (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.solutionStatus">[1]</a>, <a href="moose_classes.html#SteadyState.solutionStatus">[2]</a> - </dt> - - - <dt><a href="tmp.html#Neutral.sourceFields">sourceFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.sourceFields">[1]</a>, <a href="moose_classes.html#Neutral.sourceFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.spaceToMesh">spaceToMesh (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.spaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.spaceToMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg">SparseMsg (built-in class)</a>, <a href="moose_builtins.html#SparseMsg">[1]</a>, <a href="moose_classes.html#SparseMsg">[2]</a> - </dt> - - - <dt><a href="tmp.html#Species">Species (built-in class)</a>, <a href="moose_builtins.html#Species">[1]</a>, <a href="moose_classes.html#Species">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.species">species (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.species">[1]</a>, <a href="moose_classes.html#PoolBase.species">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.speciesId">speciesId (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.speciesId">[1]</a>, <a href="moose_classes.html#PoolBase.speciesId">[2]</a> - </dt> - - - <dt><a href="tmp.html#sphere">sphere</a>, <a href="moose_builtins.html#sphere">[1]</a>, <a href="moose_classes.html#sphere">[2]</a> - </dt> - - - <dt><a href="tmp.html#Table.spike">spike() (Table method)</a>, <a href="moose_builtins.html#Table.spike">[1]</a>, <a href="moose_classes.html#Table.spike">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen">SpikeGen (built-in class)</a>, <a href="moose_builtins.html#SpikeGen">[1]</a>, <a href="moose_classes.html#SpikeGen">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.spikeOut">spikeOut (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.spikeOut">[1]</a>, <a href="moose_classes.html#IntFire.spikeOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.spikeOut">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.spikeOut">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.spikeOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.spikeOut">(SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.spikeOut">[1]</a>, <a href="moose_classes.html#SpikeGen.spikeOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SpineMesh.spineList">spineList() (SpineMesh method)</a>, <a href="moose_builtins.html#SpineMesh.spineList">[1]</a>, <a href="moose_classes.html#SpineMesh.spineList">[2]</a> - </dt> - - - <dt><a href="tmp.html#NeuroMesh.spineListOut">spineListOut (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.spineListOut">[1]</a>, <a href="moose_classes.html#NeuroMesh.spineListOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpineMesh">SpineMesh (built-in class)</a>, <a href="moose_builtins.html#SpineMesh">[1]</a>, <a href="moose_classes.html#SpineMesh">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.src">src (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.src">[1]</a>, <a href="moose_classes.html#Finfo.src">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.srcFieldsOnE1">srcFieldsOnE1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.srcFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.srcFieldsOnE1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Msg.srcFieldsOnE2">srcFieldsOnE2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.srcFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.srcFieldsOnE2">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.start">start() (Clock method)</a>, <a href="moose_builtins.html#Clock.start">[1]</a>, <a href="moose_classes.html#Clock.start">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.startTime">startTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.startTime">[1]</a>, <a href="moose_classes.html#StimulusTable.startTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#state">state</a>, <a href="moose_builtins.html#state">[1]</a>, <a href="moose_classes.html#state">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovChannel.state">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.state">[1]</a>, <a href="moose_classes.html#MarkovChannel.state">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.state">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.state">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.state">[2]</a> - </dt> - - - <dt><a href="tmp.html#RC.state">(RC attribute)</a>, <a href="moose_builtins.html#RC.state">[1]</a>, <a href="moose_classes.html#RC.state">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#MarkovGslSolver.stateOut">stateOut (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.stateOut">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.stateOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.stateOut">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.stateOut">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.stateOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SteadyState.stateType">stateType (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.stateType">[1]</a>, <a href="moose_classes.html#SteadyState.stateType">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats">Stats (built-in class)</a>, <a href="moose_builtins.html#Stats">[1]</a>, <a href="moose_classes.html#Stats">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.status">status (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.status">[1]</a>, <a href="moose_classes.html#SteadyState.status">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState">SteadyState (built-in class)</a>, <a href="moose_builtins.html#SteadyState">[1]</a>, <a href="moose_classes.html#SteadyState">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.stencilIndex">stencilIndex (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.stencilIndex">[1]</a>, <a href="moose_classes.html#ChemCompt.stencilIndex">[2]</a> - </dt> - - - <dt><a href="tmp.html#ChemCompt.stencilRate">stencilRate (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.stencilRate">[1]</a>, <a href="moose_classes.html#ChemCompt.stencilRate">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.step">step() (Clock method)</a>, <a href="moose_builtins.html#Clock.step">[1]</a>, <a href="moose_classes.html#Clock.step">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.stepPosition">stepPosition (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.stepPosition">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.stepSize">stepSize (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.stepSize">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable">StimulusTable (built-in class)</a>, <a href="moose_builtins.html#StimulusTable">[1]</a>, <a href="moose_classes.html#StimulusTable">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich">Stoich (built-in class)</a>, <a href="moose_builtins.html#Stoich">[1]</a>, <a href="moose_classes.html#Stoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#Dsolve.stoich">stoich (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.stoich">[1]</a>, <a href="moose_classes.html#Dsolve.stoich">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Gsolve.stoich">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.stoich">[1]</a>, <a href="moose_classes.html#Gsolve.stoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#Ksolve.stoich">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.stoich">[1]</a>, <a href="moose_classes.html#Ksolve.stoich">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.stoich">(SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.stoich">[1]</a>, <a href="moose_classes.html#SteadyState.stoich">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Clock.stop">stop() (Clock method)</a>, <a href="moose_builtins.html#Clock.stop">[1]</a>, <a href="moose_classes.html#Clock.stop">[2]</a> - </dt> - - - <dt><a href="tmp.html#StimulusTable.stopTime">stopTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.stopTime">[2]</a> - </dt> - - - <dt><a href="tmp.html#storeInflux">storeInflux()</a>, <a href="moose_builtins.html#storeInflux">[1]</a>, <a href="moose_classes.html#storeInflux">[2]</a> - </dt> - - - <dt><a href="tmp.html#storeOutflux">storeOutflux()</a>, <a href="moose_builtins.html#storeOutflux">[1]</a>, <a href="moose_classes.html#storeOutflux">[2]</a> - </dt> - - - <dt><a href="tmp.html#DiagonalMsg.stride">stride (DiagonalMsg attribute)</a>, <a href="moose_builtins.html#DiagonalMsg.stride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.stride">[2]</a> - </dt> - - - <dt><a href="tmp.html#EnzBase.sub">sub (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.sub">[1]</a>, <a href="moose_classes.html#EnzBase.sub">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.sub">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.sub">[1]</a>, <a href="moose_classes.html#ReacBase.sub">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#EnzBase.subDest">subDest() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.subDest">[1]</a>, <a href="moose_classes.html#EnzBase.subDest">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.subDest">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.subDest">[1]</a>, <a href="moose_classes.html#ReacBase.subDest">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#EnzBase.subOut">subOut (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.subOut">[1]</a>, <a href="moose_classes.html#EnzBase.subOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ReacBase.subOut">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.subOut">[1]</a>, <a href="moose_classes.html#ReacBase.subOut">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#NeuroMesh.subTree">subTree (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.subTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.subTree">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stats.sum">sum (Stats attribute)</a>, <a href="moose_builtins.html#Stats.sum">[1]</a>, <a href="moose_classes.html#Stats.sum">[2]</a> - </dt> - - - <dt><a href="tmp.html#SumFunc">SumFunc (built-in class)</a>, <a href="moose_builtins.html#SumFunc">[1]</a>, <a href="moose_classes.html#SumFunc">[2]</a> - </dt> - - - <dt><a href="tmp.html#sumRaxial">sumRaxial()</a>, <a href="tmp.html#sumRaxial">[1]</a>, <a href="tmp.html#sumRaxial">[2]</a>, <a href="moose_builtins.html#sumRaxial">[3]</a>, <a href="moose_builtins.html#sumRaxial">[4]</a>, <a href="moose_builtins.html#sumRaxial">[5]</a>, <a href="moose_classes.html#sumRaxial">[6]</a>, <a href="moose_classes.html#sumRaxial">[7]</a>, <a href="moose_classes.html#sumRaxial">[8]</a> - </dt> - - - <dt><a href="tmp.html#sumRaxialOut">sumRaxialOut</a>, <a href="tmp.html#sumRaxialOut">[1]</a>, <a href="tmp.html#sumRaxialOut">[2]</a>, <a href="moose_builtins.html#sumRaxialOut">[3]</a>, <a href="moose_builtins.html#sumRaxialOut">[4]</a>, <a href="moose_builtins.html#sumRaxialOut">[5]</a>, <a href="moose_classes.html#sumRaxialOut">[6]</a>, <a href="moose_classes.html#sumRaxialOut">[7]</a>, <a href="moose_classes.html#sumRaxialOut">[8]</a> - </dt> - - - <dt><a href="tmp.html#CubeMesh.surface">surface (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.surface">[1]</a>, <a href="moose_classes.html#CubeMesh.surface">[2]</a> - </dt> - - - <dt><a href="tmp.html#SymCompartment">SymCompartment (built-in class)</a>, <a href="moose_builtins.html#SymCompartment">[1]</a>, <a href="moose_classes.html#SymCompartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#Synapse">Synapse (built-in class)</a>, <a href="moose_builtins.html#Synapse">[1]</a>, <a href="moose_classes.html#Synapse">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan">SynChan (built-in class)</a>, <a href="moose_builtins.html#SynChan">[1]</a>, <a href="moose_classes.html#SynChan">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase">SynChanBase (built-in class)</a>, <a href="moose_builtins.html#SynChanBase">[1]</a>, <a href="moose_classes.html#SynChanBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynHandler">SynHandler (built-in class)</a>, <a href="moose_builtins.html#SynHandler">[1]</a>, <a href="moose_classes.html#SynHandler">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="T">T</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Table">Table (built-in class)</a>, <a href="moose_builtins.html#Table">[1]</a>, <a href="moose_classes.html#Table">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.table">table (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.table">[1]</a>, <a href="moose_classes.html#Interpol2D.table">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#VectorTable.table">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.table">[1]</a>, <a href="moose_classes.html#VectorTable.table">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.tableA">tableA (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tableA">[1]</a>, <a href="moose_classes.html#HHGate.tableA">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.tableA">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.tableA">[1]</a>, <a href="moose_classes.html#HHGate2D.tableA">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.tableB">tableB (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tableB">[1]</a>, <a href="moose_classes.html#HHGate.tableB">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHGate2D.tableB">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.tableB">[1]</a>, <a href="moose_classes.html#HHGate2D.tableB">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#TableBase">TableBase (built-in class)</a>, <a href="moose_builtins.html#TableBase">[1]</a>, <a href="moose_classes.html#TableBase">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.tableVector2D">tableVector2D (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.tableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.tableVector2D">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.target">target (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.target">[1]</a>, <a href="moose_classes.html#HSolve.target">[2]</a> - </dt> - - - <dt><a href="tmp.html#tau">tau</a>, <a href="moose_builtins.html#tau">[1]</a>, <a href="moose_classes.html#tau">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CaConc.tau">(CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.tau">[1]</a>, <a href="moose_classes.html#CaConc.tau">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.tau">(HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tau">[1]</a>, <a href="moose_classes.html#HHGate.tau">[2]</a> - </dt> - - - <dt><a href="tmp.html#IntFire.tau">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.tau">[1]</a>, <a href="moose_classes.html#IntFire.tau">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCaConc.tau">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.tau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.tau">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#SynChan.tau1">tau1 (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.tau1">[1]</a>, <a href="moose_classes.html#SynChan.tau1">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChan.tau2">tau2 (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.tau2">[1]</a>, <a href="moose_classes.html#SynChan.tau2">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.tauD">tauD (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.tauD">[1]</a>, <a href="moose_classes.html#PIDController.tauD">[2]</a> - </dt> - - - <dt><a href="tmp.html#PIDController.tauI">tauI (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.tauI">[1]</a>, <a href="moose_classes.html#PIDController.tauI">[2]</a> - </dt> - - - <dt><a href="tmp.html#tauPump">tauPump()</a>, <a href="moose_builtins.html#tauPump">[1]</a>, <a href="moose_classes.html#tauPump">[2]</a> - </dt> - - - <dt><a href="tmp.html#td">td</a>, <a href="moose_builtins.html#td">[1]</a>, <a href="moose_classes.html#td">[2]</a> - </dt> - - - <dt><a href="tmp.html#Nernst.Temperature">Temperature (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Temperature">[1]</a>, <a href="moose_classes.html#Nernst.Temperature">[2]</a> - </dt> - - - <dt><a href="tmp.html#testSched">testSched (built-in class)</a>, <a href="moose_builtins.html#testSched">[1]</a>, <a href="moose_classes.html#testSched">[2]</a> - </dt> - - - <dt><a href="tmp.html#Annotator.textColor">textColor (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.textColor">[1]</a>, <a href="moose_classes.html#Annotator.textColor">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#CaConc.thick">thick (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.thick">[1]</a>, <a href="moose_classes.html#CaConc.thick">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieCaConc.thick">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.thick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.thick">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#thickness">thickness</a>, <a href="moose_builtins.html#thickness">[1]</a>, <a href="moose_classes.html#thickness">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#PsdMesh.thickness">(PsdMesh attribute)</a>, <a href="moose_builtins.html#PsdMesh.thickness">[1]</a>, <a href="moose_classes.html#PsdMesh.thickness">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Mstring.this">this (Mstring attribute)</a>, <a href="moose_builtins.html#Mstring.this">[1]</a>, <a href="moose_classes.html#Mstring.this">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Neutral.this">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.this">[1]</a>, <a href="moose_classes.html#Neutral.this">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#IntFire.thresh">thresh (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.thresh">[1]</a>, <a href="moose_classes.html#IntFire.thresh">[2]</a> - </dt> - - - <dt><a href="tmp.html#SpikeGen.threshold">threshold (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.threshold">[1]</a>, <a href="moose_classes.html#SpikeGen.threshold">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Table.threshold">(Table attribute)</a>, <a href="moose_builtins.html#Table.threshold">[1]</a>, <a href="moose_classes.html#Table.threshold">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ti">ti</a>, <a href="moose_builtins.html#ti">[1]</a>, <a href="moose_classes.html#ti">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.tickDt">tickDt (Clock attribute)</a>, <a href="moose_builtins.html#Clock.tickDt">[1]</a>, <a href="moose_classes.html#Clock.tickDt">[2]</a> - </dt> - - - <dt><a href="tmp.html#Clock.tickStep">tickStep (Clock attribute)</a>, <a href="moose_builtins.html#Clock.tickStep">[1]</a>, <a href="moose_classes.html#Clock.tickStep">[2]</a> - </dt> - - - <dt><a href="tmp.html#TimeTable">TimeTable (built-in class)</a>, <a href="moose_builtins.html#TimeTable">[1]</a>, <a href="moose_classes.html#TimeTable">[2]</a> - </dt> - - - <dt><a href="tmp.html#SteadyState.total">total (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.total">[1]</a>, <a href="moose_classes.html#SteadyState.total">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.totLength">totLength (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.totLength">[1]</a>, <a href="moose_classes.html#CylMesh.totLength">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.transpose">transpose() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.transpose">[1]</a>, <a href="moose_classes.html#SparseMsg.transpose">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.trigMode">trigMode (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.trigMode">[1]</a>, <a href="moose_classes.html#PulseGen.trigMode">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.tripletFill">tripletFill() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.tripletFill">[1]</a>, <a href="moose_classes.html#SparseMsg.tripletFill">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.tweakAlpha">tweakAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.tweakAlpha">[1]</a>, <a href="moose_classes.html#HHGate.tweakAlpha">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate.tweakTau">tweakTau() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.tweakTau">[1]</a>, <a href="moose_classes.html#HHGate.tweakTau">[2]</a> - </dt> - - - <dt><a href="tmp.html#Finfo.type">type (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.type">[1]</a>, <a href="moose_classes.html#Finfo.type">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="U">U</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#IzhikevichNrn.u">u (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.u">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.u">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.u0">u0 (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.u0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.u0">[2]</a> - </dt> - - - <dt><a href="tmp.html#SparseMsg.unsetEntry">unsetEntry() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.unsetEntry">[1]</a>, <a href="moose_classes.html#SparseMsg.unsetEntry">[2]</a> - </dt> - - - <dt><a href="tmp.html#Unsigned">Unsigned (built-in class)</a>, <a href="moose_builtins.html#Unsigned">[1]</a>, <a href="moose_classes.html#Unsigned">[2]</a> - </dt> - - - <dt><a href="tmp.html#Stoich.unzombify">unzombify() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.unzombify">[1]</a>, <a href="moose_classes.html#Stoich.unzombify">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Shell.useClock">useClock() (Shell method)</a>, <a href="moose_builtins.html#Shell.useClock">[1]</a>, <a href="moose_classes.html#Shell.useClock">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.useConcentration">useConcentration (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.useConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.useConcentration">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ZombieHHChannel.useConcentration">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.useConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.useConcentration">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate.useInterpolation">useInterpolation (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.useInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.useInterpolation">[2]</a> - </dt> - - - <dt><a href="tmp.html#Gsolve.useRandInit">useRandInit (Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.useRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.useRandInit">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="V">V</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#RC.V0">V0 (RC attribute)</a>, <a href="moose_builtins.html#RC.V0">[1]</a>, <a href="moose_classes.html#RC.V0">[2]</a> - </dt> - - - <dt><a href="tmp.html#valence">valence</a>, <a href="moose_builtins.html#valence">[1]</a>, <a href="moose_classes.html#valence">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Nernst.valence">(Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.valence">[1]</a>, <a href="moose_classes.html#Nernst.valence">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#value">value</a>, <a href="moose_builtins.html#value">[1]</a>, <a href="moose_classes.html#value">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Double.value">(Double attribute)</a>, <a href="moose_builtins.html#Double.value">[1]</a>, <a href="moose_classes.html#Double.value">[2]</a> - </dt> - - - <dt><a href="tmp.html#Long.value">(Long attribute)</a>, <a href="moose_builtins.html#Long.value">[1]</a>, <a href="moose_classes.html#Long.value">[2]</a> - </dt> - - - <dt><a href="tmp.html#Mstring.value">(Mstring attribute)</a>, <a href="moose_builtins.html#Mstring.value">[1]</a>, <a href="moose_classes.html#Mstring.value">[2]</a> - </dt> - - - <dt><a href="tmp.html#Unsigned.value">(Unsigned attribute)</a>, <a href="moose_builtins.html#Unsigned.value">[1]</a>, <a href="moose_classes.html#Unsigned.value">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Neutral.valueFields">valueFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.valueFields">[1]</a>, <a href="moose_classes.html#Neutral.valueFields">[2]</a> - </dt> - - - <dt><a href="tmp.html#valueOut">valueOut</a>, <a href="moose_builtins.html#valueOut">[1]</a>, <a href="moose_classes.html#valueOut">[2]</a> - </dt> - - - <dt><a href="tmp.html#var">var</a>, <a href="moose_builtins.html#var">[1]</a>, <a href="moose_classes.html#var">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.varIn">varIn() (Func method)</a>, <a href="moose_builtins.html#Func.varIn">[1]</a>, <a href="moose_classes.html#Func.varIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#vars">vars</a>, <a href="moose_builtins.html#vars">[1]</a>, <a href="moose_classes.html#vars">[2]</a> - </dt> - - - <dt><a href="tmp.html#VClamp">VClamp (built-in class)</a>, <a href="moose_builtins.html#VClamp">[1]</a>, <a href="moose_classes.html#VClamp">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.vDiv">vDiv (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vDiv">[1]</a>, <a href="moose_classes.html#HSolve.vDiv">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.vector">vector (TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.vector">[1]</a>, <a href="moose_classes.html#TableBase.vector">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#VectorTable">VectorTable (built-in class)</a>, <a href="moose_builtins.html#VectorTable">[1]</a>, <a href="moose_classes.html#VectorTable">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.Vm">Vm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Vm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Vm">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IntFire.Vm">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.Vm">[1]</a>, <a href="moose_classes.html#IntFire.Vm">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.Vm">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Vm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Vm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovChannel.Vm">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.Vm">[1]</a>, <a href="moose_classes.html#MarkovChannel.Vm">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovRateTable.Vm">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.Vm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.Vm">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChanBase.Vm">Vm() (ChanBase method)</a>, <a href="tmp.html#ChanBase.Vm">[1]</a>, <a href="moose_builtins.html#ChanBase.Vm">[2]</a>, <a href="moose_builtins.html#ChanBase.Vm">[3]</a>, <a href="moose_classes.html#ChanBase.Vm">[4]</a>, <a href="moose_classes.html#ChanBase.Vm">[5]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#SpikeGen.Vm">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.Vm">[1]</a>, <a href="moose_classes.html#SpikeGen.Vm">[2]</a> - </dt> - - - <dt><a href="tmp.html#SynChanBase.Vm">(SynChanBase method)</a>, <a href="tmp.html#SynChanBase.Vm">[1]</a>, <a href="moose_builtins.html#SynChanBase.Vm">[2]</a>, <a href="moose_builtins.html#SynChanBase.Vm">[3]</a>, <a href="moose_classes.html#SynChanBase.Vm">[4]</a>, <a href="moose_classes.html#SynChanBase.Vm">[5]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Vm1">Vm1()</a>, <a href="moose_builtins.html#Vm1">[1]</a>, <a href="moose_classes.html#Vm1">[2]</a> - </dt> - - - <dt><a href="tmp.html#Vm2">Vm2()</a>, <a href="moose_builtins.html#Vm2">[1]</a>, <a href="moose_classes.html#Vm2">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.vMax">vMax (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vMax">[1]</a>, <a href="moose_classes.html#HSolve.vMax">[2]</a> - </dt> - - - <dt><a href="tmp.html#IzhikevichNrn.Vmax">Vmax (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Vmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Vmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#HSolve.vMin">vMin (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vMin">[1]</a>, <a href="moose_classes.html#HSolve.vMin">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.VmOut">VmOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.VmOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.VmOut">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#IzhikevichNrn.VmOut">(IzhikevichNrn attribute)</a>, <a href="tmp.html#IzhikevichNrn.VmOut">[1]</a>, <a href="moose_builtins.html#IzhikevichNrn.VmOut">[2]</a>, <a href="moose_builtins.html#IzhikevichNrn.VmOut">[3]</a>, <a href="moose_classes.html#IzhikevichNrn.VmOut">[4]</a>, <a href="moose_classes.html#IzhikevichNrn.VmOut">[5]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#volume">volume</a>, <a href="moose_builtins.html#volume">[1]</a>, <a href="moose_classes.html#volume">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#ChemCompt.volume">(ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.volume">[1]</a>, <a href="moose_classes.html#ChemCompt.volume">[2]</a> - </dt> - - - <dt><a href="tmp.html#MeshEntry.volume">(MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.volume">[1]</a>, <a href="moose_classes.html#MeshEntry.volume">[2]</a> - </dt> - - - <dt><a href="tmp.html#PoolBase.volume">(PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.volume">[1]</a>, <a href="moose_classes.html#PoolBase.volume">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ChemCompt.voxelVolume">voxelVolume (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.voxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.voxelVolume">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="W">W</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#Synapse.weight">weight (Synapse attribute)</a>, <a href="moose_builtins.html#Synapse.weight">[1]</a>, <a href="moose_classes.html#Synapse.weight">[2]</a> - </dt> - - - <dt><a href="tmp.html#PulseGen.width">width (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.width">[1]</a>, <a href="moose_classes.html#PulseGen.width">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#PulseGen.widthIn">widthIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.widthIn">[1]</a>, <a href="moose_classes.html#PulseGen.widthIn">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="X">X</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#x">x</a>, <a href="moose_builtins.html#x">[1]</a>, <a href="moose_classes.html#x">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Annotator.x">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.x">[1]</a>, <a href="moose_classes.html#Annotator.x">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.x">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.x">[1]</a>, <a href="moose_classes.html#CompartmentBase.x">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.X">X (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.X">[1]</a>, <a href="moose_classes.html#HHChannel.X">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.X">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.X">[1]</a>, <a href="moose_classes.html#HHChannel2D.X">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.X">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.X">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.X">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CompartmentBase.x0">x0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.x0">[1]</a>, <a href="moose_classes.html#CompartmentBase.x0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.x0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.x0">[1]</a>, <a href="moose_classes.html#CubeMesh.x0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.x0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.x0">[1]</a>, <a href="moose_classes.html#CylMesh.x0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.x1">x1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.x1">[1]</a>, <a href="moose_classes.html#CubeMesh.x1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.x1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.x1">[1]</a>, <a href="moose_classes.html#CylMesh.x1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.xdivs">xdivs (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.xdivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.xdivs">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xdivs">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.xdivs">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xdivs">[1]</a>, <a href="moose_classes.html#VectorTable.xdivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.xdivsA">xdivsA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.xdivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.xdivsB">xdivsB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.xdivsB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Func.xIn">xIn() (Func method)</a>, <a href="moose_builtins.html#Func.xIn">[1]</a>, <a href="moose_classes.html#Func.xIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.Xindex">Xindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Xindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Xindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.xmax">xmax (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.xmax">[1]</a>, <a href="moose_classes.html#Interpol.xmax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.xmax">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xmax">[1]</a>, <a href="moose_classes.html#Interpol2D.xmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.xmax">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xmax">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.xmax">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xmax">[1]</a>, <a href="moose_classes.html#VectorTable.xmax">[2]</a> - </dt> - - </dl></dd> - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#HHGate2D.xmaxA">xmaxA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.xmaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.xmaxB">xmaxB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.xmaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol.xmin">xmin (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.xmin">[1]</a>, <a href="moose_classes.html#Interpol.xmin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Interpol2D.xmin">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xmin">[1]</a>, <a href="moose_classes.html#Interpol2D.xmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#MarkovSolverBase.xmin">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xmin">[2]</a> - </dt> - - - <dt><a href="tmp.html#VectorTable.xmin">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xmin">[1]</a>, <a href="moose_classes.html#VectorTable.xmin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.xminA">xminA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xminA">[1]</a>, <a href="moose_classes.html#HHGate2D.xminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.xminB">xminB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xminB">[1]</a>, <a href="moose_classes.html#HHGate2D.xminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#TableBase.xplot">xplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.xplot">[1]</a>, <a href="moose_classes.html#TableBase.xplot">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.Xpower">Xpower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Xpower">[1]</a>, <a href="moose_classes.html#HHChannel.Xpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.Xpower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Xpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Xpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Xpower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Xpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Xpower">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#xyIn">xyIn()</a>, <a href="moose_builtins.html#xyIn">[1]</a>, <a href="moose_classes.html#xyIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#xyzIn">xyzIn()</a>, <a href="moose_builtins.html#xyzIn">[1]</a>, <a href="moose_classes.html#xyzIn">[2]</a> - </dt> - - </dl></td> -</tr></table> - -<h2 id="Y">Y</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#y">y</a>, <a href="moose_builtins.html#y">[1]</a>, <a href="moose_classes.html#y">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Annotator.y">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.y">[1]</a>, <a href="moose_classes.html#Annotator.y">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.y">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.y">[1]</a>, <a href="moose_classes.html#CompartmentBase.y">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.Y">Y (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Y">[1]</a>, <a href="moose_classes.html#HHChannel.Y">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.Y">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Y">[1]</a>, <a href="moose_classes.html#HHChannel2D.Y">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol.y">y (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.y">[1]</a>, <a href="moose_classes.html#Interpol.y">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#TableBase.y">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.y">[1]</a>, <a href="moose_classes.html#TableBase.y">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#ZombieHHChannel.Y">Y (ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Y">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Y">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.y0">y0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.y0">[1]</a>, <a href="moose_classes.html#CompartmentBase.y0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.y0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.y0">[1]</a>, <a href="moose_classes.html#CubeMesh.y0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.y0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.y0">[1]</a>, <a href="moose_classes.html#CylMesh.y0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.y1">y1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.y1">[1]</a>, <a href="moose_classes.html#CubeMesh.y1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.y1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.y1">[1]</a>, <a href="moose_classes.html#CylMesh.y1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.ydivs">ydivs (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ydivs">[1]</a>, <a href="moose_classes.html#Interpol2D.ydivs">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.ydivs">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ydivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ydivs">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.ydivsA">ydivsA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ydivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.ydivsA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.ydivsB">ydivsB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ydivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.ydivsB">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#yIn">yIn()</a>, <a href="moose_builtins.html#yIn">[1]</a>, <a href="moose_classes.html#yIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.Yindex">Yindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Yindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Yindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.ymax">ymax (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ymax">[1]</a>, <a href="moose_classes.html#Interpol2D.ymax">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.ymax">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ymax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ymax">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.ymaxA">ymaxA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ymaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.ymaxA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.ymaxB">ymaxB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ymaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.ymaxB">[2]</a> - </dt> - - - <dt><a href="tmp.html#Interpol2D.ymin">ymin (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ymin">[1]</a>, <a href="moose_classes.html#Interpol2D.ymin">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#MarkovSolverBase.ymin">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ymin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ymin">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHGate2D.yminA">yminA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.yminA">[1]</a>, <a href="moose_classes.html#HHGate2D.yminA">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHGate2D.yminB">yminB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.yminB">[1]</a>, <a href="moose_classes.html#HHGate2D.yminB">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.Ypower">Ypower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Ypower">[1]</a>, <a href="moose_classes.html#HHChannel.Ypower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.Ypower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Ypower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Ypower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Ypower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ypower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ypower">[2]</a> - </dt> - - </dl></dd> - </dl></td> -</tr></table> - -<h2 id="Z">Z</h2> -<table style="width: 100%" class="indextable genindextable"><tr> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#z">z</a>, <a href="moose_builtins.html#z">[1]</a>, <a href="moose_classes.html#z">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#Annotator.z">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.z">[1]</a>, <a href="moose_classes.html#Annotator.z">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.z">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.z">[1]</a>, <a href="moose_classes.html#CompartmentBase.z">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#HHChannel.Z">Z (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Z">[1]</a>, <a href="moose_classes.html#HHChannel.Z">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.Z">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Z">[1]</a>, <a href="moose_classes.html#HHChannel2D.Z">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#Interpol2D.z">z (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.z">[1]</a>, <a href="moose_classes.html#Interpol2D.z">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Z">Z (ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Z">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Z">[2]</a> - </dt> - - - <dt><a href="tmp.html#CompartmentBase.z0">z0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.z0">[1]</a>, <a href="moose_classes.html#CompartmentBase.z0">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CubeMesh.z0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.z0">[1]</a>, <a href="moose_classes.html#CubeMesh.z0">[2]</a> - </dt> - - - <dt><a href="tmp.html#CylMesh.z0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.z0">[1]</a>, <a href="moose_classes.html#CylMesh.z0">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#CubeMesh.z1">z1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.z1">[1]</a>, <a href="moose_classes.html#CubeMesh.z1">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#CylMesh.z1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.z1">[1]</a>, <a href="moose_classes.html#CylMesh.z1">[2]</a> - </dt> - - </dl></dd> - - <dt><a href="tmp.html#zIn">zIn()</a>, <a href="moose_builtins.html#zIn">[1]</a>, <a href="moose_classes.html#zIn">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel2D.Zindex">Zindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Zindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Zindex">[2]</a> - </dt> - - - <dt><a href="tmp.html#MgBlock.Zk">Zk (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.Zk">[1]</a>, <a href="moose_classes.html#MgBlock.Zk">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieBufPool">ZombieBufPool (built-in class)</a>, <a href="moose_builtins.html#ZombieBufPool">[1]</a>, <a href="moose_classes.html#ZombieBufPool">[2]</a> - </dt> - - </dl></td> - <td style="width: 33%" valign="top"><dl> - - <dt><a href="tmp.html#ZombieCaConc">ZombieCaConc (built-in class)</a>, <a href="moose_builtins.html#ZombieCaConc">[1]</a>, <a href="moose_classes.html#ZombieCaConc">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieCompartment">ZombieCompartment (built-in class)</a>, <a href="moose_builtins.html#ZombieCompartment">[1]</a>, <a href="moose_classes.html#ZombieCompartment">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieEnz">ZombieEnz (built-in class)</a>, <a href="moose_builtins.html#ZombieEnz">[1]</a>, <a href="moose_classes.html#ZombieEnz">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieFuncPool">ZombieFuncPool (built-in class)</a>, <a href="moose_builtins.html#ZombieFuncPool">[1]</a>, <a href="moose_classes.html#ZombieFuncPool">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel">ZombieHHChannel (built-in class)</a>, <a href="moose_builtins.html#ZombieHHChannel">[1]</a>, <a href="moose_classes.html#ZombieHHChannel">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieMMenz">ZombieMMenz (built-in class)</a>, <a href="moose_builtins.html#ZombieMMenz">[1]</a>, <a href="moose_classes.html#ZombieMMenz">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombiePool">ZombiePool (built-in class)</a>, <a href="moose_builtins.html#ZombiePool">[1]</a>, <a href="moose_classes.html#ZombiePool">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieReac">ZombieReac (built-in class)</a>, <a href="moose_builtins.html#ZombieReac">[1]</a>, <a href="moose_classes.html#ZombieReac">[2]</a> - </dt> - - - <dt><a href="tmp.html#HHChannel.Zpower">Zpower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Zpower">[1]</a>, <a href="moose_classes.html#HHChannel.Zpower">[2]</a> - </dt> - - <dd><dl> - - <dt><a href="tmp.html#HHChannel2D.Zpower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Zpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Zpower">[2]</a> - </dt> - - - <dt><a href="tmp.html#ZombieHHChannel.Zpower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Zpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Zpower">[2]</a> - </dt> - - </dl></dd> - </dl></td> -</tr></table> - - - - </div> - </div> - </div> - <div class="sphinxsidebar"> - <div class="sphinxsidebarwrapper"> - <p class="logo"><a href="index.html"> - <img class="logo" src="_static/moose_logo.png" alt="Logo"/> - </a></p> - - - -<div id="searchbox" style="display: none"> - <h3>Quick search</h3> - <form class="search" action="search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - <p class="searchtip" style="font-size: 90%"> - Enter search terms or a module, class or function name. - </p> -</div> -<script type="text/javascript">$('#searchbox').show(0);</script> - </div> - </div> - <div class="clearer"></div> - </div> - <div class="related"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="#" title="General Index" - >index</a></li> - <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> - - <li><a href="index.html">MOOSE 3.0 documentation</a> »</li> - - </ul> - </div> - <div class="footer"> - © Copyright 2014, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray and Dilawar Singh. - 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<div class="body"> - - <div class="section" id="the-multiscale-object-oriented-simulation-environment"> -<h1>the Multiscale Object-Oriented Simulation Environment<a class="headerlink" href="#the-multiscale-object-oriented-simulation-environment" title="Permalink to this headline">¶</a></h1> -<p>Contents:</p> -<div class="toctree-wrapper compound"> -<ul> -<li class="toctree-l1"><a class="reference internal" href="moose_overview.html">MOOSE = Multiscale Object Oriented Simulation Environment.</a><ul> -<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#how-to-use-the-documentation">How to use the documentation</a></li> -</ul> -</li> -<li class="toctree-l1"><a class="reference internal" href="moose_overview.html#brief-overview-of-pymoose">Brief overview of PyMOOSE</a><ul> -<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#vec">vec</a></li> -<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#melement">melement</a></li> -<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#creating-melements">Creating melements</a></li> -<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#module-functions">module functions</a></li> -</ul> -</li> -<li class="toctree-l1"><a class="reference internal" href="moose_builtins.html">MOOSE Builtins</a></li> -<li class="toctree-l1"><a class="reference internal" href="moose_classes.html">MOOSE Classes</a></li> -</ul> -</div> -</div> -<div class="section" id="indices-and-tables"> -<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1> -<ul class="simple"> -<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li> -<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li> -<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li> -</ul> -</div> - - - </div> - </div> - </div> - <div class="sphinxsidebar"> - <div class="sphinxsidebarwrapper"> - <p class="logo"><a href="#"> - <img class="logo" src="_static/moose_logo.png" alt="Logo"/> - </a></p> - <h3><a href="#">Table Of Contents</a></h3> - <ul> -<li><a class="reference internal" href="#">the Multiscale Object-Oriented Simulation Environment</a><ul> -</ul> -</li> -<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li> -</ul> - - <h4>Next topic</h4> - <p class="topless"><a href="moose_overview.html" - title="next chapter">MOOSE = Multiscale Object Oriented Simulation Environment.</a></p> - <h3>This Page</h3> - <ul class="this-page-menu"> - <li><a href="_sources/index.txt" - rel="nofollow">Show Source</a></li> - </ul> -<div id="searchbox" style="display: none"> - <h3>Quick search</h3> - <form class="search" action="search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - <p class="searchtip" style="font-size: 90%"> - Enter search terms or a module, class or function name. - </p> -</div> -<script type="text/javascript">$('#searchbox').show(0);</script> - </div> - </div> - <div class="clearer"></div> - </div> - <div class="related"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="moose_overview.html" title="MOOSE = Multiscale Object Oriented Simulation Environment." - >next</a> |</li> - <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> - - <li><a href="#">MOOSE 3.0 documentation</a> »</li> - - </ul> - </div> - <div class="footer"> - © Copyright 2014, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray and Dilawar Singh. - Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3. - </div> - </body> -</html> \ No newline at end of file diff --git a/docs/user/html/pymoose/moose_builtins.html b/docs/user/html/pymoose/moose_builtins.html deleted file mode 100644 index 8280c4d392ac6ef373028e5de0c4c617b27ca1eb..0000000000000000000000000000000000000000 --- a/docs/user/html/pymoose/moose_builtins.html +++ /dev/null @@ -1,889 +0,0 @@ - - -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" - "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - - <title>MOOSE builtins — MOOSE 3.0 documentation</title> - - <link rel="stylesheet" href="_static/default.css" type="text/css" /> - <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> - - <script type="text/javascript"> - var DOCUMENTATION_OPTIONS = { - URL_ROOT: '', - VERSION: '3.0', - COLLAPSE_INDEX: false, - FILE_SUFFIX: '.html', - HAS_SOURCE: true - }; - </script> - <script type="text/javascript" src="_static/jquery.js"></script> - <script type="text/javascript" src="_static/underscore.js"></script> - <script type="text/javascript" src="_static/doctools.js"></script> - <link rel="top" title="MOOSE 3.0 documentation" href="index.html" /> - <link rel="next" title="MOOSE Classes" href="moose_classes.html" /> - <link rel="prev" title="Welcome to MOOSE documentation!" href="index.html" /> - </head> - <body> - <div class="related"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="right" > - <a href="moose_classes.html" title="MOOSE Classes" - accesskey="N">next</a> |</li> - <li class="right" > - <a href="index.html" title="Welcome to MOOSE documentation!" - accesskey="P">previous</a> |</li> - <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> - <li><a href="index.html">MOOSE 3.0 documentation</a> »</li> - </ul> - </div> - - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body"> - - <div class="section" id="module-moose"> -<span id="moose-builtins"></span><h1>MOOSE builtins<a class="headerlink" href="#module-moose" title="Permalink to this headline">¶</a></h1> -<div class="section" id="moose-multiscale-object-oriented-simulation-environment"> -<h2>MOOSE = Multiscale Object Oriented Simulation Environment.<a class="headerlink" href="#moose-multiscale-object-oriented-simulation-environment" title="Permalink to this headline">¶</a></h2> -<div class="section" id="how-to-use-the-documentation"> -<h3>How to use the documentation<a class="headerlink" href="#how-to-use-the-documentation" title="Permalink to this headline">¶</a></h3> -<p>MOOSE documentation is split into Python documentation and builtin -documentation. The functions and classes that are only part of the -Python interface can be viewed via Python’s builtin <tt class="docutils literal"><span class="pre">help</span></tt> -function:</p> -<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">help</span><span class="p">(</span><span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">)</span> -</pre></div> -</div> -<p>...</p> -<p>The documentation built into main C++ code of MOOSE can be accessed -via the module function <tt class="docutils literal"><span class="pre">doc</span></tt>:</p> -<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">moose</span><span class="o">.</span><span class="n">doc</span><span class="p">(</span><span class="s">'Neutral'</span><span class="p">)</span> -</pre></div> -</div> -<p>...</p> -<p>To get documentation about a particular field:</p> -<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">moose</span><span class="o">.</span><span class="n">doc</span><span class="p">(</span><span class="s">'Neutral.childMsg'</span><span class="p">)</span> -</pre></div> -</div> -</div> -</div> -<div class="section" id="brief-overview-of-pymoose"> -<h2>Brief overview of PyMOOSE<a class="headerlink" href="#brief-overview-of-pymoose" title="Permalink to this headline">¶</a></h2> -<p>Classes:</p> -<div class="section" id="vec"> -<h3>vec<a class="headerlink" href="#vec" title="Permalink to this headline">¶</a></h3> -<p>this is the unique identifier of a MOOSE object. Note that you can -create multiple references to the same MOOSE object in Python, but as -long as they have the same path/id value, they all point to the same -entity in MOOSE.</p> -<p>Constructor:</p> -<p>You can create a new vec using the constructor:</p> -<p>vec(path, dimension, classname)</p> -<p>Fields:</p> -<p>value – unsigned integer representation of id of this vec</p> -<p>path – string representing the path corresponding this vec</p> -<p>shape – tuple containing the dimensions of this vec</p> -<p>Apart from these, every vec exposes the fields of all its elements -in a vectorized form. For example:</p> -<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">iaf</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">vec</span><span class="p">(</span><span class="s">'/iaf'</span><span class="p">,</span> <span class="p">(</span><span class="mi">10</span><span class="p">),</span> <span class="s">'IntFire'</span><span class="p">)</span> -<span class="gp">>>> </span><span class="n">iaf</span><span class="o">.</span><span class="n">Vm</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span> -<span class="gp">>>> </span><span class="k">print</span> <span class="n">iaf</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">Vm</span> -<span class="go">5.0</span> -<span class="gp">>>> </span><span class="k">print</span> <span class="n">iaf</span><span class="o">.</span><span class="n">Vm</span> -<span class="go">array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])</span> -</pre></div> -</div> -<p>Methods:</p> -<p>vec implements part of the sequence protocol:</p> -<p>len(em) – the first dimension of em.</p> -<p>em[n] – the n-th element in em.</p> -<p>em[n1:n2] – a tuple containing n1 to n2-th (exclusive) element in em.</p> -<p>elem in em – True if elem is contained in em.</p> -</div> -<div class="section" id="melement"> -<h3>melement<a class="headerlink" href="#melement" title="Permalink to this headline">¶</a></h3> -<p>Single moose object. It has three numbers to uniquely identify it:</p> -<p>id - id of the vec containing this element</p> -<p>dataIndex - index of this element in the container vec</p> -<p>fieldIndex - if this is a tertiary object, i.e. acts -as a field in another element (like synapse[0] in IntFire[1]), then -the index of this field in the containing element.</p> -<p>Methods:</p> -<p>getId – vec object containing this element. -vec() – vec object containing this element.</p> -<p>getDataIndex() – unsigned integer representing the index of this -element in containing MOOSE object.</p> -<p>getFieldIndex() – unsigned integer representing the index of this -element as a field in the containing Element.</p> -<p>getFieldType(field) – human readable datatype information of field</p> -<p>getField(field) – get value of field</p> -<p>setField(field, value) – assign value to field</p> -<p>getFieldNames(fieldType) – tuple containing names of all the fields -of type fieldType. fieldType can be valueFinfo, lookupFinfo, srcFinfo, -destFinfo and sharedFinfo. If nothing is passed, a union of all of the -above is used and all the fields are returned.</p> -<p>connect(srcField, destObj, destField, msgType) – connect srcField of -this element to destField of destObj.</p> -<p>melement is something like an abstract base class in C++. The concrete -base class is Neutral. However you do not need to cast objects down to -access their fields. The PyMOOSE interface will automatically do the -check for you and raise an exception if the specified field does not -exist for the current element.</p> -</div> -<div class="section" id="creating-melements"> -<h3>Creating melements<a class="headerlink" href="#creating-melements" title="Permalink to this headline">¶</a></h3> -<p>To create the objects of concrete subclasses of melement, the class -can be called as follows:</p> -<p>melement(path, dims, dtype, parent)</p> -<p>path: This is like unix filesystem path and is the concatenation of -name of the element to be created and that of all its ancestors -spearated by <cite>/</cite>. For example, path=`/a/b` will create the element -named <cite>b</cite> under element <cite>a</cite>. Note that if <cite>a</cite> does not exist, this -will raise an error. However, if <cite>parent</cite> is specified, <cite>path</cite> should -contain only the name of the element.</p> -<p>dims: (optional) tuple specifying the dimension of the containing melement to be -created. It is (1,) by default.</p> -<p>dtype: string specifying the class name of the element to be created.</p> -<p>parent: (optional) string specifying the path of the parent element or -the Id or the ObjId of the parent element or a reference to the parent -element. If this is specified, the first argument <cite>path</cite> is treated as -the name of the element to be created.</p> -<p>All arguments can be passed as keyword arguments.</p> -<p>For concrete subclasses of melement, you do not need to pass the class -argument because the class name is passed automatically to <cite>melement</cite> -__init__ method.</p> -<p>a = Neutral(‘alpha’) # Creates element named <cite>alpha</cite> under current working element -b = Neutral(‘alpha/beta’) # Creates the element named <cite>beta</cite> under <cite>alpha</cite> -c = Cell(‘charlie’, parent=a) # creates element <cite>charlie</cite> under <cite>alpha</cite> -d = DiffAmp(‘delta’, parent=’alpha/beta’) # creates element <cite>delta</cite> under <cite>beta</cite></p> -</div> -<div class="section" id="module-functions"> -<h3>module functions<a class="headerlink" href="#module-functions" title="Permalink to this headline">¶</a></h3> -<p>element(path) - returns a reference to an existing object converted to -the right class. Raises ValueError if path does not exist.</p> -<p>copy(src=<src>, dest=<dest>, name=<name_of_the_copy>, n=<num_copies>, -copyMsg=<whether_to_copy_messages) – make a copy of source object as -a child of the destination object.</p> -<p>move(src, dest) – move src object under dest object.</p> -<p>useClock(tick, path, update_function) – schedule <update_function> of -every object that matches <path> on clock no. <tick>. Most commonly -the function is ‘process’. NOTE: unlike earlier versions, now -autoschedule is not available. You have to call useClock for every -element that should be updated during the simulation.</p> -<p>The sequence of clockticks with the same dt is according to their -number. This is utilized for controlling the order of updates in -various objects where it matters.</p> -<p>The following convention should be observed when assigning clockticks -to various components of a model:</p> -<p>Clock ticks 0-3 are for electrical (biophysical) components, 4 and 5 -are for chemical kinetics, 6 and 7 are for lookup tables and stimulus, -8 and 9 are for recording tables.</p> -<p>Generally, ‘process’ is the method to be assigned a clock -tick. Notable exception is ‘init’ method of Compartment class which is -assigned tick 0.</p> -<p>0 : Compartment: ‘init’ -1 : Compartment: ‘process’ -2 : HHChannel and other channels: ‘process’ -3 : CaConc : ‘process’ -4,5 : Elements for chemical kinetics : ‘process’ -6,7 : Lookup (tables), stimulus : ‘process’ -8,9 : Tables for plotting : process</p> -<p>Example: -moose.useClock(0, ‘/model/compartment_1’, ‘init’) -moose.useClock(1, ‘/model/compartment_1’, ‘process’)</p> -<p>setClock(tick, dt) – set dt of clock no <tick>.</p> -<p>start(runtime) – start simulation of <runtime> time.</p> -<p>reinit() – reinitialize simulation.</p> -<p>stop() – stop simulation</p> -<p>isRunning() – true if simulation is in progress, false otherwise.</p> -<p>exists(path) – true if there is a pre-existing object with the specified path.</p> -<p>loadModel(filepath, modelpath) – load file in <filepath> into node -<modelpath> of the moose model-tree.</p> -<p>setCwe(obj) – set the current working element to <obj> - which can be -either a string representing the path of the object in the moose -model-tree, or an vec. -ce(obj) – an alias for setCwe.</p> -<p>getCwe() – returns vec containing the current working element. -pwe() – an alias for getCwe.</p> -<p>showfields(obj) – print the fields in object in human readable format</p> -<p>le(obj) – list element under object, if no parameter specified, list -elements under current working element</p> -<dl class="function"> -<dt id="moose.pwe"> -<tt class="descclassname">moose.</tt><tt class="descname">pwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.pwe" title="Permalink to this definition">¶</a></dt> -<dd><p>Print present working element. Convenience function for GENESIS -users. If you want to retrieve the element in stead of printing -the path, use moose.getCwe()</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.le"> -<tt class="descclassname">moose.</tt><tt class="descname">le</tt><big>(</big><em>el=None</em><big>)</big><a class="headerlink" href="#moose.le" title="Permalink to this definition">¶</a></dt> -<dd><p>List elements under <cite>el</cite> or current element if no argument -specified.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : str/melement/vec/None</p> -<blockquote> -<div><dl class="docutils"> -<dt>The element or the path under which to look. If <cite>None</cite>, children</dt> -<dd><p class="first last">of current working element are displayed.</p> -</dd> -</dl> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.ce"> -<tt class="descclassname">moose.</tt><tt class="descname">ce</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.ce" title="Permalink to this definition">¶</a></dt> -<dd><p>Set the current working element. ‘ce’ is an alias of this function</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.showfield"> -<tt class="descclassname">moose.</tt><tt class="descname">showfield</tt><big>(</big><em>el</em>, <em>field='*'</em>, <em>showtype=False</em><big>)</big><a class="headerlink" href="#moose.showfield" title="Permalink to this definition">¶</a></dt> -<dd><p>Show the fields of the element <cite>el</cite>, their data types and -values in human readable format. Convenience function for GENESIS -users.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : melement/str</p> -<blockquote> -<div><p>Element or path of an existing element.</p> -</div></blockquote> -<p><strong>field</strong> : str</p> -<blockquote> -<div><p>Field to be displayed. If ‘*’ (default), all fields are displayed.</p> -</div></blockquote> -<p><strong>showtype</strong> : bool</p> -<blockquote> -<div><p>If True show the data type of each field. False by default.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.showmsg"> -<tt class="descclassname">moose.</tt><tt class="descname">showmsg</tt><big>(</big><em>el</em><big>)</big><a class="headerlink" href="#moose.showmsg" title="Permalink to this definition">¶</a></dt> -<dd><p>Print the incoming and outgoing messages of <cite>el</cite>.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : melement/vec/str</p> -<blockquote> -<div><p>Object whose messages are to be displayed.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.doc"> -<tt class="descclassname">moose.</tt><tt class="descname">doc</tt><big>(</big><em>arg</em>, <em>inherited=True</em>, <em>paged=True</em><big>)</big><a class="headerlink" href="#moose.doc" title="Permalink to this definition">¶</a></dt> -<dd><p>Display the documentation for class or field in a class.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>arg</strong> : str/class/melement/vec</p> -<blockquote> -<div><p>A string specifying a moose class name and a field name -separated by a dot. e.g., ‘Neutral.name’. Prepending <cite>moose.</cite> -is allowed. Thus moose.doc(‘moose.Neutral.name’) is equivalent -to the above. -It can also be string specifying just a moose class name or a -moose class or a moose object (instance of melement or vec -or there subclasses). In that case, the builtin documentation -for the corresponding moose class is displayed.</p> -</div></blockquote> -<p><strong>paged: bool</strong></p> -<blockquote> -<div><p>Whether to display the docs via builtin pager or print and -exit. If not specified, it defaults to False and -moose.doc(xyz) will print help on xyz and return control to -command line.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">None</p> -</td> -</tr> -<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first"><strong>NameError</strong></p> -<blockquote class="last"> -<div><p>If class or field does not exist.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.element"> -<tt class="descclassname">moose.</tt><tt class="descname">element</tt><big>(</big><em>arg</em><big>)</big> → moose object<a class="headerlink" href="#moose.element" title="Permalink to this definition">¶</a></dt> -<dd><p>Convert a path or an object to the appropriate builtin moose class -instance</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>arg</strong> : str/vec/moose object</p> -<blockquote> -<div><p>path of the moose element to be converted or another element (possibly -available as a superclass instance).</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">melement</p> -<blockquote class="last"> -<div><p>MOOSE element (object) corresponding to the <cite>arg</cite> converted to write subclass.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.getFieldNames"> -<tt class="descclassname">moose.</tt><tt class="descname">getFieldNames</tt><big>(</big><em>className</em>, <em>finfoType='valueFinfo'</em><big>)</big> → tuple<a class="headerlink" href="#moose.getFieldNames" title="Permalink to this definition">¶</a></dt> -<dd><p>Get a tuple containing the name of all the fields of <cite>finfoType</cite> -kind.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>className</strong> : string</p> -<blockquote> -<div><p>Name of the class to look up.</p> -</div></blockquote> -<p><strong>finfoType</strong> : string</p> -<blockquote> -<div><p>The kind of field (<cite>valueFinfo</cite>, <cite>srcFinfo</cite>, <cite>destFinfo</cite>, -<cite>lookupFinfo</cite>, <cite>fieldElementFinfo</cite>.).</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">tuple</p> -<blockquote class="last"> -<div><p>Names of the fields of type <cite>finfoType</cite> in class <cite>className</cite>.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.copy"> -<tt class="descclassname">moose.</tt><tt class="descname">copy</tt><big>(</big><em>src</em>, <em>dest</em>, <em>name</em>, <em>n</em>, <em>toGlobal</em>, <em>copyExtMsg</em><big>)</big> → bool<a class="headerlink" href="#moose.copy" title="Permalink to this definition">¶</a></dt> -<dd><p>Make copies of a moose object.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>src</strong> : vec, element or str</p> -<blockquote> -<div><p>source object.</p> -</div></blockquote> -<p><strong>dest</strong> : vec, element or str</p> -<blockquote> -<div><p>Destination object to copy into.</p> -</div></blockquote> -<p><strong>name</strong> : str</p> -<blockquote> -<div><p>Name of the new object. If omitted, name of the original will be used.</p> -</div></blockquote> -<p><strong>n</strong> : int</p> -<blockquote> -<div><p>Number of copies to make.</p> -</div></blockquote> -<p><strong>toGlobal</strong> : int</p> -<blockquote> -<div><p>Relevant for parallel environments only. If false, the copies will -reside on local node, otherwise all nodes get the copies.</p> -</div></blockquote> -<p><strong>copyExtMsg</strong> : int</p> -<blockquote> -<div><p>If true, messages to/from external objects are also copied.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">vec</p> -<blockquote class="last"> -<div><p>newly copied vec</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.move"> -<tt class="descclassname">moose.</tt><tt class="descname">move</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.move" title="Permalink to this definition">¶</a></dt> -<dd><p>Move a vec object to a destination.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.delete"> -<tt class="descclassname">moose.</tt><tt class="descname">delete</tt><big>(</big><em>obj</em><big>)</big> → None<a class="headerlink" href="#moose.delete" title="Permalink to this definition">¶</a></dt> -<dd><p>Delete the underlying moose object. This does not delete any of the -Python objects referring to this vec but does invalidate them. Any -attempt to access them will raise a ValueError.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>id</strong> : vec</p> -<blockquote> -<div><p>vec of the object to be deleted.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.useClock"> -<tt class="descclassname">moose.</tt><tt class="descname">useClock</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.useClock" title="Permalink to this definition">¶</a></dt> -<dd><p>Schedule objects on a specified clock</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.setClock"> -<tt class="descclassname">moose.</tt><tt class="descname">setClock</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.setClock" title="Permalink to this definition">¶</a></dt> -<dd><p>Set the dt of a clock.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.start"> -<tt class="descclassname">moose.</tt><tt class="descname">start</tt><big>(</big><em>time</em><big>)</big> → None<a class="headerlink" href="#moose.start" title="Permalink to this definition">¶</a></dt> -<dd><p>Run simulation for <cite>t</cite> time. Advances the simulator clock by <cite>t</cite> -time.</p> -<p>After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before -CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the -simulator behaviour will be undefined. Once moose.reinit() has been -called, you can call moose.start(t) as many time as you like. This -will continue the simulation from the last state for <cite>t</cite> time.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>t</strong> : float</p> -<blockquote> -<div><p>duration of simulation.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -<div class="admonition-see-also admonition seealso"> -<p class="first admonition-title">See also</p> -<dl class="last docutils"> -<dt><a class="reference internal" href="#moose.reinit" title="moose.reinit"><tt class="xref py py-obj docutils literal"><span class="pre">moose.reinit</span></tt></a></dt> -<dd>(Re)initialize simulation</dd> -</dl> -</div> -</dd></dl> - -<dl class="function"> -<dt id="moose.reinit"> -<tt class="descclassname">moose.</tt><tt class="descname">reinit</tt><big>(</big><big>)</big> → None<a class="headerlink" href="#moose.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>Reinitialize simulation.</p> -<p>This function (re)initializes moose simulation. It must be called -before you start the simulation (see moose.start). If you want to -continue simulation after you have called moose.reinit() and -moose.start(), you must NOT call moose.reinit() again. Calling -moose.reinit() again will take the system back to initial setting -(like clear out all data recording tables, set state variables to -their initial values, etc.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.stop"> -<tt class="descclassname">moose.</tt><tt class="descname">stop</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.stop" title="Permalink to this definition">¶</a></dt> -<dd><p>Stop simulation</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.isRunning"> -<tt class="descclassname">moose.</tt><tt class="descname">isRunning</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.isRunning" title="Permalink to this definition">¶</a></dt> -<dd><p>True if the simulation is currently running.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.exists"> -<tt class="descclassname">moose.</tt><tt class="descname">exists</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.exists" title="Permalink to this definition">¶</a></dt> -<dd><p>True if there is an object with specified path.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.writeSBML"> -<tt class="descclassname">moose.</tt><tt class="descname">writeSBML</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.writeSBML" title="Permalink to this definition">¶</a></dt> -<dd><p>Export biochemical model to an SBML file.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.readSBML"> -<tt class="descclassname">moose.</tt><tt class="descname">readSBML</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.readSBML" title="Permalink to this definition">¶</a></dt> -<dd><p>Import SBML model to Moose.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.loadModel"> -<tt class="descclassname">moose.</tt><tt class="descname">loadModel</tt><big>(</big><em>filename</em>, <em>modelpath</em>, <em>solverclass</em><big>)</big> → vec<a class="headerlink" href="#moose.loadModel" title="Permalink to this definition">¶</a></dt> -<dd><p>Load model from a file to a specified path.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>filename</strong> : str</p> -<blockquote> -<div><p>model description file.</p> -</div></blockquote> -<p><strong>modelpath</strong> : str</p> -<blockquote> -<div><p>moose path for the top level element of the model to be created.</p> -</div></blockquote> -<p><strong>solverclass</strong> : str, optional</p> -<blockquote> -<div><p>solver type to be used for simulating the model.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">vec</p> -<blockquote class="last"> -<div><p>loaded model container vec.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.saveModel"> -<tt class="descclassname">moose.</tt><tt class="descname">saveModel</tt><big>(</big><em>source</em>, <em>filename</em><big>)</big> → None<a class="headerlink" href="#moose.saveModel" title="Permalink to this definition">¶</a></dt> -<dd><p>Save model rooted at <cite>source</cite> to file <cite>filename</cite>.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>source</strong> : vec/element/str</p> -<blockquote> -<div><p>root of the model tree</p> -</div></blockquote> -<p><strong>filename</strong> : str</p> -<blockquote> -<div><p>destination file to save the model in.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.connect"> -<tt class="descclassname">moose.</tt><tt class="descname">connect</tt><big>(</big><em>src</em>, <em>src_field</em>, <em>dest</em>, <em>dest_field</em>, <em>message_type</em><big>)</big> → bool<a class="headerlink" href="#moose.connect" title="Permalink to this definition">¶</a></dt> -<dd><p>Create a message between <cite>src_field</cite> on <cite>src</cite> object to <cite>dest_field</cite> -on <cite>dest</cite> object.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>src</strong> : element/vec/string</p> -<blockquote> -<div><p>the source object (or its path)</p> -</div></blockquote> -<p><strong>src_field</strong> : str</p> -<blockquote> -<div><p>the source field name. Fields listed under <cite>srcFinfo</cite> and -<cite>sharedFinfo</cite> qualify for this.</p> -</div></blockquote> -<p><strong>dest</strong> : element/vec/string</p> -<blockquote> -<div><p>the destination object.</p> -</div></blockquote> -<p><strong>dest_field</strong> : str</p> -<blockquote> -<div><p>the destination field name. Fields listed under <cite>destFinfo</cite> -and <cite>sharedFinfo</cite> qualify for this.</p> -</div></blockquote> -<p><strong>message_type</strong> : str (optional)</p> -<blockquote> -<div><p>Type of the message. Can be <cite>Single</cite>, <cite>OneToOne</cite>, <cite>OneToAll</cite>. -If not specified, it defaults to <cite>Single</cite>.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">melement</p> -<blockquote class="last"> -<div><p>message-manager for the newly created message.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.getCwe"> -<tt class="descclassname">moose.</tt><tt class="descname">getCwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.getCwe" title="Permalink to this definition">¶</a></dt> -<dd><p>Get the current working element. ‘pwe’ is an alias of this function.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.setCwe"> -<tt class="descclassname">moose.</tt><tt class="descname">setCwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.setCwe" title="Permalink to this definition">¶</a></dt> -<dd><p>Set the current working element. ‘ce’ is an alias of this function</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.getFieldDict"> -<tt class="descclassname">moose.</tt><tt class="descname">getFieldDict</tt><big>(</big><em>className</em>, <em>finfoType</em><big>)</big> → dict<a class="headerlink" href="#moose.getFieldDict" title="Permalink to this definition">¶</a></dt> -<dd><p>Get dictionary of field names and types for specified class.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>className</strong> : str</p> -<blockquote> -<div><p>MOOSE class to find the fields of.</p> -</div></blockquote> -<p><strong>finfoType</strong> : str (optional)</p> -<blockquote> -<div><p>Finfo type of the fields to find. If empty or not specified, all -fields will be retrieved.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">dict</p> -<blockquote class="last"> -<div><p>field names and their types.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -<p class="rubric">Notes</p> -<p>This behaviour is different from <cite>getFieldNames</cite> where only -<cite>valueFinfo`s are returned when `finfoType</cite> remains unspecified.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.getField"> -<tt class="descclassname">moose.</tt><tt class="descname">getField</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.getField" title="Permalink to this definition">¶</a></dt> -<dd><p>getField(element, field, fieldtype) – Get specified field of specified type from object vec.</p> -</dd></dl> - -<dl class="function"> -<dt id="moose.seed"> -<tt class="descclassname">moose.</tt><tt class="descname">seed</tt><big>(</big><em>seedvalue</em><big>)</big> → None<a class="headerlink" href="#moose.seed" title="Permalink to this definition">¶</a></dt> -<dd><p>Reseed MOOSE random number generator.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>seed</strong> : int</p> -<blockquote> -<div><p>Optional value to use for seeding. If 0, a random seed is -automatically created using the current system time and other -information. If not specified, it defaults to 0.</p> -</div></blockquote> -</td> -</tr> -<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.rand"> -<tt class="descclassname">moose.</tt><tt class="descname">rand</tt><big>(</big><em>) -> [0</em>, <em>1</em><big>)</big><a class="headerlink" href="#moose.rand" title="Permalink to this definition">¶</a></dt> -<dd><table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">float in [0, 1) real interval generated by MT19937.</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.wildcardFind"> -<tt class="descclassname">moose.</tt><tt class="descname">wildcardFind</tt><big>(</big><em>expression</em><big>)</big> → tuple of melements.<a class="headerlink" href="#moose.wildcardFind" title="Permalink to this definition">¶</a></dt> -<dd><p>Find an object by wildcard.</p> -<table class="docutils field-list" frame="void" rules="none"> -<col class="field-name" /> -<col class="field-body" /> -<tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>expression</strong> : str</p> -<blockquote class="last"> -<div><p>MOOSE allows wildcard expressions of the form:</p> -<div class="highlight-python"><div class="highlight"><pre><span class="p">{</span><span class="n">PATH</span><span class="p">}</span><span class="o">/</span><span class="p">{</span><span class="n">WILDCARD</span><span class="p">}[{</span><span class="n">CONDITION</span><span class="p">}]</span> -</pre></div> -</div> -<p>where {PATH} is valid path in the element tree. -{WILDCARD} can be <cite>#</cite> or <cite>##</cite>.</p> -<p><cite>#</cite> causes the search to be restricted to the children of the -element specified by {PATH}.</p> -<p><cite>##</cite> makes the search to recursively go through all the descendants -of the {PATH} element. -{CONDITION} can be:</p> -<div class="highlight-python"><pre>TYPE={CLASSNAME} : an element satisfies this condition if it is of -class {CLASSNAME}. -ISA={CLASSNAME} : alias for TYPE={CLASSNAME} -CLASS={CLASSNAME} : alias for TYPE={CLASSNAME} -FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with -{VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=, -!=, >, <, >=, <=).</pre> -</div> -<p>For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all -the objects under /mymodel whose Vm field is >= -65.</p> -</div></blockquote> -</td> -</tr> -</tbody> -</table> -</dd></dl> - -<dl class="function"> -<dt id="moose.quit"> -<tt class="descclassname">moose.</tt><tt class="descname">quit</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.quit" title="Permalink to this definition">¶</a></dt> -<dd><p>Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.</p> -</dd></dl> - -</div> -</div> -<p>,</p> -</div> - - - </div> - </div> - </div> - <div class="sphinxsidebar"> - <div class="sphinxsidebarwrapper"> - <h3><a href="index.html">Table Of Contents</a></h3> - <ul> -<li><a class="reference internal" href="#">MOOSE builtins</a><ul> -<li><a class="reference internal" href="#moose-multiscale-object-oriented-simulation-environment">MOOSE = Multiscale Object Oriented Simulation Environment.</a><ul> -<li><a class="reference internal" href="#how-to-use-the-documentation">How to use the documentation</a></li> -</ul> -</li> -<li><a class="reference internal" href="#brief-overview-of-pymoose">Brief overview of PyMOOSE</a><ul> -<li><a class="reference internal" href="#vec">vec</a></li> -<li><a class="reference internal" href="#melement">melement</a></li> -<li><a class="reference internal" href="#creating-melements">Creating melements</a></li> -<li><a class="reference internal" href="#module-functions">module functions</a></li> -</ul> -</li> -</ul> -</li> -</ul> - - <h4>Previous topic</h4> - <p class="topless"><a href="index.html" - title="previous chapter">Welcome to MOOSE documentation!</a></p> - <h4>Next topic</h4> - <p class="topless"><a href="moose_classes.html" - title="next chapter">MOOSE Classes</a></p> - <h3>This Page</h3> - <ul class="this-page-menu"> - <li><a href="_sources/moose_builtins.txt" - rel="nofollow">Show Source</a></li> - </ul> -<div id="searchbox" style="display: none"> - <h3>Quick search</h3> - <form class="search" action="search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - <p class="searchtip" style="font-size: 90%"> - Enter search terms or a module, class or function name. - </p> -</div> -<script type="text/javascript">$('#searchbox').show(0);</script> - </div> - </div> - <div class="clearer"></div> - </div> - <div class="related"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="right" > - <a href="moose_classes.html" title="MOOSE Classes" - >next</a> |</li> - <li class="right" > - <a href="index.html" title="Welcome to MOOSE documentation!" - >previous</a> |</li> - <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> - <li><a href="index.html">MOOSE 3.0 documentation</a> »</li> - </ul> - </div> - <div class="footer"> - © Copyright 2014, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray and Dilawar Singh. - Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3. - </div> - </body> -</html> \ No newline at end of file diff --git a/docs/user/html/pymoose/moose_classes.html b/docs/user/html/pymoose/moose_classes.html deleted file mode 100644 index da20c04767a5e07fb2cd515858627154a94a221d..0000000000000000000000000000000000000000 --- a/docs/user/html/pymoose/moose_classes.html +++ /dev/null @@ -1,11794 +0,0 @@ - - -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" - "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="Content-Type" content="text/html; 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The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.setOutputOffset"> -<tt class="descname">setOutputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.setOutputOffset" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.getOutputOffset"> -<tt class="descname">getOutputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getOutputOffset" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.setScale"> -<tt class="descname">setScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.setScale" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.getScale"> -<tt class="descname">getScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getScale" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Input message to the adaptor. If multiple inputs are received, the system averages the inputs.</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p> -</dd></dl> - -<dl class="method"> -<dt id="Adaptor.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.output"> -<tt class="descname">output</tt><a class="headerlink" href="#Adaptor.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends the output value every timestep.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.requestInput"> -<tt class="descname">requestInput</tt><a class="headerlink" href="#Adaptor.requestInput" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>source message field</em>) Sends out the request. Issued from the process call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.requestField"> -<tt class="descname">requestField</tt><a class="headerlink" href="#Adaptor.requestField" title="Permalink to this definition">¶</a></dt> -<dd><p>Pd (<em>source message field</em>) Sends out a request to a generic double field. Issued from the process call.Works for any number of targets.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.inputOffset"> -<tt class="descname">inputOffset</tt><a class="headerlink" href="#Adaptor.inputOffset" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Offset to apply to input message, before scaling</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.outputOffset"> -<tt class="descname">outputOffset</tt><a class="headerlink" href="#Adaptor.outputOffset" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Offset to apply at output, after scaling</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.scale"> -<tt class="descname">scale</tt><a class="headerlink" href="#Adaptor.scale" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Scaling factor to apply to input</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Adaptor.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#Adaptor.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) This is the linearly transformed output.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Annotator"> -<em class="property">class </em><tt class="descname">Annotator</tt><a class="headerlink" href="#Annotator" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Annotator.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setNotes"> -<tt class="descname">setNotes</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setNotes" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getNotes"> -<tt class="descname">getNotes</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getNotes" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setColor"> -<tt class="descname">setColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setColor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getColor"> -<tt class="descname">getColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getColor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setTextColor"> -<tt class="descname">setTextColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setTextColor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getTextColor"> -<tt class="descname">getTextColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getTextColor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.setIcon"> -<tt class="descname">setIcon</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setIcon" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Annotator.getIcon"> -<tt class="descname">getIcon</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getIcon" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.x"> -<tt class="descname">x</tt><a class="headerlink" href="#Annotator.x" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) x field. Typically display coordinate x</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.y"> -<tt class="descname">y</tt><a class="headerlink" href="#Annotator.y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) y field. Typically display coordinate y</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.z"> -<tt class="descname">z</tt><a class="headerlink" href="#Annotator.z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) z field. Typically display coordinate z</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.notes"> -<tt class="descname">notes</tt><a class="headerlink" href="#Annotator.notes" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) A string to hold some text notes about parent object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.color"> -<tt class="descname">color</tt><a class="headerlink" href="#Annotator.color" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.textColor"> -<tt class="descname">textColor</tt><a class="headerlink" href="#Annotator.textColor" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Annotator.icon"> -<tt class="descname">icon</tt><a class="headerlink" href="#Annotator.icon" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) A string to specify icon to use for display</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Arith"> -<em class="property">class </em><tt class="descname">Arith</tt><a class="headerlink" href="#Arith" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Arith.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Arith.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.setFunction"> -<tt class="descname">setFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setFunction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.getFunction"> -<tt class="descname">getFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getFunction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.setOutputValue"> -<tt class="descname">setOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.getArg1Value"> -<tt class="descname">getArg1Value</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getArg1Value" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.setAnyValue"> -<tt class="descname">setAnyValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setAnyValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.getAnyValue"> -<tt class="descname">getAnyValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getAnyValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.arg1"> -<tt class="descname">arg1</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles argument 1. This just assigns it</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.arg2"> -<tt class="descname">arg2</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles argument 2. This just assigns it</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.arg3"> -<tt class="descname">arg3</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg3" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles argument 3. This sums in each input, and clears each clock tick.</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.arg1x2"> -<tt class="descname">arg1x2</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg1x2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Store the product of the two arguments in <a href="#id13"><span class="problematic" id="id14">output_</span></a></p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="Arith.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Arith.output"> -<tt class="descname">output</tt><a class="headerlink" href="#Arith.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out the computed value</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Arith.function"> -<tt class="descname">function</tt><a class="headerlink" href="#Arith.function" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Arithmetic function to perform on inputs.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Arith.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#Arith.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Value of output as computed last timestep.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Arith.arg1Value"> -<tt class="descname">arg1Value</tt><a class="headerlink" href="#Arith.arg1Value" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Value of arg1 as computed last timestep.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Arith.anyValue"> -<tt class="descname">anyValue</tt><a class="headerlink" href="#Arith.anyValue" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="BufPool"> -<em class="property">class </em><tt class="descname">BufPool</tt><a class="headerlink" href="#BufPool" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="BufPool.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#BufPool.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="BufPool.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#BufPool.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="BufPool.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#BufPool.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="CaConc"> -<em class="property">class </em><tt class="descname">CaConc</tt><a class="headerlink" href="#CaConc" title="Permalink to this definition">¶</a></dt> -<dd><p>CaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.</p> -<dl class="attribute"> -<dt id="CaConc.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#CaConc.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setCa"> -<tt class="descname">setCa</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getCa"> -<tt class="descname">getCa</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setCaBasal"> -<tt class="descname">setCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getCaBasal"> -<tt class="descname">getCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setCa_base"> -<tt class="descname">setCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCa_base" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getCa_base"> -<tt class="descname">getCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCa_base" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setTau"> -<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getTau"> -<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setB"> -<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getB"> -<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setThick"> -<tt class="descname">setThick</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setThick" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getThick"> -<tt class="descname">getThick</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getThick" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setCeiling"> -<tt class="descname">setCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCeiling" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getCeiling"> -<tt class="descname">getCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCeiling" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.setFloor"> -<tt class="descname">setFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setFloor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.getFloor"> -<tt class="descname">getFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getFloor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.current"> -<tt class="descname">current</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.current" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Calcium Ion current, due to be converted to conc.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.currentFraction"> -<tt class="descname">currentFraction</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.currentFraction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fraction of total Ion current, that is carried by Ca2+.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.increase"> -<tt class="descname">increase</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.increase" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Any input current that increases the concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.decrease"> -<tt class="descname">decrease</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.decrease" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Any input current that decreases the concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="CaConc.basal"> -<tt class="descname">basal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.basal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Synonym for assignment of basal conc.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.concOut"> -<tt class="descname">concOut</tt><a class="headerlink" href="#CaConc.concOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Concentration of Ca in pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.Ca"> -<tt class="descname">Ca</tt><a class="headerlink" href="#CaConc.Ca" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Calcium concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.CaBasal"> -<tt class="descname">CaBasal</tt><a class="headerlink" href="#CaConc.CaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Basal Calcium concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.Ca_base"> -<tt class="descname">Ca_base</tt><a class="headerlink" href="#CaConc.Ca_base" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Basal Calcium concentration, synonym for CaBasal</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.tau"> -<tt class="descname">tau</tt><a class="headerlink" href="#CaConc.tau" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Settling time for Ca concentration</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.B"> -<tt class="descname">B</tt><a class="headerlink" href="#CaConc.B" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Volume scaling factor</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.thick"> -<tt class="descname">thick</tt><a class="headerlink" href="#CaConc.thick" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Thickness of Ca shell.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.ceiling"> -<tt class="descname">ceiling</tt><a class="headerlink" href="#CaConc.ceiling" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CaConc.floor"> -<tt class="descname">floor</tt><a class="headerlink" href="#CaConc.floor" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Floor value for Ca concentration. If Ca < floor, Ca = floor</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="ChanBase"> -<em class="property">class </em><tt class="descname">ChanBase</tt><a class="headerlink" href="#ChanBase" title="Permalink to this definition">¶</a></dt> -<dd><p>ChanBase: Base class for assorted ion channels.Presents a common interface for all of them.</p> -<dl class="attribute"> -<dt id="ChanBase.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#ChanBase.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.ghk"> -<tt class="descname">ghk</tt><a class="headerlink" href="#ChanBase.ghk" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Message to Goldman-Hodgkin-Katz object</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.Vm"> -<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">Vm</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.setGbar"> -<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.getGbar"> -<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.setEk"> -<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.getEk"> -<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.setGk"> -<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.getGk"> -<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChanBase.getIk"> -<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getIk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.channelOut"> -<tt class="descname">channelOut</tt><a class="headerlink" href="#ChanBase.channelOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends channel variables Gk and Ek to compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.permeabilityOut"> -<tt class="descname">permeabilityOut</tt><a class="headerlink" href="#ChanBase.permeabilityOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Conductance term going out to GHK object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.IkOut"> -<tt class="descname">IkOut</tt><a class="headerlink" href="#ChanBase.IkOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Channel current. This message typically goes to concenobjects that keep track of ion concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.Gbar"> -<tt class="descname">Gbar</tt><a class="headerlink" href="#ChanBase.Gbar" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximal channel conductance</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.Ek"> -<tt class="descname">Ek</tt><a class="headerlink" href="#ChanBase.Ek" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reversal potential of channel</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.Gk"> -<tt class="descname">Gk</tt><a class="headerlink" href="#ChanBase.Gk" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel conductance variable</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChanBase.Ik"> -<tt class="descname">Ik</tt><a class="headerlink" href="#ChanBase.Ik" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel current variable</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="ChemCompt"> -<em class="property">class </em><tt class="descname">ChemCompt</tt><a class="headerlink" href="#ChemCompt" title="Permalink to this definition">¶</a></dt> -<dd><p>Pure virtual base class for chemical compartments</p> -<dl class="method"> -<dt id="ChemCompt.setVolume"> -<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getVolume"> -<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getVoxelVolume"> -<tt class="descname">getVoxelVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getVoxelVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getOneVoxelVolume"> -<tt class="descname">getOneVoxelVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getOneVoxelVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getNumDimensions"> -<tt class="descname">getNumDimensions</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getNumDimensions" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getStencilRate"> -<tt class="descname">getStencilRate</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getStencilRate" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getStencilIndex"> -<tt class="descname">getStencilIndex</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getStencilIndex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.buildDefaultMesh"> -<tt class="descname">buildDefaultMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.buildDefaultMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Tells ChemCompt derived class to build a default mesh with thespecified volume and number of meshEntries.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.setVolumeNotRates"> -<tt class="descname">setVolumeNotRates</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setVolumeNotRates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Changes volume but does not notify any child objects.Only works if the ChemCompt has just one voxel.This function will invalidate any concentration term inthe model. If you don’t know why you would want to do this,then you shouldn’t use this function.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.resetStencil"> -<tt class="descname">resetStencil</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.resetStencil" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Resets the diffusion stencil to the core stencil that only includes the within-mesh diffusion. This is needed prior to building up the cross-mesh diffusion through junctions.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.setNumMesh"> -<tt class="descname">setNumMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setNumMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="ChemCompt.getNumMesh"> -<tt class="descname">getNumMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getNumMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.volume"> -<tt class="descname">volume</tt><a class="headerlink" href="#ChemCompt.volume" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Volume of entire chemical domain.Assigning this only works if the chemical compartment hasonly a single voxel. Otherwise ignored.This function goes through all objects below this on thetree, and rescales their molecule #s and rates as per thevolume change. This keeps concentration the same, and alsomaintains rates as expressed in volume units.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.voxelVolume"> -<tt class="descname">voxelVolume</tt><a class="headerlink" href="#ChemCompt.voxelVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Vector of volumes of each of the voxels.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.numDimensions"> -<tt class="descname">numDimensions</tt><a class="headerlink" href="#ChemCompt.numDimensions" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of spatial dimensions of this compartment. Usually 3 or 2</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.oneVoxelVolume"> -<tt class="descname">oneVoxelVolume</tt><a class="headerlink" href="#ChemCompt.oneVoxelVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Volume of specified voxel.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.stencilRate"> -<tt class="descname">stencilRate</tt><a class="headerlink" href="#ChemCompt.stencilRate" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of diffusion rates in the stencil for specified voxel.The identity of the coupled voxels is given by the partner field ‘stencilIndex’.Returns an empty vector for non-voxelized compartments.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ChemCompt.stencilIndex"> -<tt class="descname">stencilIndex</tt><a class="headerlink" href="#ChemCompt.stencilIndex" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,vector<unsigned int> (<em>lookup field</em>) vector of voxels diffusively coupled to the specified voxel.The diffusion rates into the coupled voxels is given by the partner field ‘stencilRate’.Returns an empty vector for non-voxelized compartments.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Cinfo"> -<em class="property">class </em><tt class="descname">Cinfo</tt><a class="headerlink" href="#Cinfo" title="Permalink to this definition">¶</a></dt> -<dd><p>Class information object.</p> -<dl class="method"> -<dt id="Cinfo.getDocs"> -<tt class="descname">getDocs</tt><big>(</big><big>)</big><a class="headerlink" href="#Cinfo.getDocs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Cinfo.getBaseClass"> -<tt class="descname">getBaseClass</tt><big>(</big><big>)</big><a class="headerlink" href="#Cinfo.getBaseClass" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Cinfo.docs"> -<tt class="descname">docs</tt><a class="headerlink" href="#Cinfo.docs" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Documentation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Cinfo.baseClass"> -<tt class="descname">baseClass</tt><a class="headerlink" href="#Cinfo.baseClass" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Name of base class</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Clock"> -<em class="property">class </em><tt class="descname">Clock</tt><a class="headerlink" href="#Clock" title="Permalink to this definition">¶</a></dt> -<dd><p>Clock: Clock class. Handles sequencing of operations in simulations.Every object scheduled for operations in MOOSE is connected to oneof the ‘Tick’ entries on the Clock.The Clock manages ten ‘Ticks’, each of which has its own dt,which is an integral multiple of the base clock <a href="#id15"><span class="problematic" id="id16">dt_</span></a>. On every clock step the ticks are examined to see which of themis due for updating. When a tick is updated, the ‘process’ call of all the objects scheduled on that tick is called.The default scheduling (should not be overridden) has the following assignment of classes to Ticks:0. Biophysics: Init call on Compartments in EE method1. Biophysics: Channels2. Biophysics: Process call on Compartments3. Undefined 4. Kinetics: Pools, or in ksolve mode: Mesh to handle diffusion5. Kinetics: Reacs, enzymes, etc, or in ksolve mode: Stoich/GSL6. Stimulus tables7. More stimulus tables8. Plots9. Postmaster. This must be called last of all and nothing else should use this Tick. The Postmaster is automatically scheduled at set up time. The Tick should be given the longest possible value, typically but not always equal to one of the other ticks, so as to batch the communications. For spiking-only communications, it is usually possible to space the communication tick by as much as 1-2 ms which is the axonal + synaptic delay.</p> -<dl class="attribute"> -<dt id="Clock.clockControl"> -<tt class="descname">clockControl</tt><a class="headerlink" href="#Clock.clockControl" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Controls all scheduling aspects of Clock, usually from Shell</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc0"> -<tt class="descname">proc0</tt><a class="headerlink" href="#Clock.proc0" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc1"> -<tt class="descname">proc1</tt><a class="headerlink" href="#Clock.proc1" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc2"> -<tt class="descname">proc2</tt><a class="headerlink" href="#Clock.proc2" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc3"> -<tt class="descname">proc3</tt><a class="headerlink" href="#Clock.proc3" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc4"> -<tt class="descname">proc4</tt><a class="headerlink" href="#Clock.proc4" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc5"> -<tt class="descname">proc5</tt><a class="headerlink" href="#Clock.proc5" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc6"> -<tt class="descname">proc6</tt><a class="headerlink" href="#Clock.proc6" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc7"> -<tt class="descname">proc7</tt><a class="headerlink" href="#Clock.proc7" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc8"> -<tt class="descname">proc8</tt><a class="headerlink" href="#Clock.proc8" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.proc9"> -<tt class="descname">proc9</tt><a class="headerlink" href="#Clock.proc9" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.setDt"> -<tt class="descname">setDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getDt"> -<tt class="descname">getDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getRunTime"> -<tt class="descname">getRunTime</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getRunTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getCurrentTime"> -<tt class="descname">getCurrentTime</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getCurrentTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getNsteps"> -<tt class="descname">getNsteps</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getNsteps" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getNumTicks"> -<tt class="descname">getNumTicks</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getNumTicks" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getCurrentStep"> -<tt class="descname">getCurrentStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getCurrentStep" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getDts"> -<tt class="descname">getDts</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getDts" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getIsRunning"> -<tt class="descname">getIsRunning</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getIsRunning" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.setTickStep"> -<tt class="descname">setTickStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setTickStep" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getTickStep"> -<tt class="descname">getTickStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getTickStep" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.setTickDt"> -<tt class="descname">setTickDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setTickDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.getTickDt"> -<tt class="descname">getTickDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getTickDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.start"> -<tt class="descname">start</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.start" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sets off the simulation for the specified duration</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.step"> -<tt class="descname">step</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.step" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sets off the simulation for the specified # of steps</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.stop"> -<tt class="descname">stop</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.stop" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Halts the simulation, with option to restart seamlessly</p> -</dd></dl> - -<dl class="method"> -<dt id="Clock.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Zeroes out all ticks, starts at t = 0</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.finished"> -<tt class="descname">finished</tt><a class="headerlink" href="#Clock.finished" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>source message field</em>) Signal for completion of run</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process0"> -<tt class="descname">process0</tt><a class="headerlink" href="#Clock.process0" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 0</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit0"> -<tt class="descname">reinit0</tt><a class="headerlink" href="#Clock.reinit0" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 0</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process1"> -<tt class="descname">process1</tt><a class="headerlink" href="#Clock.process1" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 1</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit1"> -<tt class="descname">reinit1</tt><a class="headerlink" href="#Clock.reinit1" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 1</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process2"> -<tt class="descname">process2</tt><a class="headerlink" href="#Clock.process2" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 2</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit2"> -<tt class="descname">reinit2</tt><a class="headerlink" href="#Clock.reinit2" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 2</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process3"> -<tt class="descname">process3</tt><a class="headerlink" href="#Clock.process3" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 3</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit3"> -<tt class="descname">reinit3</tt><a class="headerlink" href="#Clock.reinit3" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 3</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process4"> -<tt class="descname">process4</tt><a class="headerlink" href="#Clock.process4" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 4</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit4"> -<tt class="descname">reinit4</tt><a class="headerlink" href="#Clock.reinit4" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 4</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process5"> -<tt class="descname">process5</tt><a class="headerlink" href="#Clock.process5" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 5</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit5"> -<tt class="descname">reinit5</tt><a class="headerlink" href="#Clock.reinit5" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 5</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process6"> -<tt class="descname">process6</tt><a class="headerlink" href="#Clock.process6" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 6</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit6"> -<tt class="descname">reinit6</tt><a class="headerlink" href="#Clock.reinit6" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 6</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process7"> -<tt class="descname">process7</tt><a class="headerlink" href="#Clock.process7" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 7</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit7"> -<tt class="descname">reinit7</tt><a class="headerlink" href="#Clock.reinit7" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 7</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process8"> -<tt class="descname">process8</tt><a class="headerlink" href="#Clock.process8" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 8</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit8"> -<tt class="descname">reinit8</tt><a class="headerlink" href="#Clock.reinit8" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 8</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.process9"> -<tt class="descname">process9</tt><a class="headerlink" href="#Clock.process9" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 9</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.reinit9"> -<tt class="descname">reinit9</tt><a class="headerlink" href="#Clock.reinit9" title="Permalink to this definition">¶</a></dt> -<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 9</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.dt"> -<tt class="descname">dt</tt><a class="headerlink" href="#Clock.dt" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Base timestep for simulation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.runTime"> -<tt class="descname">runTime</tt><a class="headerlink" href="#Clock.runTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Duration to run the simulation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.currentTime"> -<tt class="descname">currentTime</tt><a class="headerlink" href="#Clock.currentTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current simulation time</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.nsteps"> -<tt class="descname">nsteps</tt><a class="headerlink" href="#Clock.nsteps" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.numTicks"> -<tt class="descname">numTicks</tt><a class="headerlink" href="#Clock.numTicks" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of clock ticks</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.currentStep"> -<tt class="descname">currentStep</tt><a class="headerlink" href="#Clock.currentStep" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Current simulation step</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.dts"> -<tt class="descname">dts</tt><a class="headerlink" href="#Clock.dts" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Utility function returning the dt (timestep) of all ticks.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.isRunning"> -<tt class="descname">isRunning</tt><a class="headerlink" href="#Clock.isRunning" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Utility function to report if simulation is in progress.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.tickStep"> -<tt class="descname">tickStep</tt><a class="headerlink" href="#Clock.tickStep" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,unsigned int (<em>lookup field</em>) Step size of specified Tick, as integral multiple of <a href="#id17"><span class="problematic" id="id18">dt_</span></a> A zero step size means that the Tick is inactive</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Clock.tickDt"> -<tt class="descname">tickDt</tt><a class="headerlink" href="#Clock.tickDt" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Timestep dt of specified Tick. Always integral multiple of <a href="#id19"><span class="problematic" id="id20">dt_</span></a>. If you assign a non-integer multiple it will round off. A zero timestep means that the Tick is inactive</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Compartment"> -<em class="property">class </em><tt class="descname">Compartment</tt><a class="headerlink" href="#Compartment" title="Permalink to this definition">¶</a></dt> -<dd><p>Compartment object, for branching neuron models.</p> -</dd></dl> - -<dl class="class"> -<dt id="CompartmentBase"> -<em class="property">class </em><tt class="descname">CompartmentBase</tt><a class="headerlink" href="#CompartmentBase" title="Permalink to this definition">¶</a></dt> -<dd><p>CompartmentBase object, for branching neuron models.</p> -<dl class="attribute"> -<dt id="CompartmentBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#CompartmentBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.init"> -<tt class="descname">init</tt><a class="headerlink" href="#CompartmentBase.init" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn’t really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#CompartmentBase.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.axial"> -<tt class="descname">axial</tt><a class="headerlink" href="#CompartmentBase.axial" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.raxial"> -<tt class="descname">raxial</tt><a class="headerlink" href="#CompartmentBase.raxial" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setVm"> -<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getVm"> -<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setCm"> -<tt class="descname">setCm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setCm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getCm"> -<tt class="descname">getCm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getCm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setEm"> -<tt class="descname">setEm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setEm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getEm"> -<tt class="descname">getEm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getEm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getIm"> -<tt class="descname">getIm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getIm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setInject"> -<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getInject"> -<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setInitVm"> -<tt class="descname">setInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setInitVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getInitVm"> -<tt class="descname">getInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getInitVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setRm"> -<tt class="descname">setRm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setRm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getRm"> -<tt class="descname">getRm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getRm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setRa"> -<tt class="descname">setRa</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setRa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getRa"> -<tt class="descname">getRa</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getRa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setDiameter"> -<tt class="descname">setDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setDiameter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getDiameter"> -<tt class="descname">getDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getDiameter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setLength"> -<tt class="descname">setLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getLength"> -<tt class="descname">getLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setX0"> -<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getX0"> -<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setY0"> -<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getY0"> -<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setZ0"> -<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getZ0"> -<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.injectMsg"> -<tt class="descname">injectMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.injectMsg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.randInject"> -<tt class="descname">randInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.randInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">injectMsg</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.cable"> -<tt class="descname">cable</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.cable" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Message for organizing compartments into groups, calledcables. Doesn’t do anything.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.initProc"> -<tt class="descname">initProc</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.initProc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Process call for the ‘init’ phase of the CompartmentBase calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.initReinit"> -<tt class="descname">initReinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.initReinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Reinit call for the ‘init’ phase of the CompartmentBase calculations.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.handleChannel"> -<tt class="descname">handleChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleChannel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles conductance and Reversal potential arguments from Channel</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.handleRaxial"> -<tt class="descname">handleRaxial</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleRaxial" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Raxial info: arguments are Ra and Vm.</p> -</dd></dl> - -<dl class="method"> -<dt id="CompartmentBase.handleAxial"> -<tt class="descname">handleAxial</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleAxial" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Axial information. Argument is just Vm.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.VmOut"> -<tt class="descname">VmOut</tt><a class="headerlink" href="#CompartmentBase.VmOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out Vm value of compartment on each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.axialOut"> -<tt class="descname">axialOut</tt><a class="headerlink" href="#CompartmentBase.axialOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out Vm value of compartment to adjacent compartments,on each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.raxialOut"> -<tt class="descname">raxialOut</tt><a class="headerlink" href="#CompartmentBase.raxialOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Raxial information on each timestep, fields are Ra and Vm</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Vm"> -<tt class="descname">Vm</tt><a class="headerlink" href="#CompartmentBase.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) membrane potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Cm"> -<tt class="descname">Cm</tt><a class="headerlink" href="#CompartmentBase.Cm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane capacitance</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Em"> -<tt class="descname">Em</tt><a class="headerlink" href="#CompartmentBase.Em" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Resting membrane potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Im"> -<tt class="descname">Im</tt><a class="headerlink" href="#CompartmentBase.Im" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current going through membrane</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.inject"> -<tt class="descname">inject</tt><a class="headerlink" href="#CompartmentBase.inject" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current injection to deliver into compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.initVm"> -<tt class="descname">initVm</tt><a class="headerlink" href="#CompartmentBase.initVm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial value for membrane potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Rm"> -<tt class="descname">Rm</tt><a class="headerlink" href="#CompartmentBase.Rm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane resistance</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.Ra"> -<tt class="descname">Ra</tt><a class="headerlink" href="#CompartmentBase.Ra" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Axial resistance of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.diameter"> -<tt class="descname">diameter</tt><a class="headerlink" href="#CompartmentBase.diameter" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Diameter of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.length"> -<tt class="descname">length</tt><a class="headerlink" href="#CompartmentBase.length" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Length of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.x0"> -<tt class="descname">x0</tt><a class="headerlink" href="#CompartmentBase.x0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) X coordinate of start of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.y0"> -<tt class="descname">y0</tt><a class="headerlink" href="#CompartmentBase.y0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Y coordinate of start of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.z0"> -<tt class="descname">z0</tt><a class="headerlink" href="#CompartmentBase.z0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Z coordinate of start of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.x"> -<tt class="descname">x</tt><a class="headerlink" href="#CompartmentBase.x" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) x coordinate of end of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.y"> -<tt class="descname">y</tt><a class="headerlink" href="#CompartmentBase.y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) y coordinate of end of compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CompartmentBase.z"> -<tt class="descname">z</tt><a class="headerlink" href="#CompartmentBase.z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) z coordinate of end of compartment</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="CplxEnzBase"> -<em class="property">class </em><tt class="descname">CplxEnzBase</tt><a class="headerlink" href="#CplxEnzBase" title="Permalink to this definition">¶</a></dt> -<dd><p>: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S —-> E + P</p> -<dl class="attribute"> -<dt id="CplxEnzBase.enz"> -<tt class="descname">enz</tt><a class="headerlink" href="#CplxEnzBase.enz" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to enzyme pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.cplx"> -<tt class="descname">cplx</tt><a class="headerlink" href="#CplxEnzBase.cplx" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to enz-sub complex pool</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.setK1"> -<tt class="descname">setK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.getK1"> -<tt class="descname">getK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.setK2"> -<tt class="descname">setK2</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.getK2"> -<tt class="descname">getK2</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.setK3"> -<tt class="descname">setK3</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK3" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.getK3"> -<tt class="descname">getK3</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK3" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.setRatio"> -<tt class="descname">setRatio</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setRatio" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.getRatio"> -<tt class="descname">getRatio</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getRatio" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.setConcK1"> -<tt class="descname">setConcK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setConcK1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.getConcK1"> -<tt class="descname">getConcK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getConcK1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.enzDest"> -<tt class="descname">enzDest</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.enzDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of Enzyme</p> -</dd></dl> - -<dl class="method"> -<dt id="CplxEnzBase.cplxDest"> -<tt class="descname">cplxDest</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.cplxDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of enz-sub complex</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.enzOut"> -<tt class="descname">enzOut</tt><a class="headerlink" href="#CplxEnzBase.enzOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.cplxOut"> -<tt class="descname">cplxOut</tt><a class="headerlink" href="#CplxEnzBase.cplxOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.k1"> -<tt class="descname">k1</tt><a class="headerlink" href="#CplxEnzBase.k1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Forward reaction from enz + sub to complex, in # units.This parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result k1 must change. It is only whenk1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.k1 is also subordinate to the ‘ratio’ field, since setting the ratio reassigns k2.Should you wish to assign the elementary rates k1, k2, k3,of an enzyme directly, always assign k1 last.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.k2"> -<tt class="descname">k2</tt><a class="headerlink" href="#CplxEnzBase.k2" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reverse reaction from complex to enz + sub</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.k3"> -<tt class="descname">k3</tt><a class="headerlink" href="#CplxEnzBase.k3" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Forward rate constant from complex to product + enz</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.ratio"> -<tt class="descname">ratio</tt><a class="headerlink" href="#CplxEnzBase.ratio" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Ratio of k2/k3</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CplxEnzBase.concK1"> -<tt class="descname">concK1</tt><a class="headerlink" href="#CplxEnzBase.concK1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) K1 expressed in concentration (1/millimolar.sec) unitsThis parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result concK1 must change. It is only whenconcK1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.concK1 is also subordinate to the ‘ratio’ field, sincesetting the ratio reassigns k2.Should you wish to assign the elementary rates concK1, k2, k3,of an enzyme directly, always assign concK1 last.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="CubeMesh"> -<em class="property">class </em><tt class="descname">CubeMesh</tt><a class="headerlink" href="#CubeMesh" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="CubeMesh.setIsToroid"> -<tt class="descname">setIsToroid</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setIsToroid" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getIsToroid"> -<tt class="descname">getIsToroid</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getIsToroid" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setPreserveNumEntries"> -<tt class="descname">setPreserveNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setPreserveNumEntries" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getPreserveNumEntries"> -<tt class="descname">getPreserveNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getPreserveNumEntries" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setAlwaysDiffuse"> -<tt class="descname">setAlwaysDiffuse</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setAlwaysDiffuse" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getAlwaysDiffuse"> -<tt class="descname">getAlwaysDiffuse</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getAlwaysDiffuse" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setX0"> -<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getX0"> -<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setY0"> -<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getY0"> -<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setZ0"> -<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getZ0"> -<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setX1"> -<tt class="descname">setX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setX1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getX1"> -<tt class="descname">getX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getX1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setY1"> -<tt class="descname">setY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setY1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getY1"> -<tt class="descname">getY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getY1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setZ1"> -<tt class="descname">setZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setZ1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getZ1"> -<tt class="descname">getZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getZ1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setDx"> -<tt class="descname">setDx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getDx"> -<tt class="descname">getDx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setDy"> -<tt class="descname">setDy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getDy"> -<tt class="descname">getDy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setDz"> -<tt class="descname">setDz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDz" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getDz"> -<tt class="descname">getDz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDz" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setNx"> -<tt class="descname">setNx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getNx"> -<tt class="descname">getNx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setNy"> -<tt class="descname">setNy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getNy"> -<tt class="descname">getNy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setNz"> -<tt class="descname">setNz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNz" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getNz"> -<tt class="descname">getNz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNz" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setCoords"> -<tt class="descname">setCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setCoords" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getCoords"> -<tt class="descname">getCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getCoords" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setMeshToSpace"> -<tt class="descname">setMeshToSpace</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setMeshToSpace" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getMeshToSpace"> -<tt class="descname">getMeshToSpace</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getMeshToSpace" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setSpaceToMesh"> -<tt class="descname">setSpaceToMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setSpaceToMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getSpaceToMesh"> -<tt class="descname">getSpaceToMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getSpaceToMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.setSurface"> -<tt class="descname">setSurface</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setSurface" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CubeMesh.getSurface"> -<tt class="descname">getSurface</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getSurface" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.isToroid"> -<tt class="descname">isToroid</tt><a class="headerlink" href="#CubeMesh.isToroid" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.preserveNumEntries"> -<tt class="descname">preserveNumEntries</tt><a class="headerlink" href="#CubeMesh.preserveNumEntries" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.alwaysDiffuse"> -<tt class="descname">alwaysDiffuse</tt><a class="headerlink" href="#CubeMesh.alwaysDiffuse" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag. When it is true, the mesh matches up sequential mesh entries for diffusion and chmestry. This is regardless of spatial location, and is guaranteed to set up at least the home reaction systemDefault is false</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.x0"> -<tt class="descname">x0</tt><a class="headerlink" href="#CubeMesh.x0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) X coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.y0"> -<tt class="descname">y0</tt><a class="headerlink" href="#CubeMesh.y0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Y coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.z0"> -<tt class="descname">z0</tt><a class="headerlink" href="#CubeMesh.z0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Z coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.x1"> -<tt class="descname">x1</tt><a class="headerlink" href="#CubeMesh.x1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) X coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.y1"> -<tt class="descname">y1</tt><a class="headerlink" href="#CubeMesh.y1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Y coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.z1"> -<tt class="descname">z1</tt><a class="headerlink" href="#CubeMesh.z1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Z coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.dx"> -<tt class="descname">dx</tt><a class="headerlink" href="#CubeMesh.dx" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) X size for mesh</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.dy"> -<tt class="descname">dy</tt><a class="headerlink" href="#CubeMesh.dy" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Y size for mesh</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.dz"> -<tt class="descname">dz</tt><a class="headerlink" href="#CubeMesh.dz" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Z size for mesh</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.nx"> -<tt class="descname">nx</tt><a class="headerlink" href="#CubeMesh.nx" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in X</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.ny"> -<tt class="descname">ny</tt><a class="headerlink" href="#CubeMesh.ny" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in Y</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.nz"> -<tt class="descname">nz</tt><a class="headerlink" href="#CubeMesh.nz" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in Z</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.coords"> -<tt class="descname">coords</tt><a class="headerlink" href="#CubeMesh.coords" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dzWhen this is done, it recalculates the numEntries since dx, dy and dz are given explicitly.As a special hack, you can leave out dx, dy and dz and use a vector of size 6. In this case the operation assumes that nx, ny and nz are to be preserved and dx, dy and dz will be recalculated.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.meshToSpace"> -<tt class="descname">meshToSpace</tt><a class="headerlink" href="#CubeMesh.meshToSpace" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Array in which each mesh entry stores spatial (cubic) index</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.spaceToMesh"> -<tt class="descname">spaceToMesh</tt><a class="headerlink" href="#CubeMesh.spaceToMesh" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CubeMesh.surface"> -<tt class="descname">surface</tt><a class="headerlink" href="#CubeMesh.surface" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="CylMesh"> -<em class="property">class </em><tt class="descname">CylMesh</tt><a class="headerlink" href="#CylMesh" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="CylMesh.setX0"> -<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getX0"> -<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getX0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setY0"> -<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getY0"> -<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getY0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setZ0"> -<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getZ0"> -<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getZ0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setR0"> -<tt class="descname">setR0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setR0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getR0"> -<tt class="descname">getR0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getR0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setX1"> -<tt class="descname">setX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setX1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getX1"> -<tt class="descname">getX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getX1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setY1"> -<tt class="descname">setY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setY1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getY1"> -<tt class="descname">getY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getY1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setZ1"> -<tt class="descname">setZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setZ1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getZ1"> -<tt class="descname">getZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getZ1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setR1"> -<tt class="descname">setR1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setR1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getR1"> -<tt class="descname">getR1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getR1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setDiffLength"> -<tt class="descname">setDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setDiffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getDiffLength"> -<tt class="descname">getDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getDiffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.setCoords"> -<tt class="descname">setCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setCoords" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getCoords"> -<tt class="descname">getCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getCoords" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getNumDiffCompts"> -<tt class="descname">getNumDiffCompts</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getNumDiffCompts" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="CylMesh.getTotLength"> -<tt class="descname">getTotLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getTotLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.x0"> -<tt class="descname">x0</tt><a class="headerlink" href="#CylMesh.x0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) x coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.y0"> -<tt class="descname">y0</tt><a class="headerlink" href="#CylMesh.y0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) y coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.z0"> -<tt class="descname">z0</tt><a class="headerlink" href="#CylMesh.z0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) z coord of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.r0"> -<tt class="descname">r0</tt><a class="headerlink" href="#CylMesh.r0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Radius of one end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.x1"> -<tt class="descname">x1</tt><a class="headerlink" href="#CylMesh.x1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) x coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.y1"> -<tt class="descname">y1</tt><a class="headerlink" href="#CylMesh.y1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) y coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.z1"> -<tt class="descname">z1</tt><a class="headerlink" href="#CylMesh.z1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) z coord of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.r1"> -<tt class="descname">r1</tt><a class="headerlink" href="#CylMesh.r1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Radius of other end</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.diffLength"> -<tt class="descname">diffLength</tt><a class="headerlink" href="#CylMesh.diffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength diffLength on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute diffLength as totLength/numEntries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.coords"> -<tt class="descname">coords</tt><a class="headerlink" href="#CylMesh.coords" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 diffLength</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.numDiffCompts"> -<tt class="descname">numDiffCompts</tt><a class="headerlink" href="#CylMesh.numDiffCompts" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of diffusive compartments in model</p> -</dd></dl> - -<dl class="attribute"> -<dt id="CylMesh.totLength"> -<tt class="descname">totLength</tt><a class="headerlink" href="#CylMesh.totLength" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Total length of cylinder</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="DiagonalMsg"> -<em class="property">class </em><tt class="descname">DiagonalMsg</tt><a class="headerlink" href="#DiagonalMsg" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="DiagonalMsg.setStride"> -<tt class="descname">setStride</tt><big>(</big><big>)</big><a class="headerlink" href="#DiagonalMsg.setStride" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiagonalMsg.getStride"> -<tt class="descname">getStride</tt><big>(</big><big>)</big><a class="headerlink" href="#DiagonalMsg.getStride" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DiagonalMsg.stride"> -<tt class="descname">stride</tt><a class="headerlink" href="#DiagonalMsg.stride" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="DifShell"> -<em class="property">class </em><tt class="descname">DifShell</tt><a class="headerlink" href="#DifShell" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>DifShell object: Models diffusion of an ion (typically calcium) within an electric compartment. A DifShell is an iso-concentration region with respect to the ion. Adjoining DifShells exchange flux of this ion, and also keep track of changes in concentration due to pumping, buffering and channel currents, by talking to the appropriate objects.</p> -<dl class="attribute"> -<dt id="DifShell.process_0"> -<tt class="descname">process_0</tt><a class="headerlink" href="#DifShell.process_0" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifShell computations in 2 stages, much as in the Compartment object. In the first stage we send out the concentration value to other DifShells and Buffer elements. We also receive fluxes and currents and sum them up to compute ( dC / dt ). In the second stage we find the new C value using an explicit integration method. This 2-stage procedure eliminates the need to store and send prev_C values, as was common in GENESIS.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DifShell.process_1"> -<tt class="descname">process_1</tt><a class="headerlink" href="#DifShell.process_1" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Second process call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DifShell.buffer"> -<tt class="descname">buffer</tt><a class="headerlink" href="#DifShell.buffer" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). During stage 0:</p> -</dd></dl> - -</div></blockquote> -<ul class="simple"> -<li>DifShell sends ion concentration</li> -</ul> -</dd></dl> - -<ul class="simple"> -<li>Buffer updates buffer concentration and sends it back immediately using a call-back.</li> -<li>DifShell updates the time-derivative ( dC / dt )</li> -</ul> -<p>During stage 1: -- DifShell advances concentration C -This scheme means that the Buffer does not need to be scheduled, and it does its computations when it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above computations in 3 stages instead of 2.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="innerDif"> -<tt class="descname">innerDif</tt><a class="headerlink" href="#innerDif" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This shared message (and the next) is between DifShells: adjoining shells exchange information to find out the flux between them. Using this message, an inner shell sends to, and receives from its outer shell.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="outerDif"> -<tt class="descname">outerDif</tt><a class="headerlink" href="#outerDif" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Using this message, an outer shell sends to, and receives from its inner shell.</p> -</dd></dl> - -<dl class="method"> -<dt id="getC"> -<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#getC" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setCeq"> -<tt class="descname">setCeq</tt><big>(</big><big>)</big><a class="headerlink" href="#setCeq" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getCeq"> -<tt class="descname">getCeq</tt><big>(</big><big>)</big><a class="headerlink" href="#getCeq" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setD"> -<tt class="descname">setD</tt><big>(</big><big>)</big><a class="headerlink" href="#setD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getD"> -<tt class="descname">getD</tt><big>(</big><big>)</big><a class="headerlink" href="#getD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setValence"> -<tt class="descname">setValence</tt><big>(</big><big>)</big><a class="headerlink" href="#setValence" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getValence"> -<tt class="descname">getValence</tt><big>(</big><big>)</big><a class="headerlink" href="#getValence" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setLeak"> -<tt class="descname">setLeak</tt><big>(</big><big>)</big><a class="headerlink" href="#setLeak" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getLeak"> -<tt class="descname">getLeak</tt><big>(</big><big>)</big><a class="headerlink" href="#getLeak" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setShapeMode"> -<tt class="descname">setShapeMode</tt><big>(</big><big>)</big><a class="headerlink" href="#setShapeMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getShapeMode"> -<tt class="descname">getShapeMode</tt><big>(</big><big>)</big><a class="headerlink" href="#getShapeMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setLength"> -<tt class="descname">setLength</tt><big>(</big><big>)</big><a class="headerlink" href="#setLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getLength"> -<tt class="descname">getLength</tt><big>(</big><big>)</big><a class="headerlink" href="#getLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setDiameter"> -<tt class="descname">setDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#setDiameter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getDiameter"> -<tt class="descname">getDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#getDiameter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setThickness"> -<tt class="descname">setThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#setThickness" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getThickness"> -<tt class="descname">getThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#getThickness" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setVolume"> -<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#setVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getVolume"> -<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#getVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setOuterArea"> -<tt class="descname">setOuterArea</tt><big>(</big><big>)</big><a class="headerlink" href="#setOuterArea" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getOuterArea"> -<tt class="descname">getOuterArea</tt><big>(</big><big>)</big><a class="headerlink" href="#getOuterArea" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="setInnerArea"> -<tt class="descname">setInnerArea</tt><big>(</big><big>)</big><a class="headerlink" href="#setInnerArea" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getInnerArea"> -<tt class="descname">getInnerArea</tt><big>(</big><big>)</big><a class="headerlink" href="#getInnerArea" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reinit happens only in stage 0</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">process</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handle process call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">reinit</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Reinit happens only in stage 0</p> -</dd></dl> - -<dl class="method"> -<dt id="reaction"> -<tt class="descname">reaction</tt><big>(</big><big>)</big><a class="headerlink" href="#reaction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Here the DifShell receives reaction rates (forward and backward), and concentrations for the free-buffer and bound-buffer molecules.</p> -</dd></dl> - -<dl class="method"> -<dt id="fluxFromOut"> -<tt class="descname">fluxFromOut</tt><big>(</big><big>)</big><a class="headerlink" href="#fluxFromOut" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message</p> -</dd></dl> - -<dl class="method"> -<dt id="fluxFromIn"> -<tt class="descname">fluxFromIn</tt><big>(</big><big>)</big><a class="headerlink" href="#fluxFromIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="influx"> -<tt class="descname">influx</tt><big>(</big><big>)</big><a class="headerlink" href="#influx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="outflux"> -<tt class="descname">outflux</tt><big>(</big><big>)</big><a class="headerlink" href="#outflux" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="fInflux"> -<tt class="descname">fInflux</tt><big>(</big><big>)</big><a class="headerlink" href="#fInflux" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="fOutflux"> -<tt class="descname">fOutflux</tt><big>(</big><big>)</big><a class="headerlink" href="#fOutflux" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="storeInflux"> -<tt class="descname">storeInflux</tt><big>(</big><big>)</big><a class="headerlink" href="#storeInflux" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="storeOutflux"> -<tt class="descname">storeOutflux</tt><big>(</big><big>)</big><a class="headerlink" href="#storeOutflux" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="tauPump"> -<tt class="descname">tauPump</tt><big>(</big><big>)</big><a class="headerlink" href="#tauPump" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="eqTauPump"> -<tt class="descname">eqTauPump</tt><big>(</big><big>)</big><a class="headerlink" href="#eqTauPump" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="mmPump"> -<tt class="descname">mmPump</tt><big>(</big><big>)</big><a class="headerlink" href="#mmPump" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="hillPump"> -<tt class="descname">hillPump</tt><big>(</big><big>)</big><a class="headerlink" href="#hillPump" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="concentrationOut"> -<tt class="descname">concentrationOut</tt><a class="headerlink" href="#concentrationOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out concentration</p> -</dd></dl> - -<dl class="attribute"> -<dt id="innerDifSourceOut"> -<tt class="descname">innerDifSourceOut</tt><a class="headerlink" href="#innerDifSourceOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out source information.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="outerDifSourceOut"> -<tt class="descname">outerDifSourceOut</tt><a class="headerlink" href="#outerDifSourceOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out source information.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="C"> -<tt class="descname">C</tt><a class="headerlink" href="#C" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Concentration C is computed by the DifShell and is read-only</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ceq"> -<tt class="descname">Ceq</tt><a class="headerlink" href="#Ceq" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="D"> -<tt class="descname">D</tt><a class="headerlink" href="#D" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="valence"> -<tt class="descname">valence</tt><a class="headerlink" href="#valence" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="leak"> -<tt class="descname">leak</tt><a class="headerlink" href="#leak" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="shapeMode"> -<tt class="descname">shapeMode</tt><a class="headerlink" href="#shapeMode" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="length"> -<tt class="descname">length</tt><a class="headerlink" href="#length" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="diameter"> -<tt class="descname">diameter</tt><a class="headerlink" href="#diameter" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="thickness"> -<tt class="descname">thickness</tt><a class="headerlink" href="#thickness" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="volume"> -<tt class="descname">volume</tt><a class="headerlink" href="#volume" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="outerArea"> -<tt class="descname">outerArea</tt><a class="headerlink" href="#outerArea" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="innerArea"> -<tt class="descname">innerArea</tt><a class="headerlink" href="#innerArea" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>)</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="DiffAmp"> -<em class="property">class </em><tt class="descname">DiffAmp</tt><a class="headerlink" href="#DiffAmp" title="Permalink to this definition">¶</a></dt> -<dd><p>A difference amplifier. Output is the difference between the total plus inputs and the total minus inputs multiplied by gain. Gain can be set statically as a field or can be a destination message and thus dynamically determined by the output of another object. Same as GENESIS diffamp object.</p> -<dl class="attribute"> -<dt id="DiffAmp.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#DiffAmp.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.setGain"> -<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.setGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.getGain"> -<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.setSaturation"> -<tt class="descname">setSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.setSaturation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.getSaturation"> -<tt class="descname">getSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getSaturation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.gainIn"> -<tt class="descname">gainIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.gainIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message to control gain dynamically.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.plusIn"> -<tt class="descname">plusIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.plusIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.minusIn"> -<tt class="descname">minusIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.minusIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt id="DiffAmp.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DiffAmp.output"> -<tt class="descname">output</tt><a class="headerlink" href="#DiffAmp.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Current output level.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DiffAmp.gain"> -<tt class="descname">gain</tt><a class="headerlink" href="#DiffAmp.gain" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DiffAmp.saturation"> -<tt class="descname">saturation</tt><a class="headerlink" href="#DiffAmp.saturation" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="DiffAmp.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#DiffAmp.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Output of the amplifier, i.e. gain * (plus - minus).</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Double"> -<em class="property">class </em><tt class="descname">Double</tt><a class="headerlink" href="#Double" title="Permalink to this definition">¶</a></dt> -<dd><p>Variable for storing values.</p> -<dl class="method"> -<dt id="Double.setValue"> -<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Double.setValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Double.getValue"> -<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Double.getValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Double.value"> -<tt class="descname">value</tt><a class="headerlink" href="#Double.value" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Variable value</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Dsolve"> -<em class="property">class </em><tt class="descname">Dsolve</tt><a class="headerlink" href="#Dsolve" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Dsolve.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Dsolve.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.setStoich"> -<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getStoich"> -<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.setPath"> -<tt class="descname">setPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setPath" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getPath"> -<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getPath" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.setCompartment"> -<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getCompartment"> -<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getNumVoxels"> -<tt class="descname">getNumVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getNumAllVoxels"> -<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.setNVec"> -<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getNVec"> -<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.setNumPools"> -<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.getNumPools"> -<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.buildNeuroMeshJunctions"> -<tt class="descname">buildNeuroMeshJunctions</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.buildNeuroMeshJunctions" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Builds junctions between NeuroMesh, SpineMesh and PsdMesh</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="Dsolve.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.stoich"> -<tt class="descname">stoich</tt><a class="headerlink" href="#Dsolve.stoich" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.path"> -<tt class="descname">path</tt><a class="headerlink" href="#Dsolve.path" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Path of reaction system. Must include all the pools that are to be handled by the Dsolve, can also include other random objects, which will be ignored.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.compartment"> -<tt class="descname">compartment</tt><a class="headerlink" href="#Dsolve.compartment" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Reac-diff compartment in which this diffusion system is embedded.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.numVoxels"> -<tt class="descname">numVoxels</tt><a class="headerlink" href="#Dsolve.numVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current diffusion solver.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.numAllVoxels"> -<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Dsolve.numAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current diffusion solver.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.numPools"> -<tt class="descname">numPools</tt><a class="headerlink" href="#Dsolve.numPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Dsolve.nVec"> -<tt class="descname">nVec</tt><a class="headerlink" href="#Dsolve.nVec" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of # of molecules along diffusion length, looked up by pool index</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Enz"> -<em class="property">class </em><tt class="descname">Enz</tt><a class="headerlink" href="#Enz" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="EnzBase"> -<em class="property">class </em><tt class="descname">EnzBase</tt><a class="headerlink" href="#EnzBase" title="Permalink to this definition">¶</a></dt> -<dd><p>Abstract base class for enzymes.</p> -<dl class="attribute"> -<dt id="EnzBase.sub"> -<tt class="descname">sub</tt><a class="headerlink" href="#EnzBase.sub" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to substrate molecule</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.prd"> -<tt class="descname">prd</tt><a class="headerlink" href="#EnzBase.prd" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to product molecule</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#EnzBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.setKm"> -<tt class="descname">setKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setKm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.getKm"> -<tt class="descname">getKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getKm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.setNumKm"> -<tt class="descname">setNumKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setNumKm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.getNumKm"> -<tt class="descname">getNumKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getNumKm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.setKcat"> -<tt class="descname">setKcat</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setKcat" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.getKcat"> -<tt class="descname">getKcat</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getKcat" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.getNumSubstrates"> -<tt class="descname">getNumSubstrates</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getNumSubstrates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.enzDest"> -<tt class="descname">enzDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.enzDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of Enzyme</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.subDest"> -<tt class="descname">subDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.subDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of substrate</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.prdDest"> -<tt class="descname">prdDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.prdDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of product. Dummy.</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="EnzBase.remesh"> -<tt class="descname">remesh</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.remesh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Tells the MMEnz to recompute its numKm after remeshing</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.subOut"> -<tt class="descname">subOut</tt><a class="headerlink" href="#EnzBase.subOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.prdOut"> -<tt class="descname">prdOut</tt><a class="headerlink" href="#EnzBase.prdOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.Km"> -<tt class="descname">Km</tt><a class="headerlink" href="#EnzBase.Km" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Michaelis-Menten constant in SI conc units (milliMolar)</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.numKm"> -<tt class="descname">numKm</tt><a class="headerlink" href="#EnzBase.numKm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Michaelis-Menten constant in number units, volume dependent</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.kcat"> -<tt class="descname">kcat</tt><a class="headerlink" href="#EnzBase.kcat" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Forward rate constant for enzyme, units 1/sec</p> -</dd></dl> - -<dl class="attribute"> -<dt id="EnzBase.numSubstrates"> -<tt class="descname">numSubstrates</tt><a class="headerlink" href="#EnzBase.numSubstrates" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Finfo"> -<em class="property">class </em><tt class="descname">Finfo</tt><a class="headerlink" href="#Finfo" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Finfo.getFieldName"> -<tt class="descname">getFieldName</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getFieldName" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Finfo.getDocs"> -<tt class="descname">getDocs</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getDocs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Finfo.getType"> -<tt class="descname">getType</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getType" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Finfo.getSrc"> -<tt class="descname">getSrc</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getSrc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Finfo.getDest"> -<tt class="descname">getDest</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Finfo.fieldName"> -<tt class="descname">fieldName</tt><a class="headerlink" href="#Finfo.fieldName" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Name of field handled by Finfo</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Finfo.docs"> -<tt class="descname">docs</tt><a class="headerlink" href="#Finfo.docs" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Documentation for Finfo</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Finfo.type"> -<tt class="descname">type</tt><a class="headerlink" href="#Finfo.type" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) RTTI type info for this Finfo</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Finfo.src"> -<tt class="descname">src</tt><a class="headerlink" href="#Finfo.src" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Subsidiary SrcFinfos. Useful for SharedFinfos</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Finfo.dest"> -<tt class="descname">dest</tt><a class="headerlink" href="#Finfo.dest" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Subsidiary DestFinfos. Useful for SharedFinfos</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Func"> -<em class="property">class </em><tt class="descname">Func</tt><a class="headerlink" href="#Func" title="Permalink to this definition">¶</a></dt> -<dd><p>Func: general purpose function calculator using real numbers. It can</p> -<p>parse mathematical expression defining a function and evaluate it</p> -<p>and/or its derivative for specified variable values.</p> -<p>The variables can be input from other moose objects. In case of</p> -<p>arbitrary variable names, the source message must have the variable</p> -<p>name as the first argument. For most common cases, input messages to</p> -<p>set x, y, z and xy, xyz are made available without such</p> -<p>requirement. This class handles only real numbers</p> -<blockquote> -<div>pi=3.141592...,</div></blockquote> -<p>e=2.718281...</p> -<dl class="attribute"> -<dt id="Func.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Func.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getValue"> -<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getDerivative"> -<tt class="descname">getDerivative</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getDerivative" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setMode"> -<tt class="descname">setMode</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getMode"> -<tt class="descname">getMode</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setExpr"> -<tt class="descname">setExpr</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setExpr" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getExpr"> -<tt class="descname">getExpr</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getExpr" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setVar"> -<tt class="descname">setVar</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setVar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getVar"> -<tt class="descname">getVar</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getVar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getVars"> -<tt class="descname">getVars</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getVars" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.varIn"> -<tt class="descname">varIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.varIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for specified variable coming from other objects</p> -</dd></dl> - -<dl class="method"> -<dt id="Func.xIn"> -<tt class="descname">xIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.xIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for variable named x. This is a shorthand. If the</p> -</dd></dl> - -</dd></dl> - -<p>expression does not have any variable named x, this the first variable -in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><blockquote> -<div><dl class="method"> -<dt id="yIn"> -<tt class="descname">yIn</tt><big>(</big><big>)</big><a class="headerlink" href="#yIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for variable named y. This is a utility for two/three</p> -</dd></dl> - -</div></blockquote> -<p>variable functions where the y value comes from a source separate -from that of x. This is a shorthand. If the</p> -</div></blockquote> -<p>expression does not have any variable named y, this the second -variable in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><blockquote> -<div><dl class="method"> -<dt id="zIn"> -<tt class="descname">zIn</tt><big>(</big><big>)</big><a class="headerlink" href="#zIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for variable named z. This is a utility for three</p> -</dd></dl> - -</div></blockquote> -<p>variable functions where the z value comes from a source separate -from that of x or y. This is a shorthand. If the expression does not -have any variable named y, this the second variable in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><dl class="method"> -<dt id="xyIn"> -<tt class="descname">xyIn</tt><big>(</big><big>)</big><a class="headerlink" href="#xyIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for variables x and y for two-variable function</p> -</dd></dl> - -<dl class="method"> -<dt id="xyzIn"> -<tt class="descname">xyzIn</tt><big>(</big><big>)</big><a class="headerlink" href="#xyzIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle value for variables x, y and z for three-variable function</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">process</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">reinit</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="valueOut"> -<tt class="descname">valueOut</tt><a class="headerlink" href="#valueOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Evaluated value of the function for the current variable values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="derivativeOut"> -<tt class="descname">derivativeOut</tt><a class="headerlink" href="#derivativeOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Value of derivative of the function for the current variable values</p> -</dd></dl> - -<dl class="attribute"> -<dt id="value"> -<tt class="descname">value</tt><a class="headerlink" href="#value" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Result of the function evaluation with current variable values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="derivative"> -<tt class="descname">derivative</tt><a class="headerlink" href="#derivative" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Derivative of the function at given variable values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="mode"> -<tt class="descname">mode</tt><a class="headerlink" href="#mode" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Mode of operation:</p> -</dd></dl> - -</div></blockquote> -<p>1: only the function value will be funculated -2: only the derivative will be funculated -3: both function value and derivative at current variable values will be funculated.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="expr"> -<tt class="descname">expr</tt><a class="headerlink" href="#expr" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Mathematical expression defining the function. The underlying parser</p> -</dd></dl> - -</div></blockquote> -</div></blockquote> -<p>is muParser. Hence the available functions and operators are (from -muParser docs):</p> -<p>Functions -Name args explanation -sin 1 sine function -cos 1 cosine function -tan 1 tangens function -asin 1 arcus sine function -acos 1 arcus cosine function -atan 1 arcus tangens function -sinh 1 hyperbolic sine function -cosh 1 hyperbolic cosine -tanh 1 hyperbolic tangens function -asinh 1 hyperbolic arcus sine function -acosh 1 hyperbolic arcus tangens function -atanh 1 hyperbolic arcur tangens function -log2 1 logarithm to the base 2 -log10 1 logarithm to the base 10 -log 1 logarithm to the base 10 -ln 1 logarithm to base e (2.71828...) -exp 1 e raised to the power of x -sqrt 1 square root of a value -sign 1 sign function -1 if x<0; 1 if x>0 -rint 1 round to nearest integer -abs 1 absolute value -min var. min of all arguments -max var. max of all arguments -sum var. sum of all arguments -avg var. mean value of all arguments</p> -<p>Operators -Op meaning prioroty -= assignement -1 -&& logical and 1 -|| logical or 2 -<= less or equal 4 ->= greater or equal 4 -!= not equal 4 -== equal 4 -> greater than 4 -< less than 4 -+ addition 5 -- subtraction 5 -* multiplication 6 -/ division 6 -^ raise x to the power of y 7</p> -<p>?: if then else operator C++ style syntax</p> -<blockquote> -<div><dl class="attribute"> -<dt id="vars"> -<tt class="descname">vars</tt><a class="headerlink" href="#vars" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Variable names in the expression</p> -</dd></dl> - -<dl class="attribute"> -<dt id="x"> -<tt class="descname">x</tt><a class="headerlink" href="#x" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Value for variable named x. This is a shorthand. If the</p> -</dd></dl> - -</div></blockquote> -<p>expression does not have any variable named x, this the first variable -in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><blockquote> -<div><dl class="attribute"> -<dt id="y"> -<tt class="descname">y</tt><a class="headerlink" href="#y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Value for variable named y. This is a utility for two/three</p> -</dd></dl> - -</div></blockquote> -<p>variable functions where the y value comes from a source separate -from that of x. This is a shorthand. If the</p> -</div></blockquote> -<p>expression does not have any variable named y, this the second -variable in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><blockquote> -<div><dl class="attribute"> -<dt id="z"> -<tt class="descname">z</tt><a class="headerlink" href="#z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Value for variable named z. This is a utility for three</p> -</dd></dl> - -</div></blockquote> -<p>variable functions where the z value comes from a source separate -from that of x or z. This is a shorthand. If the expression does not -have any variable named z, this the third variable in the sequence <cite>vars</cite>.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="var"> -<tt class="descname">var</tt><a class="headerlink" href="#var" title="Permalink to this definition">¶</a></dt> -<dd><p>string,double (<em>lookup field</em>) Lookup table for variable values.</p> -</dd></dl> - -</div></blockquote> -</div></blockquote> -<dl class="class"> -<dt id="FuncBase"> -<em class="property">class </em><tt class="descname">FuncBase</tt><a class="headerlink" href="#FuncBase" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="FuncBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#FuncBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="FuncBase.getResult"> -<tt class="descname">getResult</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.getResult" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="FuncBase.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</p> -</dd></dl> - -<dl class="method"> -<dt id="FuncBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="FuncBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="FuncBase.output"> -<tt class="descname">output</tt><a class="headerlink" href="#FuncBase.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out sum on each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="FuncBase.result"> -<tt class="descname">result</tt><a class="headerlink" href="#FuncBase.result" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Outcome of function computation</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="FuncPool"> -<em class="property">class </em><tt class="descname">FuncPool</tt><a class="headerlink" href="#FuncPool" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="FuncPool.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncPool.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles input to control value of <a href="#id21"><span class="problematic" id="id22">n_</span></a></p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="GapJunction"> -<em class="property">class </em><tt class="descname">GapJunction</tt><a class="headerlink" href="#GapJunction" title="Permalink to this definition">¶</a></dt> -<dd><p>Implementation of gap junction between two compartments. The shared</p> -<p>fields, ‘channel1’ and ‘channel2’ can be connected to the ‘channel’</p> -<p>message of the compartments at either end of the gap junction. The</p> -<p>compartments will send their Vm to the gap junction and receive the</p> -<p>conductance ‘Gk’ of the gap junction and the Vm of the other</p> -<p>compartment.</p> -<dl class="attribute"> -<dt id="GapJunction.channel1"> -<tt class="descname">channel1</tt><a class="headerlink" href="#GapJunction.channel1" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to couple the conductance and Vm from</p> -</dd></dl> - -</dd></dl> - -<p>terminal 2 to the compartment at terminal 1. The first entry is source -sending out Gk and Vm2, the second entry is destination for Vm1.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="channel2"> -<tt class="descname">channel2</tt><a class="headerlink" href="#channel2" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to couple the conductance and Vm from</p> -</dd></dl> - -</div></blockquote> -<p>terminal 1 to the compartment at terminal 2. The first entry is source -sending out Gk and Vm1, the second entry is destination for Vm2.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="Vm1"> -<tt class="descname">Vm1</tt><big>(</big><big>)</big><a class="headerlink" href="#Vm1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message from compartment</p> -</dd></dl> - -<dl class="method"> -<dt id="Vm2"> -<tt class="descname">Vm2</tt><big>(</big><big>)</big><a class="headerlink" href="#Vm2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message from another compartment</p> -</dd></dl> - -<dl class="method"> -<dt id="setGk"> -<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#setGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="getGk"> -<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#getGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">process</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">reinit</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="channel1Out"> -<tt class="descname">channel1Out</tt><a class="headerlink" href="#channel1Out" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends Gk and Vm from one compartment to the other</p> -</dd></dl> - -<dl class="attribute"> -<dt id="channel2Out"> -<tt class="descname">channel2Out</tt><a class="headerlink" href="#channel2Out" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends Gk and Vm from one compartment to the other</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gk"> -<tt class="descname">Gk</tt><a class="headerlink" href="#Gk" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Conductance of the gap junction</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="Group"> -<em class="property">class </em><tt class="descname">Group</tt><a class="headerlink" href="#Group" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Group.group"> -<tt class="descname">group</tt><a class="headerlink" href="#Group.group" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>source message field</em>) Handle for grouping Elements</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Gsolve"> -<em class="property">class </em><tt class="descname">Gsolve</tt><a class="headerlink" href="#Gsolve" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Gsolve.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Gsolve.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.setStoich"> -<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getStoich"> -<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getNumLocalVoxels"> -<tt class="descname">getNumLocalVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumLocalVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.setNVec"> -<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getNVec"> -<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.setNumAllVoxels"> -<tt class="descname">setNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNumAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getNumAllVoxels"> -<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.setNumPools"> -<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getNumPools"> -<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.setUseRandInit"> -<tt class="descname">setUseRandInit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setUseRandInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Gsolve.getUseRandInit"> -<tt class="descname">getUseRandInit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getUseRandInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.stoich"> -<tt class="descname">stoich</tt><a class="headerlink" href="#Gsolve.stoich" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.numLocalVoxels"> -<tt class="descname">numLocalVoxels</tt><a class="headerlink" href="#Gsolve.numLocalVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current solver.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.numAllVoxels"> -<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Gsolve.numAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.numPools"> -<tt class="descname">numPools</tt><a class="headerlink" href="#Gsolve.numPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.useRandInit"> -<tt class="descname">useRandInit</tt><a class="headerlink" href="#Gsolve.useRandInit" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag: True when using probabilistic (random) rounding. When initializing the mol# from floating-point Sinit values, we have two options. One is to look at each Sinit, and round to the nearest integer. The other is to look at each Sinit, and probabilistically round up or down depending on the value. For example, if we had a Sinit value of 1.49, this would always be rounded to 1.0 if the flag is false, and would be rounded to 1.0 and 2.0 in the ratio 51:49 if the flag is true.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Gsolve.nVec"> -<tt class="descname">nVec</tt><a class="headerlink" href="#Gsolve.nVec" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of pool counts</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="HHChannel"> -<em class="property">class </em><tt class="descname">HHChannel</tt><a class="headerlink" href="#HHChannel" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>HHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p> -<dl class="attribute"> -<dt id="HHChannel.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#HHChannel.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p> -</dd></dl> - -</div></blockquote> -<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -<blockquote> -<div><dl class="method"> -<dt id="HHChannel.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setXpower"> -<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getXpower"> -<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setYpower"> -<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getYpower"> -<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setZpower"> -<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getZpower"> -<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setInstant"> -<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getInstant"> -<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setUseConcentration"> -<tt class="descname">setUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setUseConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getUseConcentration"> -<tt class="descname">getUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getUseConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.concen"> -<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.concen" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to usein the Z gate calculations</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.createGate"> -<tt class="descname">createGate</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.createGate" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Function to create specified gate.Argument: Gate type [X Y Z]</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setNumGateX"> -<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getNumGateX"> -<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setNumGateY"> -<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getNumGateY"> -<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.setNumGateZ"> -<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel.getNumGateZ"> -<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.Xpower"> -<tt class="descname">Xpower</tt><a class="headerlink" href="#HHChannel.Xpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.Ypower"> -<tt class="descname">Ypower</tt><a class="headerlink" href="#HHChannel.Ypower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.Zpower"> -<tt class="descname">Zpower</tt><a class="headerlink" href="#HHChannel.Zpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Z gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.instant"> -<tt class="descname">instant</tt><a class="headerlink" href="#HHChannel.instant" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.X"> -<tt class="descname">X</tt><a class="headerlink" href="#HHChannel.X" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.Y"> -<tt class="descname">Y</tt><a class="headerlink" href="#HHChannel.Y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.Z"> -<tt class="descname">Z</tt><a class="headerlink" href="#HHChannel.Z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel.useConcentration"> -<tt class="descname">useConcentration</tt><a class="headerlink" href="#HHChannel.useConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Flag: when true, use concentration message rather than Vm tocontrol Z gate</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="class"> -<dt id="HHChannel2D"> -<em class="property">class </em><tt class="descname">HHChannel2D</tt><a class="headerlink" href="#HHChannel2D" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>HHChannel2D: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p> -<dl class="attribute"> -<dt id="HHChannel2D.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#HHChannel2D.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p> -</dd></dl> - -</div></blockquote> -<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -<blockquote> -<div><dl class="method"> -<dt id="HHChannel2D.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setXindex"> -<tt class="descname">setXindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setXindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getXindex"> -<tt class="descname">getXindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getXindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setYindex"> -<tt class="descname">setYindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setYindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getYindex"> -<tt class="descname">getYindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getYindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setZindex"> -<tt class="descname">setZindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getZindex"> -<tt class="descname">getZindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setXpower"> -<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getXpower"> -<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setYpower"> -<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getYpower"> -<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setZpower"> -<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getZpower"> -<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setInstant"> -<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getInstant"> -<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.concen"> -<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.concen" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to useas the first concen variable</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.concen2"> -<tt class="descname">concen2</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.concen2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to useas the second concen variable</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setNumGateX"> -<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getNumGateX"> -<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setNumGateY"> -<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getNumGateY"> -<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.setNumGateZ"> -<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHChannel2D.getNumGateZ"> -<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Xindex"> -<tt class="descname">Xindex</tt><a class="headerlink" href="#HHChannel2D.Xindex" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) String for setting X index.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Yindex"> -<tt class="descname">Yindex</tt><a class="headerlink" href="#HHChannel2D.Yindex" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) String for setting Y index.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Zindex"> -<tt class="descname">Zindex</tt><a class="headerlink" href="#HHChannel2D.Zindex" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) String for setting Z index.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Xpower"> -<tt class="descname">Xpower</tt><a class="headerlink" href="#HHChannel2D.Xpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Ypower"> -<tt class="descname">Ypower</tt><a class="headerlink" href="#HHChannel2D.Ypower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Zpower"> -<tt class="descname">Zpower</tt><a class="headerlink" href="#HHChannel2D.Zpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Z gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.instant"> -<tt class="descname">instant</tt><a class="headerlink" href="#HHChannel2D.instant" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.X"> -<tt class="descname">X</tt><a class="headerlink" href="#HHChannel2D.X" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Y"> -<tt class="descname">Y</tt><a class="headerlink" href="#HHChannel2D.Y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHChannel2D.Z"> -<tt class="descname">Z</tt><a class="headerlink" href="#HHChannel2D.Z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="class"> -<dt id="HHGate"> -<em class="property">class </em><tt class="descname">HHGate</tt><a class="headerlink" href="#HHGate" title="Permalink to this definition">¶</a></dt> -<dd><p>HHGate: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance.</p> -<dl class="method"> -<dt id="HHGate.getA"> -<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getB"> -<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setAlpha"> -<tt class="descname">setAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getAlpha"> -<tt class="descname">getAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setBeta"> -<tt class="descname">setBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setBeta" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getBeta"> -<tt class="descname">getBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getBeta" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setTau"> -<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getTau"> -<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setMInfinity"> -<tt class="descname">setMInfinity</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMInfinity" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getMInfinity"> -<tt class="descname">getMInfinity</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMInfinity" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setMin"> -<tt class="descname">setMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getMin"> -<tt class="descname">getMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setMax"> -<tt class="descname">setMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getMax"> -<tt class="descname">getMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setDivs"> -<tt class="descname">setDivs</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setDivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getDivs"> -<tt class="descname">getDivs</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getDivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setTableA"> -<tt class="descname">setTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTableA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getTableA"> -<tt class="descname">getTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTableA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setTableB"> -<tt class="descname">setTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTableB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getTableB"> -<tt class="descname">getTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTableB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setUseInterpolation"> -<tt class="descname">setUseInterpolation</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setUseInterpolation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getUseInterpolation"> -<tt class="descname">getUseInterpolation</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getUseInterpolation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setAlphaParms"> -<tt class="descname">setAlphaParms</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setAlphaParms" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.getAlphaParms"> -<tt class="descname">getAlphaParms</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getAlphaParms" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setupAlpha"> -<tt class="descname">setupAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setupTau"> -<tt class="descname">setupTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.tweakAlpha"> -<tt class="descname">tweakAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.tweakAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.tweakTau"> -<tt class="descname">tweakTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.tweakTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate.setupGate"> -<tt class="descname">setupGate</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupGate" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.alpha"> -<tt class="descname">alpha</tt><a class="headerlink" href="#HHGate.alpha" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.beta"> -<tt class="descname">beta</tt><a class="headerlink" href="#HHGate.beta" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.tau"> -<tt class="descname">tau</tt><a class="headerlink" href="#HHGate.tau" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.mInfinity"> -<tt class="descname">mInfinity</tt><a class="headerlink" href="#HHGate.mInfinity" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.min"> -<tt class="descname">min</tt><a class="headerlink" href="#HHGate.min" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.max"> -<tt class="descname">max</tt><a class="headerlink" href="#HHGate.max" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.divs"> -<tt class="descname">divs</tt><a class="headerlink" href="#HHGate.divs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.tableA"> -<tt class="descname">tableA</tt><a class="headerlink" href="#HHGate.tableA" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Table of A entries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.tableB"> -<tt class="descname">tableB</tt><a class="headerlink" href="#HHGate.tableB" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Table of alpha + beta entries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.useInterpolation"> -<tt class="descname">useInterpolation</tt><a class="headerlink" href="#HHGate.useInterpolation" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag: use linear interpolation if true, else direct lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.alphaParms"> -<tt class="descname">alphaParms</tt><a class="headerlink" href="#HHGate.alphaParms" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.A"> -<tt class="descname">A</tt><a class="headerlink" href="#HHGate.A" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>lookup field</em>) lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate.B"> -<tt class="descname">B</tt><a class="headerlink" href="#HHGate.B" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>lookup field</em>) lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="HHGate2D"> -<em class="property">class </em><tt class="descname">HHGate2D</tt><a class="headerlink" href="#HHGate2D" title="Permalink to this definition">¶</a></dt> -<dd><p>HHGate2D: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance. These two terms are sent right back in a message to the channel.</p> -<dl class="method"> -<dt id="HHGate2D.getA"> -<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getB"> -<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setTableA"> -<tt class="descname">setTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setTableA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getTableA"> -<tt class="descname">getTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getTableA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setTableB"> -<tt class="descname">setTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setTableB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getTableB"> -<tt class="descname">getTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getTableB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXminA"> -<tt class="descname">setXminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXminA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXminA"> -<tt class="descname">getXminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXminA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXmaxA"> -<tt class="descname">setXmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXmaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXmaxA"> -<tt class="descname">getXmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXmaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXdivsA"> -<tt class="descname">setXdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXdivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXdivsA"> -<tt class="descname">getXdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXdivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYminA"> -<tt class="descname">setYminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYminA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYminA"> -<tt class="descname">getYminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYminA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYmaxA"> -<tt class="descname">setYmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYmaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYmaxA"> -<tt class="descname">getYmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYmaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYdivsA"> -<tt class="descname">setYdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYdivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYdivsA"> -<tt class="descname">getYdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYdivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXminB"> -<tt class="descname">setXminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXminB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXminB"> -<tt class="descname">getXminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXminB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXmaxB"> -<tt class="descname">setXmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXmaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXmaxB"> -<tt class="descname">getXmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXmaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setXdivsB"> -<tt class="descname">setXdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXdivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getXdivsB"> -<tt class="descname">getXdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXdivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYminB"> -<tt class="descname">setYminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYminB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYminB"> -<tt class="descname">getYminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYminB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYmaxB"> -<tt class="descname">setYmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYmaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYmaxB"> -<tt class="descname">getYmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYmaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.setYdivsB"> -<tt class="descname">setYdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYdivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HHGate2D.getYdivsB"> -<tt class="descname">getYdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYdivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.tableA"> -<tt class="descname">tableA</tt><a class="headerlink" href="#HHGate2D.tableA" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>value field</em>) Table of A entries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.tableB"> -<tt class="descname">tableB</tt><a class="headerlink" href="#HHGate2D.tableB" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>value field</em>) Table of B entries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xminA"> -<tt class="descname">xminA</tt><a class="headerlink" href="#HHGate2D.xminA" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xmaxA"> -<tt class="descname">xmaxA</tt><a class="headerlink" href="#HHGate2D.xmaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xdivsA"> -<tt class="descname">xdivsA</tt><a class="headerlink" href="#HHGate2D.xdivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.yminA"> -<tt class="descname">yminA</tt><a class="headerlink" href="#HHGate2D.yminA" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.ymaxA"> -<tt class="descname">ymaxA</tt><a class="headerlink" href="#HHGate2D.ymaxA" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.ydivsA"> -<tt class="descname">ydivsA</tt><a class="headerlink" href="#HHGate2D.ydivsA" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xminB"> -<tt class="descname">xminB</tt><a class="headerlink" href="#HHGate2D.xminB" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xmaxB"> -<tt class="descname">xmaxB</tt><a class="headerlink" href="#HHGate2D.xmaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.xdivsB"> -<tt class="descname">xdivsB</tt><a class="headerlink" href="#HHGate2D.xdivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.yminB"> -<tt class="descname">yminB</tt><a class="headerlink" href="#HHGate2D.yminB" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.ymaxB"> -<tt class="descname">ymaxB</tt><a class="headerlink" href="#HHGate2D.ymaxB" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum range for lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.ydivsB"> -<tt class="descname">ydivsB</tt><a class="headerlink" href="#HHGate2D.ydivsB" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.A"> -<tt class="descname">A</tt><a class="headerlink" href="#HHGate2D.A" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double>,double (<em>lookup field</em>) lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HHGate2D.B"> -<tt class="descname">B</tt><a class="headerlink" href="#HHGate2D.B" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double>,double (<em>lookup field</em>) lookupB: Look up B gate value from two doubles in a vector.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="HSolve"> -<em class="property">class </em><tt class="descname">HSolve</tt><a class="headerlink" href="#HSolve" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="HSolve.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#HSolve.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Handles ‘reinit’ and ‘process’ calls from a clock.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setSeed"> -<tt class="descname">setSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setSeed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getSeed"> -<tt class="descname">getSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getSeed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setTarget"> -<tt class="descname">setTarget</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setTarget" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getTarget"> -<tt class="descname">getTarget</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getTarget" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setDt"> -<tt class="descname">setDt</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getDt"> -<tt class="descname">getDt</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setCaAdvance"> -<tt class="descname">setCaAdvance</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaAdvance" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getCaAdvance"> -<tt class="descname">getCaAdvance</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaAdvance" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setVDiv"> -<tt class="descname">setVDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getVDiv"> -<tt class="descname">getVDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setVMin"> -<tt class="descname">setVMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getVMin"> -<tt class="descname">getVMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setVMax"> -<tt class="descname">setVMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getVMax"> -<tt class="descname">getVMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setCaDiv"> -<tt class="descname">setCaDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getCaDiv"> -<tt class="descname">getCaDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setCaMin"> -<tt class="descname">setCaMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getCaMin"> -<tt class="descname">getCaMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaMin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.setCaMax"> -<tt class="descname">setCaMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.getCaMax"> -<tt class="descname">getCaMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaMax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘process’ call: Solver advances by one time-step.</p> -</dd></dl> - -<dl class="method"> -<dt id="HSolve.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call: Solver reads in model.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.seed"> -<tt class="descname">seed</tt><a class="headerlink" href="#HSolve.seed" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Use this field to specify path to a ‘seed’ compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.target"> -<tt class="descname">target</tt><a class="headerlink" href="#HSolve.target" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.dt"> -<tt class="descname">dt</tt><a class="headerlink" href="#HSolve.dt" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The time-step for this solver.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.caAdvance"> -<tt class="descname">caAdvance</tt><a class="headerlink" href="#HSolve.caAdvance" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.vDiv"> -<tt class="descname">vDiv</tt><a class="headerlink" href="#HSolve.vDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Specifies number of divisions for lookup tables of voltage-sensitive channels.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.vMin"> -<tt class="descname">vMin</tt><a class="headerlink" href="#HSolve.vMin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.vMax"> -<tt class="descname">vMax</tt><a class="headerlink" href="#HSolve.vMax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.caDiv"> -<tt class="descname">caDiv</tt><a class="headerlink" href="#HSolve.caDiv" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Specifies number of divisions for lookup tables of calcium-sensitive channels.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.caMin"> -<tt class="descname">caMin</tt><a class="headerlink" href="#HSolve.caMin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="HSolve.caMax"> -<tt class="descname">caMax</tt><a class="headerlink" href="#HSolve.caMax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="IntFire"> -<em class="property">class </em><tt class="descname">IntFire</tt><a class="headerlink" href="#IntFire" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="IntFire.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#IntFire.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.setVm"> -<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.getVm"> -<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.setTau"> -<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.getTau"> -<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.setThresh"> -<tt class="descname">setThresh</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setThresh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.getThresh"> -<tt class="descname">getThresh</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getThresh" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.setRefractoryPeriod"> -<tt class="descname">setRefractoryPeriod</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setRefractoryPeriod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.getRefractoryPeriod"> -<tt class="descname">getRefractoryPeriod</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getRefractoryPeriod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.setBufferTime"> -<tt class="descname">setBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setBufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.getBufferTime"> -<tt class="descname">getBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getBufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="IntFire.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.spikeOut"> -<tt class="descname">spikeOut</tt><a class="headerlink" href="#IntFire.spikeOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out spike events</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.Vm"> -<tt class="descname">Vm</tt><a class="headerlink" href="#IntFire.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.tau"> -<tt class="descname">tau</tt><a class="headerlink" href="#IntFire.tau" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) charging time-course</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.thresh"> -<tt class="descname">thresh</tt><a class="headerlink" href="#IntFire.thresh" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) firing threshold</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.refractoryPeriod"> -<tt class="descname">refractoryPeriod</tt><a class="headerlink" href="#IntFire.refractoryPeriod" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum time between successive spikes</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IntFire.bufferTime"> -<tt class="descname">bufferTime</tt><a class="headerlink" href="#IntFire.bufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Duration of spike buffer.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Interpol"> -<em class="property">class </em><tt class="descname">Interpol</tt><a class="headerlink" href="#Interpol" title="Permalink to this definition">¶</a></dt> -<dd><p>Interpol: Interpolation class. Handles lookup from a 1-dimensional array of real-numbered values.Returns ‘y’ value based on given ‘x’ value. Can either use interpolation or roundoff to the nearest index.</p> -<dl class="attribute"> -<dt id="Interpol.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Interpol.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.setXmin"> -<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.setXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.getXmin"> -<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.setXmax"> -<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.setXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.getXmax"> -<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Interpolates using the input as x value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol.lookupOut"> -<tt class="descname">lookupOut</tt><a class="headerlink" href="#Interpol.lookupOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) respond to a request for a value lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol.xmin"> -<tt class="descname">xmin</tt><a class="headerlink" href="#Interpol.xmin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value of x. x below this will result in y[0] being returned.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol.xmax"> -<tt class="descname">xmax</tt><a class="headerlink" href="#Interpol.xmax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value of x. x above this will result in y[last] being returned.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol.y"> -<tt class="descname">y</tt><a class="headerlink" href="#Interpol.y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Looked up value.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Interpol2D"> -<em class="property">class </em><tt class="descname">Interpol2D</tt><a class="headerlink" href="#Interpol2D" title="Permalink to this definition">¶</a></dt> -<dd><p>Interpol2D: Interpolation class. Handles lookup from a 2-dimensional grid of real-numbered values. Returns ‘z’ value based on given ‘x’ and ‘y’ values. Can either use interpolation or roundoff to the nearest index.</p> -<dl class="attribute"> -<dt id="Interpol2D.lookupReturn2D"> -<tt class="descname">lookupReturn2D</tt><a class="headerlink" href="#Interpol2D.lookupReturn2D" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.lookup"> -<tt class="descname">lookup</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.lookup" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Looks up table value based on indices v1 and v2, and sendsvalue back using the ‘lookupOut’ message</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setXmin"> -<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getXmin"> -<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setXmax"> -<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getXmax"> -<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setXdivs"> -<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getXdivs"> -<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setDx"> -<tt class="descname">setDx</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setDx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getDx"> -<tt class="descname">getDx</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getDx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setYmin"> -<tt class="descname">setYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getYmin"> -<tt class="descname">getYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setYmax"> -<tt class="descname">setYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getYmax"> -<tt class="descname">getYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setYdivs"> -<tt class="descname">setYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getYdivs"> -<tt class="descname">getYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setDy"> -<tt class="descname">setDy</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setDy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getDy"> -<tt class="descname">getDy</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getDy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setTable"> -<tt class="descname">setTable</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setTable" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getTable"> -<tt class="descname">getTable</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getTable" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.setTableVector2D"> -<tt class="descname">setTableVector2D</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setTableVector2D" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Interpol2D.getTableVector2D"> -<tt class="descname">getTableVector2D</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getTableVector2D" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.lookupOut"> -<tt class="descname">lookupOut</tt><a class="headerlink" href="#Interpol2D.lookupOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) respond to a request for a value lookup</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.xmin"> -<tt class="descname">xmin</tt><a class="headerlink" href="#Interpol2D.xmin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value for x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.xmax"> -<tt class="descname">xmax</tt><a class="headerlink" href="#Interpol2D.xmax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value for x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.xdivs"> -<tt class="descname">xdivs</tt><a class="headerlink" href="#Interpol2D.xdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) # of divisions on x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.dx"> -<tt class="descname">dx</tt><a class="headerlink" href="#Interpol2D.dx" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Increment on x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.ymin"> -<tt class="descname">ymin</tt><a class="headerlink" href="#Interpol2D.ymin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value for y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.ymax"> -<tt class="descname">ymax</tt><a class="headerlink" href="#Interpol2D.ymax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value for y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.ydivs"> -<tt class="descname">ydivs</tt><a class="headerlink" href="#Interpol2D.ydivs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) # of divisions on y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.dy"> -<tt class="descname">dy</tt><a class="headerlink" href="#Interpol2D.dy" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Increment on y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.tableVector2D"> -<tt class="descname">tableVector2D</tt><a class="headerlink" href="#Interpol2D.tableVector2D" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>value field</em>) Get the entire table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.table"> -<tt class="descname">table</tt><a class="headerlink" href="#Interpol2D.table" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int>,double (<em>lookup field</em>) Lookup an entry on the table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Interpol2D.z"> -<tt class="descname">z</tt><a class="headerlink" href="#Interpol2D.z" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double>,double (<em>lookup field</em>) Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="IzhikevichNrn"> -<em class="property">class </em><tt class="descname">IzhikevichNrn</tt><a class="headerlink" href="#IzhikevichNrn" title="Permalink to this definition">¶</a></dt> -<dd><p>Izhikevich model of spiking neuron (Izhikevich,EM. 2003. Simple model of spiking neurons. Neural Networks, IEEE Transactions on 14(6). pp 1569-1572).</p> -<blockquote> -<div><blockquote> -<div><p>dVm/dt = 0.04 * Vm^2 + 5 * Vm + 140 - u + inject</p> -<p>du/dt = a * (b * Vm - u)</p> -</div></blockquote> -<p>if Vm >= Vmax then Vm = c and u = u + d</p> -<p>Vmax = 30 mV in the paper.</p> -</div></blockquote> -<dl class="attribute"> -<dt id="IzhikevichNrn.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#IzhikevichNrn.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#IzhikevichNrn.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message from a IzhikevichNrn to channels.The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setVmax"> -<tt class="descname">setVmax</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setVmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getVmax"> -<tt class="descname">getVmax</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getVmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setC"> -<tt class="descname">setC</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setC" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getC"> -<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getC" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setD"> -<tt class="descname">setD</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getD"> -<tt class="descname">getD</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setA"> -<tt class="descname">setA</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getA"> -<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getA" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setB"> -<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getB"> -<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getU"> -<tt class="descname">getU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getU" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setVm"> -<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getVm"> -<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getIm"> -<tt class="descname">getIm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getIm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setInject"> -<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getInject"> -<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setRmByTau"> -<tt class="descname">setRmByTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setRmByTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getRmByTau"> -<tt class="descname">getRmByTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getRmByTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setAccommodating"> -<tt class="descname">setAccommodating</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setAccommodating" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getAccommodating"> -<tt class="descname">getAccommodating</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getAccommodating" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setU0"> -<tt class="descname">setU0</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setU0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getU0"> -<tt class="descname">getU0</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getU0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setInitVm"> -<tt class="descname">setInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInitVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getInitVm"> -<tt class="descname">getInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInitVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setInitU"> -<tt class="descname">setInitU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInitU" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getInitU"> -<tt class="descname">getInitU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInitU" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setAlpha"> -<tt class="descname">setAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getAlpha"> -<tt class="descname">getAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getAlpha" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setBeta"> -<tt class="descname">setBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setBeta" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getBeta"> -<tt class="descname">getBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getBeta" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.setGamma"> -<tt class="descname">setGamma</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setGamma" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.getGamma"> -<tt class="descname">getGamma</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getGamma" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.injectMsg"> -<tt class="descname">injectMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.injectMsg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Injection current into the neuron.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.cDest"> -<tt class="descname">cDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.cDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message to modify parameter c at runtime.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.dDest"> -<tt class="descname">dDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.dDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message to modify parameter d at runtime.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.bDest"> -<tt class="descname">bDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.bDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message to modify parameter b at runtime</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.aDest"> -<tt class="descname">aDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.aDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message modify parameter a at runtime.</p> -</dd></dl> - -<dl class="method"> -<dt id="IzhikevichNrn.handleChannel"> -<tt class="descname">handleChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.handleChannel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles conductance and reversal potential arguments from Channel</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.VmOut"> -<tt class="descname">VmOut</tt><a class="headerlink" href="#IzhikevichNrn.VmOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out Vm</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.spikeOut"> -<tt class="descname">spikeOut</tt><a class="headerlink" href="#IzhikevichNrn.spikeOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out spike events</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">VmOut</tt></dt> -<dd><p>double (<em>source message field</em>) Sends out Vm</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.Vmax"> -<tt class="descname">Vmax</tt><a class="headerlink" href="#IzhikevichNrn.Vmax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.c"> -<tt class="descname">c</tt><a class="headerlink" href="#IzhikevichNrn.c" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reset potential. Membrane potential is reset to c whenever it reaches Vmax.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.d"> -<tt class="descname">d</tt><a class="headerlink" href="#IzhikevichNrn.d" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Parameter d in Izhikevich model. Unit is V/s.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.a"> -<tt class="descname">a</tt><a class="headerlink" href="#IzhikevichNrn.a" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Parameter a in Izhikevich model. Unit is s^{-1}</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.b"> -<tt class="descname">b</tt><a class="headerlink" href="#IzhikevichNrn.b" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Parameter b in Izhikevich model. Unit is s^{-1}</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.u"> -<tt class="descname">u</tt><a class="headerlink" href="#IzhikevichNrn.u" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Parameter u in Izhikevich equation. Unit is V/s</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.Vm"> -<tt class="descname">Vm</tt><a class="headerlink" href="#IzhikevichNrn.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane potential, equivalent to v in Izhikevich equation.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.Im"> -<tt class="descname">Im</tt><a class="headerlink" href="#IzhikevichNrn.Im" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Total current going through the membrane. Unit is A.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.inject"> -<tt class="descname">inject</tt><a class="headerlink" href="#IzhikevichNrn.inject" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) External current injection into the neuron</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.RmByTau"> -<tt class="descname">RmByTau</tt><a class="headerlink" href="#IzhikevichNrn.RmByTau" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Hidden coefficient of input current term (I) in Izhikevich model. Defaults to 1e9 Ohm/s.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.accommodating"> -<tt class="descname">accommodating</tt><a class="headerlink" href="#IzhikevichNrn.accommodating" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) True if this neuron is an accommodating one. The equation for recovery variable u is special in this case.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.u0"> -<tt class="descname">u0</tt><a class="headerlink" href="#IzhikevichNrn.u0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) This is used for accommodating neurons where recovery variables u is computed as: u += tau*a*(b*(Vm-u0))</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.initVm"> -<tt class="descname">initVm</tt><a class="headerlink" href="#IzhikevichNrn.initVm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial membrane potential. Unit is V.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.initU"> -<tt class="descname">initU</tt><a class="headerlink" href="#IzhikevichNrn.initU" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial value of u.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.alpha"> -<tt class="descname">alpha</tt><a class="headerlink" href="#IzhikevichNrn.alpha" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.beta"> -<tt class="descname">beta</tt><a class="headerlink" href="#IzhikevichNrn.beta" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}</p> -</dd></dl> - -<dl class="attribute"> -<dt id="IzhikevichNrn.gamma"> -<tt class="descname">gamma</tt><a class="headerlink" href="#IzhikevichNrn.gamma" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Ksolve"> -<em class="property">class </em><tt class="descname">Ksolve</tt><a class="headerlink" href="#Ksolve" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Ksolve.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Ksolve.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setMethod"> -<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getMethod"> -<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setEpsAbs"> -<tt class="descname">setEpsAbs</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setEpsAbs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getEpsAbs"> -<tt class="descname">getEpsAbs</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getEpsAbs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setEpsRel"> -<tt class="descname">setEpsRel</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setEpsRel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getEpsRel"> -<tt class="descname">getEpsRel</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getEpsRel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setStoich"> -<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getStoich"> -<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setDsolve"> -<tt class="descname">setDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setDsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getDsolve"> -<tt class="descname">getDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getDsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setCompartment"> -<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getCompartment"> -<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getNumLocalVoxels"> -<tt class="descname">getNumLocalVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumLocalVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setNVec"> -<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getNVec"> -<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setNumAllVoxels"> -<tt class="descname">setNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNumAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getNumAllVoxels"> -<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.setNumPools"> -<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.getNumPools"> -<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="Ksolve.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.method"> -<tt class="descname">method</tt><a class="headerlink" href="#Ksolve.method" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Integration method, using GSL. So far only explict. Options are:rk5: The default Runge-Kutta-Fehlberg 5th order adaptive dt methodgsl: alias for the aboverk4: The Runge-Kutta 4th order fixed dt methodrk2: The Runge-Kutta 2,3 embedded fixed dt methodrkck: The Runge-Kutta Cash-Karp (4,5) methodrk8: The Runge-Kutta Prince-Dormand (8,9) method</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.epsAbs"> -<tt class="descname">epsAbs</tt><a class="headerlink" href="#Ksolve.epsAbs" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Absolute permissible integration error range.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.epsRel"> -<tt class="descname">epsRel</tt><a class="headerlink" href="#Ksolve.epsRel" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Relative permissible integration error range.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.stoich"> -<tt class="descname">stoich</tt><a class="headerlink" href="#Ksolve.stoich" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.dsolve"> -<tt class="descname">dsolve</tt><a class="headerlink" href="#Ksolve.dsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Diffusion solver object handling this reactin system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.compartment"> -<tt class="descname">compartment</tt><a class="headerlink" href="#Ksolve.compartment" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Compartment in which the Ksolve reaction system lives.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.numLocalVoxels"> -<tt class="descname">numLocalVoxels</tt><a class="headerlink" href="#Ksolve.numLocalVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current solver.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.numAllVoxels"> -<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Ksolve.numAllVoxels" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.numPools"> -<tt class="descname">numPools</tt><a class="headerlink" href="#Ksolve.numPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Ksolve.nVec"> -<tt class="descname">nVec</tt><a class="headerlink" href="#Ksolve.nVec" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of pool counts. Index specifies which voxel.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Leakage"> -<em class="property">class </em><tt class="descname">Leakage</tt><a class="headerlink" href="#Leakage" title="Permalink to this definition">¶</a></dt> -<dd><p>Leakage: Passive leakage channel.</p> -<dl class="attribute"> -<dt id="Leakage.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Leakage.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from the scheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on.</p> -</dd></dl> - -</dd></dl> - -<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -<blockquote> -<div><dl class="method"> -<dt> -<tt class="descname">process</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">reinit</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="Long"> -<em class="property">class </em><tt class="descname">Long</tt><a class="headerlink" href="#Long" title="Permalink to this definition">¶</a></dt> -<dd><p>Variable for storing values.</p> -<dl class="method"> -<dt id="Long.setValue"> -<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Long.setValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Long.getValue"> -<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Long.getValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Long.value"> -<tt class="descname">value</tt><a class="headerlink" href="#Long.value" title="Permalink to this definition">¶</a></dt> -<dd><p>long (<em>value field</em>) Variable value</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MMenz"> -<em class="property">class </em><tt class="descname">MMenz</tt><a class="headerlink" href="#MMenz" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="MarkovChannel"> -<em class="property">class </em><tt class="descname">MarkovChannel</tt><a class="headerlink" href="#MarkovChannel" title="Permalink to this definition">¶</a></dt> -<dd><p>MarkovChannel : Multistate ion channel class.It deals with ion channels which can be found in one of multiple states, some of which are conducting. This implementation assumes the occurence of first order kinetics to calculate the probabilities of the channel being found in all states. Further, the rates of transition between these states can be constant, voltage-dependent or ligand dependent (only one ligand species). The current flow obtained from the channel is calculated in a deterministic method by solving the system of differential equations obtained from the assumptions above.</p> -<dl class="attribute"> -<dt id="MarkovChannel.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MarkovChannel.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setLigandConc"> -<tt class="descname">setLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getLigandConc"> -<tt class="descname">getLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setVm"> -<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getVm"> -<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setNumStates"> -<tt class="descname">setNumStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setNumStates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getNumStates"> -<tt class="descname">getNumStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getNumStates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setNumOpenStates"> -<tt class="descname">setNumOpenStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setNumOpenStates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getNumOpenStates"> -<tt class="descname">getNumOpenStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getNumOpenStates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getState"> -<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setInitialState"> -<tt class="descname">setInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setInitialState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getInitialState"> -<tt class="descname">getInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getInitialState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setLabels"> -<tt class="descname">setLabels</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setLabels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getLabels"> -<tt class="descname">getLabels</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getLabels" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.setGbar"> -<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.getGbar"> -<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.handleLigandConc"> -<tt class="descname">handleLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.handleLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Deals with incoming messages containing information of ligand concentration</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovChannel.handleState"> -<tt class="descname">handleState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.handleState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Deals with incoming message from MarkovSolver object containing state information of the channel.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.ligandConc"> -<tt class="descname">ligandConc</tt><a class="headerlink" href="#MarkovChannel.ligandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Ligand concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.Vm"> -<tt class="descname">Vm</tt><a class="headerlink" href="#MarkovChannel.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane voltage.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.numStates"> -<tt class="descname">numStates</tt><a class="headerlink" href="#MarkovChannel.numStates" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) The number of states that the channel can occupy.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.numOpenStates"> -<tt class="descname">numOpenStates</tt><a class="headerlink" href="#MarkovChannel.numOpenStates" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) The number of states which are open/conducting.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.state"> -<tt class="descname">state</tt><a class="headerlink" href="#MarkovChannel.state" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) This is a row vector that contains the probabilities of finding the channel in each state.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.initialState"> -<tt class="descname">initialState</tt><a class="headerlink" href="#MarkovChannel.initialState" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.labels"> -<tt class="descname">labels</tt><a class="headerlink" href="#MarkovChannel.labels" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Labels for each state.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovChannel.gbar"> -<tt class="descname">gbar</tt><a class="headerlink" href="#MarkovChannel.gbar" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) A row vector containing the conductance associated with each of the open/conducting states.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MarkovGslSolver"> -<em class="property">class </em><tt class="descname">MarkovGslSolver</tt><a class="headerlink" href="#MarkovGslSolver" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="MarkovGslSolver.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MarkovGslSolver.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.getIsInitialized"> -<tt class="descname">getIsInitialized</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getIsInitialized" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.setMethod"> -<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.getMethod"> -<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.setRelativeAccuracy"> -<tt class="descname">setRelativeAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setRelativeAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.getRelativeAccuracy"> -<tt class="descname">getRelativeAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getRelativeAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.setAbsoluteAccuracy"> -<tt class="descname">setAbsoluteAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setAbsoluteAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.getAbsoluteAccuracy"> -<tt class="descname">getAbsoluteAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getAbsoluteAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.setInternalDt"> -<tt class="descname">setInternalDt</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setInternalDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.getInternalDt"> -<tt class="descname">getInternalDt</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getInternalDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.init"> -<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.init" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Initialize solver parameters.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.handleQ"> -<tt class="descname">handleQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.handleQ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovGslSolver.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.stateOut"> -<tt class="descname">stateOut</tt><a class="headerlink" href="#MarkovGslSolver.stateOut" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>source message field</em>) Sends updated state to the MarkovChannel class.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.isInitialized"> -<tt class="descname">isInitialized</tt><a class="headerlink" href="#MarkovGslSolver.isInitialized" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) True if the message has come in to set solver parameters.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.method"> -<tt class="descname">method</tt><a class="headerlink" href="#MarkovGslSolver.method" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Numerical method to use.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.relativeAccuracy"> -<tt class="descname">relativeAccuracy</tt><a class="headerlink" href="#MarkovGslSolver.relativeAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Accuracy criterion</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.absoluteAccuracy"> -<tt class="descname">absoluteAccuracy</tt><a class="headerlink" href="#MarkovGslSolver.absoluteAccuracy" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Another accuracy criterion</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovGslSolver.internalDt"> -<tt class="descname">internalDt</tt><a class="headerlink" href="#MarkovGslSolver.internalDt" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) internal timestep to use.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MarkovRateTable"> -<em class="property">class </em><tt class="descname">MarkovRateTable</tt><a class="headerlink" href="#MarkovRateTable" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="MarkovRateTable.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#MarkovRateTable.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MarkovRateTable.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.handleVm"> -<tt class="descname">handleVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.handleVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles incoming message containing voltage information.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.init"> -<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.init" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Initialization of the class. Allocates memory for all the tables.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.handleLigandConc"> -<tt class="descname">handleLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.handleLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles incoming message containing ligand concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.set1d"> -<tt class="descname">set1d</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.set1d" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Setting up of 1D lookup table for the (i,j)’th rate.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.set2d"> -<tt class="descname">set2d</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.set2d" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Setting up of 2D lookup table for the (i,j)’th rate.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.setconst"> -<tt class="descname">setconst</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setconst" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Setting a constant value for the (i,j)’th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.setVm"> -<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.getVm"> -<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.setLigandConc"> -<tt class="descname">setLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.getLigandConc"> -<tt class="descname">getLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getLigandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.getQ"> -<tt class="descname">getQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getQ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovRateTable.getSize"> -<tt class="descname">getSize</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.instratesOut"> -<tt class="descname">instratesOut</tt><a class="headerlink" href="#MarkovRateTable.instratesOut" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>source message field</em>) Sends out instantaneous rate information of varying transition ratesat each time step.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.Vm"> -<tt class="descname">Vm</tt><a class="headerlink" href="#MarkovRateTable.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane voltage.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.ligandConc"> -<tt class="descname">ligandConc</tt><a class="headerlink" href="#MarkovRateTable.ligandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Ligand concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.Q"> -<tt class="descname">Q</tt><a class="headerlink" href="#MarkovRateTable.Q" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>value field</em>) Instantaneous rate matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovRateTable.size"> -<tt class="descname">size</tt><a class="headerlink" href="#MarkovRateTable.size" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Dimension of the families of lookup tables. Is always equal to the number of states in the model.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MarkovSolver"> -<em class="property">class </em><tt class="descname">MarkovSolver</tt><a class="headerlink" href="#MarkovSolver" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="MarkovSolver.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MarkovSolver.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolver.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolver.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolver.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolver.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MarkovSolverBase"> -<em class="property">class </em><tt class="descname">MarkovSolverBase</tt><a class="headerlink" href="#MarkovSolverBase" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="MarkovSolverBase.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#MarkovSolverBase.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MarkovSolverBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.handleVm"> -<tt class="descname">handleVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.handleVm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles incoming message containing voltage information.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.ligandConc"> -<tt class="descname">ligandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.ligandConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles incoming message containing ligand concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.init"> -<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.init" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Setups the table of matrix exponentials associated with the solver object.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getQ"> -<tt class="descname">getQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getQ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getState"> -<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setInitialState"> -<tt class="descname">setInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setInitialState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getInitialState"> -<tt class="descname">getInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInitialState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setXmin"> -<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getXmin"> -<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setXmax"> -<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getXmax"> -<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setXdivs"> -<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getXdivs"> -<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getInvdx"> -<tt class="descname">getInvdx</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInvdx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setYmin"> -<tt class="descname">setYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getYmin"> -<tt class="descname">getYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setYmax"> -<tt class="descname">setYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getYmax"> -<tt class="descname">getYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.setYdivs"> -<tt class="descname">setYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getYdivs"> -<tt class="descname">getYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MarkovSolverBase.getInvdy"> -<tt class="descname">getInvdy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInvdy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.stateOut"> -<tt class="descname">stateOut</tt><a class="headerlink" href="#MarkovSolverBase.stateOut" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>source message field</em>) Sends updated state to the MarkovChannel class.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.Q"> -<tt class="descname">Q</tt><a class="headerlink" href="#MarkovSolverBase.Q" title="Permalink to this definition">¶</a></dt> -<dd><p>vector< vector<double> > (<em>value field</em>) Instantaneous rate matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.state"> -<tt class="descname">state</tt><a class="headerlink" href="#MarkovSolverBase.state" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Current state of the channel.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.initialState"> -<tt class="descname">initialState</tt><a class="headerlink" href="#MarkovSolverBase.initialState" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Initial state of the channel.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.xmin"> -<tt class="descname">xmin</tt><a class="headerlink" href="#MarkovSolverBase.xmin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value for x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.xmax"> -<tt class="descname">xmax</tt><a class="headerlink" href="#MarkovSolverBase.xmax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value for x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.xdivs"> -<tt class="descname">xdivs</tt><a class="headerlink" href="#MarkovSolverBase.xdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) # of divisions on x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.invdx"> -<tt class="descname">invdx</tt><a class="headerlink" href="#MarkovSolverBase.invdx" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reciprocal of increment on x axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.ymin"> -<tt class="descname">ymin</tt><a class="headerlink" href="#MarkovSolverBase.ymin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value for y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.ymax"> -<tt class="descname">ymax</tt><a class="headerlink" href="#MarkovSolverBase.ymax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value for y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.ydivs"> -<tt class="descname">ydivs</tt><a class="headerlink" href="#MarkovSolverBase.ydivs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) # of divisions on y axis of lookup table</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MarkovSolverBase.invdy"> -<tt class="descname">invdy</tt><a class="headerlink" href="#MarkovSolverBase.invdy" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reciprocal of increment on y axis of lookup table</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MathFunc"> -<em class="property">class </em><tt class="descname">MathFunc</tt><a class="headerlink" href="#MathFunc" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="MathFunc.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MathFunc.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.setMathML"> -<tt class="descname">setMathML</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.setMathML" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.getMathML"> -<tt class="descname">getMathML</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getMathML" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.setFunction"> -<tt class="descname">setFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.setFunction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.getFunction"> -<tt class="descname">getFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getFunction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.getResult"> -<tt class="descname">getResult</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getResult" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.arg1"> -<tt class="descname">arg1</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle arg1</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.arg2"> -<tt class="descname">arg2</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle arg2</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.arg3"> -<tt class="descname">arg3</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg3" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle arg3</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.arg4"> -<tt class="descname">arg4</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg4" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle arg4</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MathFunc.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MathFunc.output"> -<tt class="descname">output</tt><a class="headerlink" href="#MathFunc.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out result of computation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MathFunc.mathML"> -<tt class="descname">mathML</tt><a class="headerlink" href="#MathFunc.mathML" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) MathML version of expression to compute</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MathFunc.function"> -<tt class="descname">function</tt><a class="headerlink" href="#MathFunc.function" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) function is for functions of form f(x, y) = x + y</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MathFunc.result"> -<tt class="descname">result</tt><a class="headerlink" href="#MathFunc.result" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) result value</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MeshEntry"> -<em class="property">class </em><tt class="descname">MeshEntry</tt><a class="headerlink" href="#MeshEntry" title="Permalink to this definition">¶</a></dt> -<dd><p>One voxel in a chemical reaction compartment</p> -<dl class="attribute"> -<dt id="MeshEntry.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MeshEntry.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.mesh"> -<tt class="descname">mesh</tt><a class="headerlink" href="#MeshEntry.mesh" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for updating mesh volumes and subdivisions,typically controls pool volumes</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getVolume"> -<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getDimensions"> -<tt class="descname">getDimensions</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDimensions" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getMeshType"> -<tt class="descname">getMeshType</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getMeshType" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getCoordinates"> -<tt class="descname">getCoordinates</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getCoordinates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getNeighbors"> -<tt class="descname">getNeighbors</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getNeighbors" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getDiffusionArea"> -<tt class="descname">getDiffusionArea</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDiffusionArea" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.getDiffusionScaling"> -<tt class="descname">getDiffusionScaling</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDiffusionScaling" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MeshEntry.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">getVolume</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.remeshOut"> -<tt class="descname">remeshOut</tt><a class="headerlink" href="#MeshEntry.remeshOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,unsigned int,unsigned int,vector<unsigned int>,vector<double> (<em>source message field</em>) Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.remeshReacsOut"> -<tt class="descname">remeshReacsOut</tt><a class="headerlink" href="#MeshEntry.remeshReacsOut" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>source message field</em>) Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like <a href="#id23"><span class="problematic" id="id24">numKf_</span></a> accordingly.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.volume"> -<tt class="descname">volume</tt><a class="headerlink" href="#MeshEntry.volume" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Volume of this MeshEntry</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.dimensions"> -<tt class="descname">dimensions</tt><a class="headerlink" href="#MeshEntry.dimensions" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) number of dimensions of this MeshEntry</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.meshType"> -<tt class="descname">meshType</tt><a class="headerlink" href="#MeshEntry.meshType" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.Coordinates"> -<tt class="descname">Coordinates</tt><a class="headerlink" href="#MeshEntry.Coordinates" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Coordinates that define current MeshEntry. Depend on MeshType.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.neighbors"> -<tt class="descname">neighbors</tt><a class="headerlink" href="#MeshEntry.neighbors" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Indices of other MeshEntries that this one connects to</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.DiffusionArea"> -<tt class="descname">DiffusionArea</tt><a class="headerlink" href="#MeshEntry.DiffusionArea" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Diffusion area for geometry of interface</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MeshEntry.DiffusionScaling"> -<tt class="descname">DiffusionScaling</tt><a class="headerlink" href="#MeshEntry.DiffusionScaling" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) Diffusion scaling for geometry of interface</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="MgBlock"> -<em class="property">class </em><tt class="descname">MgBlock</tt><a class="headerlink" href="#MgBlock" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>MgBlock: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p> -<dl class="attribute"> -<dt id="MgBlock.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#MgBlock.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p> -</dd></dl> - -</div></blockquote> -<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -<blockquote> -<div><dl class="method"> -<dt id="MgBlock.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.origChannel"> -<tt class="descname">origChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.origChannel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>)</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.setKMg_A"> -<tt class="descname">setKMg_A</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setKMg_A" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.getKMg_A"> -<tt class="descname">getKMg_A</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getKMg_A" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.setKMg_B"> -<tt class="descname">setKMg_B</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setKMg_B" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.getKMg_B"> -<tt class="descname">getKMg_B</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getKMg_B" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.setCMg"> -<tt class="descname">setCMg</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setCMg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.getCMg"> -<tt class="descname">getCMg</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getCMg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.setIk"> -<tt class="descname">setIk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setIk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.getIk"> -<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getIk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.setZk"> -<tt class="descname">setZk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setZk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="MgBlock.getZk"> -<tt class="descname">getZk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getZk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MgBlock.KMg_A"> -<tt class="descname">KMg_A</tt><a class="headerlink" href="#MgBlock.KMg_A" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) 1/eta</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MgBlock.KMg_B"> -<tt class="descname">KMg_B</tt><a class="headerlink" href="#MgBlock.KMg_B" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) 1/gamma</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MgBlock.CMg"> -<tt class="descname">CMg</tt><a class="headerlink" href="#MgBlock.CMg" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) [Mg] in mM</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MgBlock.Ik"> -<tt class="descname">Ik</tt><a class="headerlink" href="#MgBlock.Ik" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current through MgBlock</p> -</dd></dl> - -<dl class="attribute"> -<dt id="MgBlock.Zk"> -<tt class="descname">Zk</tt><a class="headerlink" href="#MgBlock.Zk" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Charge on ion</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="class"> -<dt id="Msg"> -<em class="property">class </em><tt class="descname">Msg</tt><a class="headerlink" href="#Msg" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Msg.getE1"> -<tt class="descname">getE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getE1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getE2"> -<tt class="descname">getE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getE2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getSrcFieldsOnE1"> -<tt class="descname">getSrcFieldsOnE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getSrcFieldsOnE1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getDestFieldsOnE2"> -<tt class="descname">getDestFieldsOnE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getDestFieldsOnE2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getSrcFieldsOnE2"> -<tt class="descname">getSrcFieldsOnE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getSrcFieldsOnE2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getDestFieldsOnE1"> -<tt class="descname">getDestFieldsOnE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getDestFieldsOnE1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Msg.getAdjacent"> -<tt class="descname">getAdjacent</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getAdjacent" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.e1"> -<tt class="descname">e1</tt><a class="headerlink" href="#Msg.e1" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id of source Element.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.e2"> -<tt class="descname">e2</tt><a class="headerlink" href="#Msg.e2" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id of source Element.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.srcFieldsOnE1"> -<tt class="descname">srcFieldsOnE1</tt><a class="headerlink" href="#Msg.srcFieldsOnE1" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.destFieldsOnE2"> -<tt class="descname">destFieldsOnE2</tt><a class="headerlink" href="#Msg.destFieldsOnE2" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.srcFieldsOnE2"> -<tt class="descname">srcFieldsOnE2</tt><a class="headerlink" href="#Msg.srcFieldsOnE2" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.destFieldsOnE1"> -<tt class="descname">destFieldsOnE1</tt><a class="headerlink" href="#Msg.destFieldsOnE1" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Msg.adjacent"> -<tt class="descname">adjacent</tt><a class="headerlink" href="#Msg.adjacent" title="Permalink to this definition">¶</a></dt> -<dd><p>ObjId,ObjId (<em>lookup field</em>) The element adjacent to the specified element</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Mstring"> -<em class="property">class </em><tt class="descname">Mstring</tt><a class="headerlink" href="#Mstring" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Mstring.setThis"> -<tt class="descname">setThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.setThis" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Mstring.getThis"> -<tt class="descname">getThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.getThis" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Mstring.setValue"> -<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.setValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Mstring.getValue"> -<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.getValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Mstring.this"> -<tt class="descname">this</tt><a class="headerlink" href="#Mstring.this" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Access function for entire Mstring object.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Mstring.value"> -<tt class="descname">value</tt><a class="headerlink" href="#Mstring.value" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Access function for value field of Mstring object,which happens also to be the entire contents of the object.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Nernst"> -<em class="property">class </em><tt class="descname">Nernst</tt><a class="headerlink" href="#Nernst" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Nernst.getE"> -<tt class="descname">getE</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getE" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.setTemperature"> -<tt class="descname">setTemperature</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setTemperature" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.getTemperature"> -<tt class="descname">getTemperature</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getTemperature" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.setValence"> -<tt class="descname">setValence</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setValence" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.getValence"> -<tt class="descname">getValence</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getValence" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.setCin"> -<tt class="descname">setCin</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setCin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.getCin"> -<tt class="descname">getCin</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getCin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.setCout"> -<tt class="descname">setCout</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setCout" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.getCout"> -<tt class="descname">getCout</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getCout" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.setScale"> -<tt class="descname">setScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setScale" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.getScale"> -<tt class="descname">getScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getScale" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.ci"> -<tt class="descname">ci</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.ci" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Set internal conc of ion, and immediately send out the updated E</p> -</dd></dl> - -<dl class="method"> -<dt id="Nernst.co"> -<tt class="descname">co</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.co" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Set external conc of ion, and immediately send out the updated E</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.Eout"> -<tt class="descname">Eout</tt><a class="headerlink" href="#Nernst.Eout" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Computed reversal potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.E"> -<tt class="descname">E</tt><a class="headerlink" href="#Nernst.E" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Computed reversal potential</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.Temperature"> -<tt class="descname">Temperature</tt><a class="headerlink" href="#Nernst.Temperature" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Temperature of cell</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.valence"> -<tt class="descname">valence</tt><a class="headerlink" href="#Nernst.valence" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Valence of ion in Nernst calculation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.Cin"> -<tt class="descname">Cin</tt><a class="headerlink" href="#Nernst.Cin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Internal conc of ion</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.Cout"> -<tt class="descname">Cout</tt><a class="headerlink" href="#Nernst.Cout" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) External conc of ion</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Nernst.scale"> -<tt class="descname">scale</tt><a class="headerlink" href="#Nernst.scale" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Voltage scale factor</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="NeuroMesh"> -<em class="property">class </em><tt class="descname">NeuroMesh</tt><a class="headerlink" href="#NeuroMesh" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="NeuroMesh.setCell"> -<tt class="descname">setCell</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setCell" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getCell"> -<tt class="descname">getCell</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getCell" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.setSubTree"> -<tt class="descname">setSubTree</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setSubTree" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getSubTree"> -<tt class="descname">getSubTree</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getSubTree" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.setSeparateSpines"> -<tt class="descname">setSeparateSpines</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setSeparateSpines" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getSeparateSpines"> -<tt class="descname">getSeparateSpines</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getSeparateSpines" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getNumSegments"> -<tt class="descname">getNumSegments</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getNumSegments" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getNumDiffCompts"> -<tt class="descname">getNumDiffCompts</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getNumDiffCompts" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getParentVoxel"> -<tt class="descname">getParentVoxel</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getParentVoxel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.setDiffLength"> -<tt class="descname">setDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setDiffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getDiffLength"> -<tt class="descname">getDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getDiffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.setGeometryPolicy"> -<tt class="descname">setGeometryPolicy</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setGeometryPolicy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.getGeometryPolicy"> -<tt class="descname">getGeometryPolicy</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getGeometryPolicy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="NeuroMesh.cellPortion"> -<tt class="descname">cellPortion</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.cellPortion" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the wildcardpath of compartments to use for the subpart.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.spineListOut"> -<tt class="descname">spineListOut</tt><a class="headerlink" href="#NeuroMesh.spineListOut" title="Permalink to this definition">¶</a></dt> -<dd><p>Id,vector<Id>,vector<Id>,vector<unsigned int> (<em>source message field</em>) Request SpineMesh to construct self based on list of electrical compartments that this NeuroMesh has determined are spine shaft and spine head respectively. Also passes in the info about where each spine is connected to the NeuroMesh. Arguments: Cell Id, shaft compartment Ids, head compartment Ids,index of matching parent voxels for each spine</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.psdListOut"> -<tt class="descname">psdListOut</tt><a class="headerlink" href="#NeuroMesh.psdListOut" title="Permalink to this definition">¶</a></dt> -<dd><p>Id,vector<double>,vector<unsigned int> (<em>source message field</em>) Tells PsdMesh to build a mesh. Arguments: Cell Id, Coordinates of each psd, index of matching parent voxels for each spineThe coordinates each have 8 entries:xyz of centre of psd, xyz of vector perpendicular to psd, psd diameter, diffusion distance from parent compartment to PSD</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.cell"> -<tt class="descname">cell</tt><a class="headerlink" href="#NeuroMesh.cell" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.subTree"> -<tt class="descname">subTree</tt><a class="headerlink" href="#NeuroMesh.subTree" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<Id> (<em>value field</em>) Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.separateSpines"> -<tt class="descname">separateSpines</tt><a class="headerlink" href="#NeuroMesh.separateSpines" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag: when separateSpines is true, the traversal separates any compartment with the strings ‘spine’, ‘head’, ‘shaft’ or ‘neck’ in its name,Allows to set up separate mesh for spines, based on the same cell model. Requires for the spineListOut message tobe sent to the target SpineMesh object.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.numSegments"> -<tt class="descname">numSegments</tt><a class="headerlink" href="#NeuroMesh.numSegments" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of cylindrical/spherical segments in model</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.numDiffCompts"> -<tt class="descname">numDiffCompts</tt><a class="headerlink" href="#NeuroMesh.numDiffCompts" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of diffusive compartments in model</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.parentVoxel"> -<tt class="descname">parentVoxel</tt><a class="headerlink" href="#NeuroMesh.parentVoxel" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Vector of indices of parents of each voxel.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.diffLength"> -<tt class="descname">diffLength</tt><a class="headerlink" href="#NeuroMesh.diffLength" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron</p> -</dd></dl> - -<dl class="attribute"> -<dt id="NeuroMesh.geometryPolicy"> -<tt class="descname">geometryPolicy</tt><a class="headerlink" href="#NeuroMesh.geometryPolicy" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don’t worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Neuron"> -<em class="property">class </em><tt class="descname">Neuron</tt><a class="headerlink" href="#Neuron" title="Permalink to this definition">¶</a></dt> -<dd><p>Neuron - A compartment container</p> -</dd></dl> - -<dl class="class"> -<dt id="Neutral"> -<em class="property">class </em><tt class="descname">Neutral</tt><a class="headerlink" href="#Neutral" title="Permalink to this definition">¶</a></dt> -<dd><p>Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.</p> -<dl class="method"> -<dt id="Neutral.parentMsg"> -<tt class="descname">parentMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.parentMsg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Message from Parent Element(s)</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.setThis"> -<tt class="descname">setThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setThis" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getThis"> -<tt class="descname">getThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getThis" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.setName"> -<tt class="descname">setName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setName" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getName"> -<tt class="descname">getName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getName" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getMe"> -<tt class="descname">getMe</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMe" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getParent"> -<tt class="descname">getParent</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getParent" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getChildren"> -<tt class="descname">getChildren</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getChildren" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getPath"> -<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getPath" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getClassName"> -<tt class="descname">getClassName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getClassName" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.setNumData"> -<tt class="descname">setNumData</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setNumData" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getNumData"> -<tt class="descname">getNumData</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNumData" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.setNumField"> -<tt class="descname">setNumField</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setNumField" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getNumField"> -<tt class="descname">getNumField</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNumField" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getValueFields"> -<tt class="descname">getValueFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getValueFields" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getSourceFields"> -<tt class="descname">getSourceFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getSourceFields" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getDestFields"> -<tt class="descname">getDestFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getDestFields" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getMsgOut"> -<tt class="descname">getMsgOut</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgOut" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getMsgIn"> -<tt class="descname">getMsgIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getNeighbors"> -<tt class="descname">getNeighbors</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNeighbors" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getMsgDests"> -<tt class="descname">getMsgDests</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgDests" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Neutral.getMsgDestFunctions"> -<tt class="descname">getMsgDestFunctions</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgDestFunctions" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.childOut"> -<tt class="descname">childOut</tt><a class="headerlink" href="#Neutral.childOut" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>source message field</em>) Message to child Elements</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.this"> -<tt class="descname">this</tt><a class="headerlink" href="#Neutral.this" title="Permalink to this definition">¶</a></dt> -<dd><p>Neutral (<em>value field</em>) Access function for entire object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.name"> -<tt class="descname">name</tt><a class="headerlink" href="#Neutral.name" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Name of object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.me"> -<tt class="descname">me</tt><a class="headerlink" href="#Neutral.me" title="Permalink to this definition">¶</a></dt> -<dd><p>ObjId (<em>value field</em>) ObjId for current object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.parent"> -<tt class="descname">parent</tt><a class="headerlink" href="#Neutral.parent" title="Permalink to this definition">¶</a></dt> -<dd><p>ObjId (<em>value field</em>) Parent ObjId for current object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.children"> -<tt class="descname">children</tt><a class="headerlink" href="#Neutral.children" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<Id> (<em>value field</em>) vector of ObjIds listing all children of current object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.path"> -<tt class="descname">path</tt><a class="headerlink" href="#Neutral.path" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) text path for object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.className"> -<tt class="descname">className</tt><a class="headerlink" href="#Neutral.className" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Class Name of object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.numData"> -<tt class="descname">numData</tt><a class="headerlink" href="#Neutral.numData" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) # of Data entries on Element.Note that on a FieldElement this does NOT refer to field entries,but to the number of DataEntries on the parent of the FieldElement.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.numField"> -<tt class="descname">numField</tt><a class="headerlink" href="#Neutral.numField" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) For a FieldElement: number of entries of self.For a regular Element: One.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.valueFields"> -<tt class="descname">valueFields</tt><a class="headerlink" href="#Neutral.valueFields" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) List of all value fields on Element.These fields are accessed through the assignment operations in the Python interface.These fields may also be accessed as functions through the set<FieldName> and get<FieldName> commands.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.sourceFields"> -<tt class="descname">sourceFields</tt><a class="headerlink" href="#Neutral.sourceFields" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) List of all source fields on Element, that is fields that can act as message sources.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.destFields"> -<tt class="descname">destFields</tt><a class="headerlink" href="#Neutral.destFields" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<string> (<em>value field</em>) List of all destination fields on Element, that is, fieldsthat are accessed as Element functions.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.msgOut"> -<tt class="descname">msgOut</tt><a class="headerlink" href="#Neutral.msgOut" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<ObjId> (<em>value field</em>) Messages going out from this Element</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.msgIn"> -<tt class="descname">msgIn</tt><a class="headerlink" href="#Neutral.msgIn" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<ObjId> (<em>value field</em>) Messages coming in to this Element</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.neighbors"> -<tt class="descname">neighbors</tt><a class="headerlink" href="#Neutral.neighbors" title="Permalink to this definition">¶</a></dt> -<dd><p>string,vector<Id> (<em>lookup field</em>) Ids of Elements connected this Element on specified field.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.msgDests"> -<tt class="descname">msgDests</tt><a class="headerlink" href="#Neutral.msgDests" title="Permalink to this definition">¶</a></dt> -<dd><p>string,vector<ObjId> (<em>lookup field</em>) ObjIds receiving messages from the specified SrcFinfo</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Neutral.msgDestFunctions"> -<tt class="descname">msgDestFunctions</tt><a class="headerlink" href="#Neutral.msgDestFunctions" title="Permalink to this definition">¶</a></dt> -<dd><p>string,vector<string> (<em>lookup field</em>) Matching function names for each ObjId receiving a msg from the specified SrcFinfo</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="OneToAllMsg"> -<em class="property">class </em><tt class="descname">OneToAllMsg</tt><a class="headerlink" href="#OneToAllMsg" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="OneToAllMsg.setI1"> -<tt class="descname">setI1</tt><big>(</big><big>)</big><a class="headerlink" href="#OneToAllMsg.setI1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="OneToAllMsg.getI1"> -<tt class="descname">getI1</tt><big>(</big><big>)</big><a class="headerlink" href="#OneToAllMsg.getI1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="OneToAllMsg.i1"> -<tt class="descname">i1</tt><a class="headerlink" href="#OneToAllMsg.i1" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) DataId of source Element.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="OneToOneDataIndexMsg"> -<em class="property">class </em><tt class="descname">OneToOneDataIndexMsg</tt><a class="headerlink" href="#OneToOneDataIndexMsg" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="OneToOneMsg"> -<em class="property">class </em><tt class="descname">OneToOneMsg</tt><a class="headerlink" href="#OneToOneMsg" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="PIDController"> -<em class="property">class </em><tt class="descname">PIDController</tt><a class="headerlink" href="#PIDController" title="Permalink to this definition">¶</a></dt> -<dd><p>PID feedback controller.PID stands for Proportional-Integral-Derivative. It is used to feedback control dynamical systems. It tries to create a feedback output such that the sensed (measured) parameter is held at command value. Refer to wikipedia (<a class="reference external" href="http://wikipedia.org">http://wikipedia.org</a>) for details on PID Controller.</p> -<dl class="attribute"> -<dt id="PIDController.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#PIDController.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.setGain"> -<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getGain"> -<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.setSaturation"> -<tt class="descname">setSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setSaturation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getSaturation"> -<tt class="descname">getSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getSaturation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.setCommand"> -<tt class="descname">setCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setCommand" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getCommand"> -<tt class="descname">getCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getCommand" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getSensed"> -<tt class="descname">getSensed</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getSensed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.setTauI"> -<tt class="descname">setTauI</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setTauI" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getTauI"> -<tt class="descname">getTauI</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getTauI" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.setTauD"> -<tt class="descname">setTauD</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setTauD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getTauD"> -<tt class="descname">getTauD</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getTauD" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getError"> -<tt class="descname">getError</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getError" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getIntegral"> -<tt class="descname">getIntegral</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getIntegral" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getDerivative"> -<tt class="descname">getDerivative</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getDerivative" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.getE_previous"> -<tt class="descname">getE_previous</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getE_previous" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.commandIn"> -<tt class="descname">commandIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.commandIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Command (desired value) input. This is known as setpoint (SP) in control theory.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.sensedIn"> -<tt class="descname">sensedIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.sensedIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.gainDest"> -<tt class="descname">gainDest</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.gainDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destination message to control the PIDController gain dynamically.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle process calls.</p> -</dd></dl> - -<dl class="method"> -<dt id="PIDController.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reinitialize the object.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.output"> -<tt class="descname">output</tt><a class="headerlink" href="#PIDController.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.gain"> -<tt class="descname">gain</tt><a class="headerlink" href="#PIDController.gain" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.saturation"> -<tt class="descname">saturation</tt><a class="headerlink" href="#PIDController.saturation" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Bound on the permissible range of output. Defaults to maximum double value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.command"> -<tt class="descname">command</tt><a class="headerlink" href="#PIDController.command" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.sensed"> -<tt class="descname">sensed</tt><a class="headerlink" href="#PIDController.sensed" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Sensed (measured) value. This is commonly known as process variable(PV) in control theory.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.tauI"> -<tt class="descname">tauI</tt><a class="headerlink" href="#PIDController.tauI" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.tauD"> -<tt class="descname">tauD</tt><a class="headerlink" href="#PIDController.tauD" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PIDController.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#PIDController.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )</p> -</dd></dl> - -</dd></dl> - -<p>Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)</p> -<blockquote> -<div><dl class="attribute"> -<dt id="error"> -<tt class="descname">error</tt><a class="headerlink" href="#error" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The error term, which is the difference between command and sensed value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="integral"> -<tt class="descname">integral</tt><a class="headerlink" href="#integral" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">derivative</tt></dt> -<dd><p>double (<em>value field</em>) The derivative term. This is (error - e_previous)/dt.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="e_previous"> -<tt class="descname">e_previous</tt><a class="headerlink" href="#e_previous" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The error term for previous step.</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="Pool"> -<em class="property">class </em><tt class="descname">Pool</tt><a class="headerlink" href="#Pool" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Pool.increment"> -<tt class="descname">increment</tt><big>(</big><big>)</big><a class="headerlink" href="#Pool.increment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Increments mol numbers by specified amount. Can be +ve or -ve</p> -</dd></dl> - -<dl class="method"> -<dt id="Pool.decrement"> -<tt class="descname">decrement</tt><big>(</big><big>)</big><a class="headerlink" href="#Pool.decrement" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Decrements mol numbers by specified amount. Can be +ve or -ve</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="PoolBase"> -<em class="property">class </em><tt class="descname">PoolBase</tt><a class="headerlink" href="#PoolBase" title="Permalink to this definition">¶</a></dt> -<dd><p>Abstract base class for pools.</p> -<dl class="attribute"> -<dt id="PoolBase.reac"> -<tt class="descname">reac</tt><a class="headerlink" href="#PoolBase.reac" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to reaction</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#PoolBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.species"> -<tt class="descname">species</tt><a class="headerlink" href="#PoolBase.species" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for connecting to species objects</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setN"> -<tt class="descname">setN</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setN" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getN"> -<tt class="descname">getN</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getN" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setNInit"> -<tt class="descname">setNInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setNInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getNInit"> -<tt class="descname">getNInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getNInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setDiffConst"> -<tt class="descname">setDiffConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setDiffConst" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getDiffConst"> -<tt class="descname">getDiffConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getDiffConst" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setMotorConst"> -<tt class="descname">setMotorConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setMotorConst" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getMotorConst"> -<tt class="descname">getMotorConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getMotorConst" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setConc"> -<tt class="descname">setConc</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getConc"> -<tt class="descname">getConc</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getConc" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setConcInit"> -<tt class="descname">setConcInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setConcInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getConcInit"> -<tt class="descname">getConcInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getConcInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setVolume"> -<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getVolume"> -<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getVolume" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.setSpeciesId"> -<tt class="descname">setSpeciesId</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setSpeciesId" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.getSpeciesId"> -<tt class="descname">getSpeciesId</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getSpeciesId" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.reacDest"> -<tt class="descname">reacDest</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.reacDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reaction input</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="PoolBase.handleMolWt"> -<tt class="descname">handleMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.handleMolWt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.nOut"> -<tt class="descname">nOut</tt><a class="headerlink" href="#PoolBase.nOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out # of molecules in pool on each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.requestMolWt"> -<tt class="descname">requestMolWt</tt><a class="headerlink" href="#PoolBase.requestMolWt" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>source message field</em>) Requests Species object for mol wt</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.n"> -<tt class="descname">n</tt><a class="headerlink" href="#PoolBase.n" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Number of molecules in pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.nInit"> -<tt class="descname">nInit</tt><a class="headerlink" href="#PoolBase.nInit" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial value of number of molecules in pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.diffConst"> -<tt class="descname">diffConst</tt><a class="headerlink" href="#PoolBase.diffConst" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Diffusion constant of molecule</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.motorConst"> -<tt class="descname">motorConst</tt><a class="headerlink" href="#PoolBase.motorConst" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Motor transport rate molecule. + is away from soma, - is towards soma. Only relevant for ZombiePool subclasses.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.conc"> -<tt class="descname">conc</tt><a class="headerlink" href="#PoolBase.conc" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Concentration of molecules in this pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.concInit"> -<tt class="descname">concInit</tt><a class="headerlink" href="#PoolBase.concInit" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial value of molecular concentration in pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.volume"> -<tt class="descname">volume</tt><a class="headerlink" href="#PoolBase.volume" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Volume of compartment. Units are SI. Utility field, the actual volume info is stored on a volume mesh entry in the parent compartment.This mapping is implicit: the parent compartment must be somewhere up the element tree, and must have matching mesh entries. If the compartment isn’tavailable the volume is just taken as 1</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PoolBase.speciesId"> -<tt class="descname">speciesId</tt><a class="headerlink" href="#PoolBase.speciesId" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Species identifier for this mol pool. Eventually link to ontology.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="PostMaster"> -<em class="property">class </em><tt class="descname">PostMaster</tt><a class="headerlink" href="#PostMaster" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="PostMaster.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#PostMaster.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.getNumNodes"> -<tt class="descname">getNumNodes</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getNumNodes" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.getMyNode"> -<tt class="descname">getMyNode</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getMyNode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.setBufferSize"> -<tt class="descname">setBufferSize</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.setBufferSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.getBufferSize"> -<tt class="descname">getBufferSize</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getBufferSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="PostMaster.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PostMaster.numNodes"> -<tt class="descname">numNodes</tt><a class="headerlink" href="#PostMaster.numNodes" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Returns number of nodes that simulation runs on.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PostMaster.myNode"> -<tt class="descname">myNode</tt><a class="headerlink" href="#PostMaster.myNode" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Returns index of current node.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PostMaster.bufferSize"> -<tt class="descname">bufferSize</tt><a class="headerlink" href="#PostMaster.bufferSize" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Size of the send a receive buffers for each node.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="PsdMesh"> -<em class="property">class </em><tt class="descname">PsdMesh</tt><a class="headerlink" href="#PsdMesh" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="PsdMesh.setThickness"> -<tt class="descname">setThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.setThickness" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PsdMesh.getThickness"> -<tt class="descname">getThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.getThickness" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PsdMesh.psdList"> -<tt class="descname">psdList</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.psdList" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Specifies the geometry of the spine,and the associated parent voxelArguments: cell container, disk params vector with 8 entriesper psd, parent voxel index</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PsdMesh.thickness"> -<tt class="descname">thickness</tt><a class="headerlink" href="#PsdMesh.thickness" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) An assumed thickness for PSD. The volume is computed as thePSD area passed in to each PSD, times this value.defaults to 50 nanometres. For reference, membranes are 5 nm.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="PulseGen"> -<em class="property">class </em><tt class="descname">PulseGen</tt><a class="headerlink" href="#PulseGen" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>PulseGen: general purpose pulse generator. This can generate any number of pulses with specified level and duration.</p> -<dl class="attribute"> -<dt id="PulseGen.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#PulseGen.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setBaseLevel"> -<tt class="descname">setBaseLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setBaseLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getBaseLevel"> -<tt class="descname">getBaseLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getBaseLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setFirstLevel"> -<tt class="descname">setFirstLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getFirstLevel"> -<tt class="descname">getFirstLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setFirstWidth"> -<tt class="descname">setFirstWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getFirstWidth"> -<tt class="descname">getFirstWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setFirstDelay"> -<tt class="descname">setFirstDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getFirstDelay"> -<tt class="descname">getFirstDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setSecondLevel"> -<tt class="descname">setSecondLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getSecondLevel"> -<tt class="descname">getSecondLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setSecondWidth"> -<tt class="descname">setSecondWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getSecondWidth"> -<tt class="descname">getSecondWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setSecondDelay"> -<tt class="descname">setSecondDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getSecondDelay"> -<tt class="descname">getSecondDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setCount"> -<tt class="descname">setCount</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setCount" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getCount"> -<tt class="descname">getCount</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getCount" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setTrigMode"> -<tt class="descname">setTrigMode</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setTrigMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getTrigMode"> -<tt class="descname">getTrigMode</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getTrigMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setLevel"> -<tt class="descname">setLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getLevel"> -<tt class="descname">getLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setWidth"> -<tt class="descname">setWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getWidth"> -<tt class="descname">getWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.setDelay"> -<tt class="descname">setDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.getDelay"> -<tt class="descname">getDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle incoming input that determines gating/triggering onset.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.levelIn"> -<tt class="descname">levelIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.levelIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle level value coming from other objects</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.widthIn"> -<tt class="descname">widthIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.widthIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle width value coming from other objects</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.delayIn"> -<tt class="descname">delayIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.delayIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle delay value coming from other objects</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt id="PulseGen.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.output"> -<tt class="descname">output</tt><a class="headerlink" href="#PulseGen.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Current output level.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#PulseGen.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Output amplitude</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.baseLevel"> -<tt class="descname">baseLevel</tt><a class="headerlink" href="#PulseGen.baseLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Basal level of the stimulus</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.firstLevel"> -<tt class="descname">firstLevel</tt><a class="headerlink" href="#PulseGen.firstLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Amplitude of the first pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.firstWidth"> -<tt class="descname">firstWidth</tt><a class="headerlink" href="#PulseGen.firstWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Width of the first pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.firstDelay"> -<tt class="descname">firstDelay</tt><a class="headerlink" href="#PulseGen.firstDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Delay to start of the first pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.secondLevel"> -<tt class="descname">secondLevel</tt><a class="headerlink" href="#PulseGen.secondLevel" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Amplitude of the second pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.secondWidth"> -<tt class="descname">secondWidth</tt><a class="headerlink" href="#PulseGen.secondWidth" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Width of the second pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.secondDelay"> -<tt class="descname">secondDelay</tt><a class="headerlink" href="#PulseGen.secondDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Delay to start of of the second pulse in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.count"> -<tt class="descname">count</tt><a class="headerlink" href="#PulseGen.count" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of pulses in a sequence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.trigMode"> -<tt class="descname">trigMode</tt><a class="headerlink" href="#PulseGen.trigMode" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Trigger mode for pulses in the sequence.</p> -</dd></dl> - -</div></blockquote> -<p>0 : free-running mode where it keeps looping its output -1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses) -2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="PulseGen.level"> -<tt class="descname">level</tt><a class="headerlink" href="#PulseGen.level" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Level of the pulse at specified index</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.width"> -<tt class="descname">width</tt><a class="headerlink" href="#PulseGen.width" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Width of the pulse at specified index</p> -</dd></dl> - -<dl class="attribute"> -<dt id="PulseGen.delay"> -<tt class="descname">delay</tt><a class="headerlink" href="#PulseGen.delay" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Delay of the pulse at specified index</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="class"> -<dt id="RC"> -<em class="property">class </em><tt class="descname">RC</tt><a class="headerlink" href="#RC" title="Permalink to this definition">¶</a></dt> -<dd><p>RC circuit: a series resistance R shunted by a capacitance C.</p> -<dl class="attribute"> -<dt id="RC.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#RC.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.setV0"> -<tt class="descname">setV0</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setV0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.getV0"> -<tt class="descname">getV0</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getV0" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.setR"> -<tt class="descname">setR</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setR" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.getR"> -<tt class="descname">getR</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getR" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.setC"> -<tt class="descname">setC</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setC" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.getC"> -<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getC" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.getState"> -<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.setInject"> -<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.getInject"> -<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getInject" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.injectIn"> -<tt class="descname">injectIn</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.injectIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Receives input to the RC circuit. All incoming messages are summed up to give the total input current.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call.</p> -</dd></dl> - -<dl class="method"> -<dt id="RC.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle reinitialization</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.output"> -<tt class="descname">output</tt><a class="headerlink" href="#RC.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Current output level.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.V0"> -<tt class="descname">V0</tt><a class="headerlink" href="#RC.V0" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Initial value of ‘state’</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.R"> -<tt class="descname">R</tt><a class="headerlink" href="#RC.R" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Series resistance of the RC circuit.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.C"> -<tt class="descname">C</tt><a class="headerlink" href="#RC.C" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Parallel capacitance of the RC circuit.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.state"> -<tt class="descname">state</tt><a class="headerlink" href="#RC.state" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Output value of the RC circuit. This is the voltage across the capacitor.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="RC.inject"> -<tt class="descname">inject</tt><a class="headerlink" href="#RC.inject" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Input value to the RC circuit.This is handled as an input current to the circuit.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Reac"> -<em class="property">class </em><tt class="descname">Reac</tt><a class="headerlink" href="#Reac" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="ReacBase"> -<em class="property">class </em><tt class="descname">ReacBase</tt><a class="headerlink" href="#ReacBase" title="Permalink to this definition">¶</a></dt> -<dd><p>Base class for reactions. Provides the MOOSE APIfunctions, but ruthlessly refers almost all of them to derivedclasses, which have to provide the man page output.</p> -<dl class="attribute"> -<dt id="ReacBase.sub"> -<tt class="descname">sub</tt><a class="headerlink" href="#ReacBase.sub" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to substrate pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.prd"> -<tt class="descname">prd</tt><a class="headerlink" href="#ReacBase.prd" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to substrate pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#ReacBase.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.setNumKf"> -<tt class="descname">setNumKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setNumKf" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getNumKf"> -<tt class="descname">getNumKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumKf" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.setNumKb"> -<tt class="descname">setNumKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setNumKb" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getNumKb"> -<tt class="descname">getNumKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumKb" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.setKf"> -<tt class="descname">setKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setKf" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getKf"> -<tt class="descname">getKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getKf" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.setKb"> -<tt class="descname">setKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setKb" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getKb"> -<tt class="descname">getKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getKb" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getNumSubstrates"> -<tt class="descname">getNumSubstrates</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumSubstrates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.getNumProducts"> -<tt class="descname">getNumProducts</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumProducts" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.subDest"> -<tt class="descname">subDest</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.subDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of substrate</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.prdDest"> -<tt class="descname">prdDest</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.prdDest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles # of molecules of product</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="ReacBase.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.subOut"> -<tt class="descname">subOut</tt><a class="headerlink" href="#ReacBase.subOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.prdOut"> -<tt class="descname">prdOut</tt><a class="headerlink" href="#ReacBase.prdOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.numKf"> -<tt class="descname">numKf</tt><a class="headerlink" href="#ReacBase.numKf" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Forward rate constant, in # units</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.numKb"> -<tt class="descname">numKb</tt><a class="headerlink" href="#ReacBase.numKb" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reverse rate constant, in # units</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.Kf"> -<tt class="descname">Kf</tt><a class="headerlink" href="#ReacBase.Kf" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Forward rate constant, in concentration units</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.Kb"> -<tt class="descname">Kb</tt><a class="headerlink" href="#ReacBase.Kb" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reverse rate constant, in concentration units</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.numSubstrates"> -<tt class="descname">numSubstrates</tt><a class="headerlink" href="#ReacBase.numSubstrates" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of substrates of reaction</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ReacBase.numProducts"> -<tt class="descname">numProducts</tt><a class="headerlink" href="#ReacBase.numProducts" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of products of reaction</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Shell"> -<em class="property">class </em><tt class="descname">Shell</tt><a class="headerlink" href="#Shell" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Shell.setclock"> -<tt class="descname">setclock</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.setclock" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns clock ticks. Args: tick#, dt</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.create"> -<tt class="descname">create</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.create" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) create( class, parent, newElm, name, numData, isGlobal )</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.delete"> -<tt class="descname">delete</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.delete" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Destroys Element, all its messages, and all its children. Args: Id</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.copy"> -<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.copy" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.move"> -<tt class="descname">move</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.move" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) handleMove( Id orig, Id newParent ): moves an Element to a new parent</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.addMsg"> -<tt class="descname">addMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.addMsg" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Makes a msg. Arguments are: msgtype, src object, src field, dest object, dest field</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.quit"> -<tt class="descname">quit</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.quit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Stops simulation running and quits the simulator</p> -</dd></dl> - -<dl class="method"> -<dt id="Shell.useClock"> -<tt class="descname">useClock</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.useClock" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Deals with assignment of path to a given clock. Arguments: path, field, tick number.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SingleMsg"> -<em class="property">class </em><tt class="descname">SingleMsg</tt><a class="headerlink" href="#SingleMsg" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="SingleMsg.setI1"> -<tt class="descname">setI1</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.setI1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SingleMsg.getI1"> -<tt class="descname">getI1</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.getI1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SingleMsg.setI2"> -<tt class="descname">setI2</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.setI2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SingleMsg.getI2"> -<tt class="descname">getI2</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.getI2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SingleMsg.i1"> -<tt class="descname">i1</tt><a class="headerlink" href="#SingleMsg.i1" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Index of source object.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SingleMsg.i2"> -<tt class="descname">i2</tt><a class="headerlink" href="#SingleMsg.i2" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Index of dest object.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SparseMsg"> -<em class="property">class </em><tt class="descname">SparseMsg</tt><a class="headerlink" href="#SparseMsg" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="SparseMsg.getNumRows"> -<tt class="descname">getNumRows</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumRows" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.getNumColumns"> -<tt class="descname">getNumColumns</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumColumns" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.getNumEntries"> -<tt class="descname">getNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumEntries" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.setProbability"> -<tt class="descname">setProbability</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setProbability" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.getProbability"> -<tt class="descname">getProbability</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getProbability" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.setSeed"> -<tt class="descname">setSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setSeed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.getSeed"> -<tt class="descname">getSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getSeed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.setRandomConnectivity"> -<tt class="descname">setRandomConnectivity</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setRandomConnectivity" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns connectivity with specified probability and seed</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.setEntry"> -<tt class="descname">setEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setEntry" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns single row,column value</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.unsetEntry"> -<tt class="descname">unsetEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.unsetEntry" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Clears single row,column entry</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.clear"> -<tt class="descname">clear</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.clear" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Clears out the entire matrix</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.transpose"> -<tt class="descname">transpose</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.transpose" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Transposes the sparse matrix</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.pairFill"> -<tt class="descname">pairFill</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.pairFill" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fills entire matrix using pairs of (x,y) indices to indicate presence of a connection. If the target is a FieldElement itautomagically assigns FieldIndices.</p> -</dd></dl> - -<dl class="method"> -<dt id="SparseMsg.tripletFill"> -<tt class="descname">tripletFill</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.tripletFill" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fills entire matrix using triplets of (x,y,fieldIndex) to fully specify every connection in the sparse matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SparseMsg.numRows"> -<tt class="descname">numRows</tt><a class="headerlink" href="#SparseMsg.numRows" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of rows in matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SparseMsg.numColumns"> -<tt class="descname">numColumns</tt><a class="headerlink" href="#SparseMsg.numColumns" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of columns in matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SparseMsg.numEntries"> -<tt class="descname">numEntries</tt><a class="headerlink" href="#SparseMsg.numEntries" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of Entries in matrix.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SparseMsg.probability"> -<tt class="descname">probability</tt><a class="headerlink" href="#SparseMsg.probability" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) connection probability for random connectivity.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SparseMsg.seed"> -<tt class="descname">seed</tt><a class="headerlink" href="#SparseMsg.seed" title="Permalink to this definition">¶</a></dt> -<dd><p>long (<em>value field</em>) Random number seed for generating probabilistic connectivity.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Species"> -<em class="property">class </em><tt class="descname">Species</tt><a class="headerlink" href="#Species" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Species.pool"> -<tt class="descname">pool</tt><a class="headerlink" href="#Species.pool" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Connects to pools of this Species type</p> -</dd></dl> - -<dl class="method"> -<dt id="Species.setMolWt"> -<tt class="descname">setMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.setMolWt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Species.getMolWt"> -<tt class="descname">getMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.getMolWt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Species.handleMolWtRequest"> -<tt class="descname">handleMolWtRequest</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.handleMolWtRequest" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle requests for molWt.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Species.molWtOut"> -<tt class="descname">molWtOut</tt><a class="headerlink" href="#Species.molWtOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) returns molWt.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Species.molWt"> -<tt class="descname">molWt</tt><a class="headerlink" href="#Species.molWt" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Molecular weight of species</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SpikeGen"> -<em class="property">class </em><tt class="descname">SpikeGen</tt><a class="headerlink" href="#SpikeGen" title="Permalink to this definition">¶</a></dt> -<dd><p>SpikeGen object, for detecting threshold crossings.The threshold detection can work in multiple modes.</p> -<blockquote> -<div>If the refractT < 0.0, then it fires an event only at the rising edge of the input voltage waveform</div></blockquote> -<dl class="attribute"> -<dt id="SpikeGen.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#SpikeGen.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.Vm"> -<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.setThreshold"> -<tt class="descname">setThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setThreshold" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.getThreshold"> -<tt class="descname">getThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getThreshold" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.setRefractT"> -<tt class="descname">setRefractT</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setRefractT" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.getRefractT"> -<tt class="descname">getRefractT</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getRefractT" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.setAbs_refract"> -<tt class="descname">setAbs_refract</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setAbs_refract" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.getAbs_refract"> -<tt class="descname">getAbs_refract</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getAbs_refract" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.getHasFired"> -<tt class="descname">getHasFired</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getHasFired" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.setEdgeTriggered"> -<tt class="descname">setEdgeTriggered</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setEdgeTriggered" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpikeGen.getEdgeTriggered"> -<tt class="descname">getEdgeTriggered</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getEdgeTriggered" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.spikeOut"> -<tt class="descname">spikeOut</tt><a class="headerlink" href="#SpikeGen.spikeOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out a trigger for an event.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.threshold"> -<tt class="descname">threshold</tt><a class="headerlink" href="#SpikeGen.threshold" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Spiking threshold, must cross it going up</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.refractT"> -<tt class="descname">refractT</tt><a class="headerlink" href="#SpikeGen.refractT" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Refractory Time.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.abs_refract"> -<tt class="descname">abs_refract</tt><a class="headerlink" href="#SpikeGen.abs_refract" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Absolute refractory time. Synonym for refractT.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.hasFired"> -<tt class="descname">hasFired</tt><a class="headerlink" href="#SpikeGen.hasFired" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) True if SpikeGen has just fired</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpikeGen.edgeTriggered"> -<tt class="descname">edgeTriggered</tt><a class="headerlink" href="#SpikeGen.edgeTriggered" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SpineMesh"> -<em class="property">class </em><tt class="descname">SpineMesh</tt><a class="headerlink" href="#SpineMesh" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="SpineMesh.getParentVoxel"> -<tt class="descname">getParentVoxel</tt><big>(</big><big>)</big><a class="headerlink" href="#SpineMesh.getParentVoxel" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SpineMesh.spineList"> -<tt class="descname">spineList</tt><big>(</big><big>)</big><a class="headerlink" href="#SpineMesh.spineList" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Specifies the list of electrical compartments for the spine,and the associated parent voxelArguments: cell container, shaft compartments, head compartments, parent voxel index</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SpineMesh.parentVoxel"> -<tt class="descname">parentVoxel</tt><a class="headerlink" href="#SpineMesh.parentVoxel" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Vector of indices of proximal voxels within this mesh.Spines are at present modeled with just one compartment,so each entry in this vector is always set to EMPTY == -1U</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Stats"> -<em class="property">class </em><tt class="descname">Stats</tt><a class="headerlink" href="#Stats" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Stats.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Stats.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.getMean"> -<tt class="descname">getMean</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getMean" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.getSdev"> -<tt class="descname">getSdev</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getSdev" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.getSum"> -<tt class="descname">getSum</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getSum" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.getNum"> -<tt class="descname">getNum</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getNum" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="Stats.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">process</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">reinit</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stats.mean"> -<tt class="descname">mean</tt><a class="headerlink" href="#Stats.mean" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Mean of all sampled values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stats.sdev"> -<tt class="descname">sdev</tt><a class="headerlink" href="#Stats.sdev" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Standard Deviation of all sampled values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stats.sum"> -<tt class="descname">sum</tt><a class="headerlink" href="#Stats.sum" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Sum of all sampled values.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stats.num"> -<tt class="descname">num</tt><a class="headerlink" href="#Stats.num" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of all sampled values.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SteadyState"> -<em class="property">class </em><tt class="descname">SteadyState</tt><a class="headerlink" href="#SteadyState" title="Permalink to this definition">¶</a></dt> -<dd><p>SteadyState: works out a steady-state value for a reaction system. It uses GSL heavily, and isn’t even compiled if the flag isn’t set. It finds the ss value closest to the initial conditions, defined by current molecular concentrations.If you want to find multiple stable states, use the MultiStable object,which operates a SteadyState object to find multiple states.If you want to carry out a dose-response calculation, use the DoseResponse object.If you want to follow a stable state in phase space, use the StateTrajectory object.</p> -<dl class="method"> -<dt id="SteadyState.setStoich"> -<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getStoich"> -<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStoich" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getBadStoichiometry"> -<tt class="descname">getBadStoichiometry</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getBadStoichiometry" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getIsInitialized"> -<tt class="descname">getIsInitialized</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getIsInitialized" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getNIter"> -<tt class="descname">getNIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNIter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getStatus"> -<tt class="descname">getStatus</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStatus" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.setMaxIter"> -<tt class="descname">setMaxIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setMaxIter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getMaxIter"> -<tt class="descname">getMaxIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getMaxIter" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.setConvergenceCriterion"> -<tt class="descname">setConvergenceCriterion</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setConvergenceCriterion" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getConvergenceCriterion"> -<tt class="descname">getConvergenceCriterion</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getConvergenceCriterion" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getNumVarPools"> -<tt class="descname">getNumVarPools</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNumVarPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getRank"> -<tt class="descname">getRank</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getRank" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getStateType"> -<tt class="descname">getStateType</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStateType" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getNNegEigenvalues"> -<tt class="descname">getNNegEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNNegEigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getNPosEigenvalues"> -<tt class="descname">getNPosEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNPosEigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getSolutionStatus"> -<tt class="descname">getSolutionStatus</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getSolutionStatus" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.setTotal"> -<tt class="descname">setTotal</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setTotal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getTotal"> -<tt class="descname">getTotal</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getTotal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.getEigenvalues"> -<tt class="descname">getEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getEigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.setupMatrix"> -<tt class="descname">setupMatrix</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setupMatrix" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) This function initializes and rebuilds the matrices used in the calculation.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.settle"> -<tt class="descname">settle</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.settle" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation only if the object has not yet been initialized.</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.resettle"> -<tt class="descname">resettle</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.resettle" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.showMatrices"> -<tt class="descname">showMatrices</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.showMatrices" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices</p> -</dd></dl> - -<dl class="method"> -<dt id="SteadyState.randomInit"> -<tt class="descname">randomInit</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.randomInit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Generate random initial conditions consistent with the massconservation rules. Typically invoked in order to scanstates</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.stoich"> -<tt class="descname">stoich</tt><a class="headerlink" href="#SteadyState.stoich" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Specify the Id of the stoichiometry system to use</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.badStoichiometry"> -<tt class="descname">badStoichiometry</tt><a class="headerlink" href="#SteadyState.badStoichiometry" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Bool: True if there is a problem with the stoichiometry</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.isInitialized"> -<tt class="descname">isInitialized</tt><a class="headerlink" href="#SteadyState.isInitialized" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) True if the model has been initialized successfully</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.nIter"> -<tt class="descname">nIter</tt><a class="headerlink" href="#SteadyState.nIter" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of iterations done by steady state solver</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.status"> -<tt class="descname">status</tt><a class="headerlink" href="#SteadyState.status" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Status of solver</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.maxIter"> -<tt class="descname">maxIter</tt><a class="headerlink" href="#SteadyState.maxIter" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Max permissible number of iterations to try before giving up</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.convergenceCriterion"> -<tt class="descname">convergenceCriterion</tt><a class="headerlink" href="#SteadyState.convergenceCriterion" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Fractional accuracy required to accept convergence</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.numVarPools"> -<tt class="descname">numVarPools</tt><a class="headerlink" href="#SteadyState.numVarPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of variable molecules in reaction system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.rank"> -<tt class="descname">rank</tt><a class="headerlink" href="#SteadyState.rank" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of independent molecules in reaction system</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.stateType"> -<tt class="descname">stateType</tt><a class="headerlink" href="#SteadyState.stateType" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) 0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.nNegEigenvalues"> -<tt class="descname">nNegEigenvalues</tt><a class="headerlink" href="#SteadyState.nNegEigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of negative eigenvalues: indicates type of solution</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.nPosEigenvalues"> -<tt class="descname">nPosEigenvalues</tt><a class="headerlink" href="#SteadyState.nPosEigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of positive eigenvalues: indicates type of solution</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.solutionStatus"> -<tt class="descname">solutionStatus</tt><a class="headerlink" href="#SteadyState.solutionStatus" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) 0: Good; 1: Failed to find steady states; 2: Failed to find eigenvalues</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.total"> -<tt class="descname">total</tt><a class="headerlink" href="#SteadyState.total" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Totals table for conservation laws. The exact mapping ofthis to various sums of molecules is given by the conservation matrix, and is currently a bit opaque.The value of ‘total’ is set to initial conditions whenthe ‘SteadyState::settle’ function is called.Assigning values to the total is a special operation:it rescales the concentrations of all the affectedmolecules so that they are at the specified total.This happens the next time ‘settle’ is called.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SteadyState.eigenvalues"> -<tt class="descname">eigenvalues</tt><a class="headerlink" href="#SteadyState.eigenvalues" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Eigenvalues computed for steady state</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="StimulusTable"> -<em class="property">class </em><tt class="descname">StimulusTable</tt><a class="headerlink" href="#StimulusTable" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="StimulusTable.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#StimulusTable.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setStartTime"> -<tt class="descname">setStartTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStartTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getStartTime"> -<tt class="descname">getStartTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStartTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setStopTime"> -<tt class="descname">setStopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getStopTime"> -<tt class="descname">getStopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setLoopTime"> -<tt class="descname">setLoopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setLoopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getLoopTime"> -<tt class="descname">getLoopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getLoopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setStepSize"> -<tt class="descname">setStepSize</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStepSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getStepSize"> -<tt class="descname">getStepSize</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStepSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setStepPosition"> -<tt class="descname">setStepPosition</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStepPosition" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getStepPosition"> -<tt class="descname">getStepPosition</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStepPosition" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.setDoLoop"> -<tt class="descname">setDoLoop</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setDoLoop" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.getDoLoop"> -<tt class="descname">getDoLoop</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getDoLoop" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt id="StimulusTable.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.output"> -<tt class="descname">output</tt><a class="headerlink" href="#StimulusTable.output" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out tabulated data according to lookup parameters.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.startTime"> -<tt class="descname">startTime</tt><a class="headerlink" href="#StimulusTable.startTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.stopTime"> -<tt class="descname">stopTime</tt><a class="headerlink" href="#StimulusTable.stopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.loopTime"> -<tt class="descname">loopTime</tt><a class="headerlink" href="#StimulusTable.loopTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.stepSize"> -<tt class="descname">stepSize</tt><a class="headerlink" href="#StimulusTable.stepSize" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.stepPosition"> -<tt class="descname">stepPosition</tt><a class="headerlink" href="#StimulusTable.stepPosition" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="StimulusTable.doLoop"> -<tt class="descname">doLoop</tt><a class="headerlink" href="#StimulusTable.doLoop" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Stoich"> -<em class="property">class </em><tt class="descname">Stoich</tt><a class="headerlink" href="#Stoich" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="Stoich.setPath"> -<tt class="descname">setPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setPath" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getPath"> -<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getPath" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.setKsolve"> -<tt class="descname">setKsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setKsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getKsolve"> -<tt class="descname">getKsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getKsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.setDsolve"> -<tt class="descname">setDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setDsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getDsolve"> -<tt class="descname">getDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getDsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.setCompartment"> -<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getCompartment"> -<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getEstimatedDt"> -<tt class="descname">getEstimatedDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getEstimatedDt" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getNumVarPools"> -<tt class="descname">getNumVarPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumVarPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getNumAllPools"> -<tt class="descname">getNumAllPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumAllPools" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getPoolIdMap"> -<tt class="descname">getPoolIdMap</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getPoolIdMap" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getNumRates"> -<tt class="descname">getNumRates</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumRates" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getMatrixEntry"> -<tt class="descname">getMatrixEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getMatrixEntry" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getColumnIndex"> -<tt class="descname">getColumnIndex</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getColumnIndex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.getRowStart"> -<tt class="descname">getRowStart</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getRowStart" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Stoich.unzombify"> -<tt class="descname">unzombify</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.unzombify" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Restore all zombies to their native state</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.path"> -<tt class="descname">path</tt><a class="headerlink" href="#Stoich.path" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) Wildcard path for reaction system handled by Stoich</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.ksolve"> -<tt class="descname">ksolve</tt><a class="headerlink" href="#Stoich.ksolve" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id of Kinetic reaction solver class that works with this Stoich. Must be of class Ksolve, or Gsolve (at present) Must be assigned before the path is set.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.dsolve"> -<tt class="descname">dsolve</tt><a class="headerlink" href="#Stoich.dsolve" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id of Diffusion solver class that works with this Stoich. Must be of class Dsolve If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.compartment"> -<tt class="descname">compartment</tt><a class="headerlink" href="#Stoich.compartment" title="Permalink to this definition">¶</a></dt> -<dd><p>Id (<em>value field</em>) Id of chemical compartment class that works with this Stoich. Must be derived from class ChemCompt. If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.estimatedDt"> -<tt class="descname">estimatedDt</tt><a class="headerlink" href="#Stoich.estimatedDt" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Estimated timestep for reac system based on Euler error</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.numVarPools"> -<tt class="descname">numVarPools</tt><a class="headerlink" href="#Stoich.numVarPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of time-varying pools to be computed by the numerical engine</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.numAllPools"> -<tt class="descname">numAllPools</tt><a class="headerlink" href="#Stoich.numAllPools" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Total number of pools handled by the numerical engine. This includes variable ones, buffered ones, and functions</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.poolIdMap"> -<tt class="descname">poolIdMap</tt><a class="headerlink" href="#Stoich.poolIdMap" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Map to look up the index of the pool from its Id.poolIndex = poolIdMap[ Id::value() - poolOffset ] where the poolOffset is the smallest Id::value. poolOffset is passed back as the last entry of this vector. Any Ids that are not pools return EMPTY=~0.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.numRates"> -<tt class="descname">numRates</tt><a class="headerlink" href="#Stoich.numRates" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Total number of rate terms in the reaction system.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.matrixEntry"> -<tt class="descname">matrixEntry</tt><a class="headerlink" href="#Stoich.matrixEntry" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<int> (<em>value field</em>) The non-zero matrix entries in the sparse matrix. Theircolumn indices are in a separate vector and the rowinformatino in a third</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.columnIndex"> -<tt class="descname">columnIndex</tt><a class="headerlink" href="#Stoich.columnIndex" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Column Index of each matrix entry</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Stoich.rowStart"> -<tt class="descname">rowStart</tt><a class="headerlink" href="#Stoich.rowStart" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<unsigned int> (<em>value field</em>) Row start for each block of entries and column indices</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SumFunc"> -<em class="property">class </em><tt class="descname">SumFunc</tt><a class="headerlink" href="#SumFunc" title="Permalink to this definition">¶</a></dt> -<dd><p>SumFunc object. Adds up all inputs</p> -</dd></dl> - -<dl class="class"> -<dt id="SymCompartment"> -<em class="property">class </em><tt class="descname">SymCompartment</tt><a class="headerlink" href="#SymCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>SymCompartment object, for branching neuron models. In symmetric</p> -<p>compartments the axial resistance is equally divided on two sides of</p> -<blockquote> -<div><p>you must use a fixed-width font like Courier for correct rendition of the diagrams below.]</p> -<blockquote> -<div><blockquote> -<div>Ra/2 B Ra/2</div></blockquote> -<p>A-///_____///– C</p> -<blockquote> -<div><blockquote> -<div><blockquote> -<div><blockquote> -<div><div class="line-block"> -<div class="line"><br /></div> -</div> -</div></blockquote> -<p>____|____</p> -</div></blockquote> -<div class="line-block"> -<div class="line"><a href="#id1"><span class="problematic" id="id2">|</span></a></div> -</div> -<div class="line-block"> -<div class="line"></div> -</div> -<div class="line-block"> -<div class="line">/ Rm</div> -</div> -</div></blockquote> -<p>—- Cm </p> -<p>—- /</p> -<blockquote> -<div><div class="line-block"> -<div class="line"><a href="#id3"><span class="problematic" id="id4">|</span></a></div> -</div> -<div class="line-block"> -<div class="line">_____</div> -</div> -<div class="line-block"> -<div class="line">— Em</div> -</div> -<p><a href="#id11"><span class="problematic" id="id12">|_________|</span></a></p> -<blockquote> -<div><blockquote> -<div><div class="line-block"> -<div class="line"><br /></div> -</div> -</div></blockquote> -<p>__|__</p> -</div></blockquote> -</div></blockquote> -</div></blockquote> -</div></blockquote> -</div></blockquote> -<p>In case of branching, the B-C part of the parent’s axial resistance</p> -<p>forms a Y with the A-B part of the children.</p> -<blockquote> -<div><blockquote> -<div><blockquote> -<div><p>B’</p> -<div class="line-block"> -<div class="line"><br /></div> -</div> -<p>/</p> -<p></p> -<p>/</p> -<p></p> -<p>/</p> -<p><a href="#id5"><span class="problematic" id="id6">|</span></a>A’</p> -</div></blockquote> -<p>B |</p> -</div></blockquote> -<p>A—–///—–///——<a href="#id7"><span class="problematic" id="id8">|</span></a>C</p> -<blockquote> -<div><div class="line-block"> -<div class="line"><br /></div> -</div> -<p><a href="#id9"><span class="problematic" id="id10">|</span></a>A”</p> -<p>/</p> -<p></p> -<p>/</p> -<p></p> -<p>/</p> -<div class="line-block"> -<div class="line"><br /></div> -</div> -<p>B”</p> -</div></blockquote> -</div></blockquote> -<p>As per basic circuit analysis techniques, the C node is replaced using</p> -<p>star-mesh transform. This requires all sibling compartments at a</p> -<p>branch point to be connected via ‘sibling’ messages by the user (or</p> -<p>by the cell reader in case of prototypes). For the same reason, the</p> -<p>child compartment must be connected to the parent by</p> -<p>distal-proximal message pair. The calculation of the</p> -<p>coefficient for computing equivalent resistances in the mesh is done</p> -<p>at reinit.</p> -<dl class="attribute"> -<dt id="SymCompartment.proximal"> -<tt class="descname">proximal</tt><a class="headerlink" href="#SymCompartment.proximal" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p> -</dd></dl> - -</dd></dl> - -<p>It goes from the proximal end of the current compartment to -distal end of the compartment closer to the soma.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="distal"> -<tt class="descname">distal</tt><a class="headerlink" href="#distal" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p> -</dd></dl> - -</div></blockquote> -<dl class="docutils"> -<dt>It goes from the distal end of the current compartment to the</dt> -<dd>proximal end of one further from the soma.</dd> -</dl> -<p>The Ra values collected from children and -sibling nodes are used for computing the equivalent resistance -between each pair of nodes using star-mesh transformation. -Mathematically this is the same as the proximal message, but -the distinction is important for traversal and clarity.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="sibling"> -<tt class="descname">sibling</tt><a class="headerlink" href="#sibling" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p> -</dd></dl> - -</div></blockquote> -<p>Conceptually, this goes from the proximal end of the current -compartment to the proximal end of a sibling compartment -on a branch in a dendrite. However, -this works out to the same as a ‘distal’ message in terms of -equivalent circuit. The Ra values collected from siblings -and parent node are used for -computing the equivalent resistance between each pair of -nodes using star-mesh transformation.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="sphere"> -<tt class="descname">sphere</tt><a class="headerlink" href="#sphere" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between a spherical compartment</p> -</dd></dl> - -</div></blockquote> -<p>(typically soma) and a number of evenly spaced cylindrical -compartments, typically primary dendrites. -The sphere contributes the usual Ra/2 to the resistance -between itself and children. The child compartments -do not connect across to each other -through sibling messages. Instead they just connect to the soma -through the ‘proximalOnly’ message</p> -<blockquote> -<div><dl class="attribute"> -<dt id="cylinder"> -<tt class="descname">cylinder</tt><a class="headerlink" href="#cylinder" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between a cylindrical compartment</p> -</dd></dl> - -</div></blockquote> -<p>(typically a dendrite) and a number of evenly spaced child -compartments, typically dendritic spines, protruding from the -curved surface of the cylinder. We assume that the resistance -from the cylinder curved surface to its axis is negligible. -The child compartments do not need to connect across to each -other through sibling messages. Instead they just connect to the -parent dendrite through the ‘proximalOnly’ message</p> -<blockquote> -<div><dl class="attribute"> -<dt id="proximalOnly"> -<tt class="descname">proximalOnly</tt><a class="headerlink" href="#proximalOnly" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message between a dendrite and a parent</p> -</dd></dl> - -</div></blockquote> -<p>compartment whose offspring are spatially separated from each -other. For example, evenly spaced dendrites emerging from a soma -or spines emerging from a common parent dendrite. In these cases -the sibling dendrites do not need to connect to each other -through ‘sibling’ messages. Instead they just connect to the -parent compartment (soma or dendrite) through this message</p> -<blockquote> -<div><dl class="method"> -<dt id="raxialSym"> -<tt class="descname">raxialSym</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialSym" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt id="sumRaxial"> -<tt class="descname">sumRaxial</tt><big>(</big><big>)</big><a class="headerlink" href="#sumRaxial" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">raxialSym</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">sumRaxial</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">raxialSym</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">sumRaxial</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p> -</dd></dl> - -<dl class="method"> -<dt id="raxialSphere"> -<tt class="descname">raxialSphere</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialSphere" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p> -</dd></dl> - -</div></blockquote> -<p>other compartments are evenly distributed on a spherical compartment.</p> -<blockquote> -<div><dl class="method"> -<dt id="raxialCylinder"> -<tt class="descname">raxialCylinder</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialCylinder" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p> -</dd></dl> - -</div></blockquote> -<p>other compartments are evenly distributed on the curved surface of the cylindrical compartment, so we assume that the cylinder does not add any further resistance.</p> -<blockquote> -<div><dl class="method"> -<dt> -<tt class="descname">raxialSphere</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p> -</dd></dl> - -</div></blockquote> -<p>other compartments are evenly distributed on a spherical compartment.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="proximalOut"> -<tt class="descname">proximalOut</tt><a class="headerlink" href="#proximalOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="sumRaxialOut"> -<tt class="descname">sumRaxialOut</tt><a class="headerlink" href="#sumRaxialOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out Ra</p> -</dd></dl> - -<dl class="attribute"> -<dt id="distalOut"> -<tt class="descname">distalOut</tt><a class="headerlink" href="#distalOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">sumRaxialOut</tt></dt> -<dd><p>double (<em>source message field</em>) Sends out Ra</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">distalOut</tt></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">sumRaxialOut</tt></dt> -<dd><p>double (<em>source message field</em>) Sends out Ra</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">distalOut</tt></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="cylinderOut"> -<tt class="descname">cylinderOut</tt><a class="headerlink" href="#cylinderOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm to compartments (typically spines) on thecurved surface of a cylinder. Ra is set to nearly zero,since we assume that the resistance from axis to surface isnegligible.</p> -</dd></dl> - -<dl class="attribute"> -<dt> -<tt class="descname">proximalOut</tt></dt> -<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="SynChan"> -<em class="property">class </em><tt class="descname">SynChan</tt><a class="headerlink" href="#SynChan" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="SynChan.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#SynChan.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.setTau1"> -<tt class="descname">setTau1</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setTau1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.getTau1"> -<tt class="descname">getTau1</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getTau1" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.setTau2"> -<tt class="descname">setTau2</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setTau2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.getTau2"> -<tt class="descname">getTau2</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getTau2" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.setNormalizeWeights"> -<tt class="descname">setNormalizeWeights</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setNormalizeWeights" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.getNormalizeWeights"> -<tt class="descname">getNormalizeWeights</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getNormalizeWeights" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.activation"> -<tt class="descname">activation</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.activation" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Sometimes we want to continuously activate the channel</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChan.modulator"> -<tt class="descname">modulator</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.modulator" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Modulate channel response</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChan.tau1"> -<tt class="descname">tau1</tt><a class="headerlink" href="#SynChan.tau1" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Decay time constant for the synaptic conductance, tau1 >= tau2.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChan.tau2"> -<tt class="descname">tau2</tt><a class="headerlink" href="#SynChan.tau2" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Rise time constant for the synaptic conductance, tau1 >= tau2.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChan.normalizeWeights"> -<tt class="descname">normalizeWeights</tt><a class="headerlink" href="#SynChan.normalizeWeights" title="Permalink to this definition">¶</a></dt> -<dd><p>bool (<em>value field</em>) Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SynChanBase"> -<em class="property">class </em><tt class="descname">SynChanBase</tt><a class="headerlink" href="#SynChanBase" title="Permalink to this definition">¶</a></dt> -<dd><p>SynChanBase: Base class for assorted ion channels.Presents a common interface for all of them.</p> -<dl class="attribute"> -<dt id="SynChanBase.channel"> -<tt class="descname">channel</tt><a class="headerlink" href="#SynChanBase.channel" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.ghk"> -<tt class="descname">ghk</tt><a class="headerlink" href="#SynChanBase.ghk" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Message to Goldman-Hodgkin-Katz object</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.Vm"> -<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.Vm" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p> -</dd></dl> - -<dl class="method"> -<dt> -<tt class="descname">Vm</tt><big>(</big><big>)</big></dt> -<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.setGbar"> -<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.getGbar"> -<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.setEk"> -<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.getEk"> -<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.setGk"> -<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.getGk"> -<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.getIk"> -<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getIk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.setBufferTime"> -<tt class="descname">setBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setBufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynChanBase.getBufferTime"> -<tt class="descname">getBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getBufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.channelOut"> -<tt class="descname">channelOut</tt><a class="headerlink" href="#SynChanBase.channelOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>source message field</em>) Sends channel variables Gk and Ek to compartment</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.permeabilityOut"> -<tt class="descname">permeabilityOut</tt><a class="headerlink" href="#SynChanBase.permeabilityOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Conductance term going out to GHK object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.IkOut"> -<tt class="descname">IkOut</tt><a class="headerlink" href="#SynChanBase.IkOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Channel current. This message typically goes to concenobjects that keep track of ion concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.Gbar"> -<tt class="descname">Gbar</tt><a class="headerlink" href="#SynChanBase.Gbar" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximal channel conductance</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.Ek"> -<tt class="descname">Ek</tt><a class="headerlink" href="#SynChanBase.Ek" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reversal potential of channel</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.Gk"> -<tt class="descname">Gk</tt><a class="headerlink" href="#SynChanBase.Gk" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel conductance variable</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.Ik"> -<tt class="descname">Ik</tt><a class="headerlink" href="#SynChanBase.Ik" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel current variable</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynChanBase.bufferTime"> -<tt class="descname">bufferTime</tt><a class="headerlink" href="#SynChanBase.bufferTime" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Duration of spike buffer.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="SynHandler"> -<em class="property">class </em><tt class="descname">SynHandler</tt><a class="headerlink" href="#SynHandler" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="SynHandler.setNumSynapses"> -<tt class="descname">setNumSynapses</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.setNumSynapses" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynHandler.getNumSynapses"> -<tt class="descname">getNumSynapses</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.getNumSynapses" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynHandler.setNumSynapse"> -<tt class="descname">setNumSynapse</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.setNumSynapse" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="SynHandler.getNumSynapse"> -<tt class="descname">getNumSynapse</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.getNumSynapse" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="SynHandler.numSynapses"> -<tt class="descname">numSynapses</tt><a class="headerlink" href="#SynHandler.numSynapses" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of synapses on SynHandler. Duplicate field for num_synapse</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Synapse"> -<em class="property">class </em><tt class="descname">Synapse</tt><a class="headerlink" href="#Synapse" title="Permalink to this definition">¶</a></dt> -<dd><p>Synapse using ring buffer for events.</p> -<dl class="method"> -<dt id="Synapse.setWeight"> -<tt class="descname">setWeight</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.setWeight" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Synapse.getWeight"> -<tt class="descname">getWeight</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.getWeight" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Synapse.setDelay"> -<tt class="descname">setDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.setDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Synapse.getDelay"> -<tt class="descname">getDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.getDelay" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Synapse.addSpike"> -<tt class="descname">addSpike</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.addSpike" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles arriving spike messages, inserts into event queue.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Synapse.weight"> -<tt class="descname">weight</tt><a class="headerlink" href="#Synapse.weight" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Synaptic weight</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Synapse.delay"> -<tt class="descname">delay</tt><a class="headerlink" href="#Synapse.delay" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Axonal propagation delay to this synapse</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="Table"> -<em class="property">class </em><tt class="descname">Table</tt><a class="headerlink" href="#Table" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="Table.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#Table.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.setThreshold"> -<tt class="descname">setThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.setThreshold" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.getThreshold"> -<tt class="descname">getThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.getThreshold" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fills data into table. Also handles data sent back following request</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.spike"> -<tt class="descname">spike</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.spike" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fills spike timings into the Table. Signal has to exceed thresh</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p> -</dd></dl> - -<dl class="method"> -<dt id="Table.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Table.requestOut"> -<tt class="descname">requestOut</tt><a class="headerlink" href="#Table.requestOut" title="Permalink to this definition">¶</a></dt> -<dd><p>Pd (<em>source message field</em>) Sends request for a field to target object</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Table.threshold"> -<tt class="descname">threshold</tt><a class="headerlink" href="#Table.threshold" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) threshold used when Table acts as a buffer for spikes</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="TableBase"> -<em class="property">class </em><tt class="descname">TableBase</tt><a class="headerlink" href="#TableBase" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="TableBase.setVector"> -<tt class="descname">setVector</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.setVector" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.getVector"> -<tt class="descname">getVector</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getVector" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.getOutputValue"> -<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getOutputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.getSize"> -<tt class="descname">getSize</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getSize" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.linearTransform"> -<tt class="descname">linearTransform</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.linearTransform" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Linearly scales and offsets data. Scale first, then offset.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.xplot"> -<tt class="descname">xplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.xplot" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.plainPlot"> -<tt class="descname">plainPlot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.plainPlot" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.loadCSV"> -<tt class="descname">loadCSV</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadCSV" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.loadXplot"> -<tt class="descname">loadXplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadXplot" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.loadXplotRange"> -<tt class="descname">loadXplotRange</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadXplotRange" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.compareXplot"> -<tt class="descname">compareXplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.compareXplot" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Reads a plot from an xplot file and compares with contents of TableBase.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.compareVec"> -<tt class="descname">compareVec</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.compareVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Compares contents of TableBase with a vector of doubles.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</p> -</dd></dl> - -<dl class="method"> -<dt id="TableBase.clearVec"> -<tt class="descname">clearVec</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.clearVec" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles request to clear the data vector</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TableBase.vector"> -<tt class="descname">vector</tt><a class="headerlink" href="#TableBase.vector" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) vector with all table entries</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TableBase.outputValue"> -<tt class="descname">outputValue</tt><a class="headerlink" href="#TableBase.outputValue" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Output value holding current table entry or output of a calculation</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TableBase.size"> -<tt class="descname">size</tt><a class="headerlink" href="#TableBase.size" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TableBase.y"> -<tt class="descname">y</tt><a class="headerlink" href="#TableBase.y" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Value of table at specified index</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="TimeTable"> -<em class="property">class </em><tt class="descname">TimeTable</tt><a class="headerlink" href="#TimeTable" title="Permalink to this definition">¶</a></dt> -<dd><p>TimeTable: Read in spike times from file and send out eventOut messages</p> -<p>at the specified times.</p> -<dl class="attribute"> -<dt id="TimeTable.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#TimeTable.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.setFilename"> -<tt class="descname">setFilename</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.setFilename" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.getFilename"> -<tt class="descname">getFilename</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getFilename" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.setMethod"> -<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.setMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.getMethod"> -<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getMethod" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.getState"> -<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getState" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handle process call</p> -</dd></dl> - -<dl class="method"> -<dt id="TimeTable.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TimeTable.eventOut"> -<tt class="descname">eventOut</tt><a class="headerlink" href="#TimeTable.eventOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out spike time if it falls in current timestep.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="TimeTable.filename"> -<tt class="descname">filename</tt><a class="headerlink" href="#TimeTable.filename" title="Permalink to this definition">¶</a></dt> -<dd><p>string (<em>value field</em>) File to read lookup data from. The file should be contain two columns</p> -</dd></dl> - -</dd></dl> - -<p>separated by any space character.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="method"> -<tt class="descname">method</tt><a class="headerlink" href="#method" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Method to use for filling up the entries. Currently only method 4</p> -</dd></dl> - -</div></blockquote> -<p>(loading from file) is supported.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="state"> -<tt class="descname">state</tt><a class="headerlink" href="#state" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Current state of the time table.</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="Unsigned"> -<em class="property">class </em><tt class="descname">Unsigned</tt><a class="headerlink" href="#Unsigned" title="Permalink to this definition">¶</a></dt> -<dd><p>Variable for storing values.</p> -<dl class="method"> -<dt id="Unsigned.setValue"> -<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Unsigned.setValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="Unsigned.getValue"> -<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Unsigned.getValue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="Unsigned.value"> -<tt class="descname">value</tt><a class="headerlink" href="#Unsigned.value" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned long (<em>value field</em>) Variable value</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="VClamp"> -<em class="property">class </em><tt class="descname">VClamp</tt><a class="headerlink" href="#VClamp" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><p>Voltage clamp object for holding neuronal compartments at a specific voltage. This implementation uses a builtin RC circuit to filter the</p> -<p>command input and then use a PID to bring the sensed voltage (Vm from</p> -<p>compartment) to the filtered command potential.</p> -<blockquote> -<div>Connect the <cite>currentOut</cite> source of VClamp to <cite>injectMsg</cite></div></blockquote> -<p>dest of Compartment. Connect the <cite>VmOut</cite> source of Compartment to</p> -<p><cite>set_sensed</cite> dest of VClamp. Either set <cite>command</cite> field to a</p> -<p>fixed value, or connect an appropriate source of command potential</p> -<p>(like the <cite>outputOut</cite> message of an appropriately configured</p> -<p>PulseGen) to <cite>set_command</cite> dest.</p> -<blockquote> -<div>The default settings for the RC filter and PID controller should be</div></blockquote> -<p>time constant of RC filter, tau = 5 * dt</p> -<p>proportional gain of PID, gain = Cm/dt where Cm is the membrane</p> -<blockquote> -<div>capacitance of the compartment</div></blockquote> -<p>integration time of PID, ti = dt</p> -<p>derivative time of PID, td = 0</p> -<dl class="attribute"> -<dt id="VClamp.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#VClamp.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process messages from the scheduler</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getCommand"> -<tt class="descname">getCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getCommand" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getCurrent"> -<tt class="descname">getCurrent</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getCurrent" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getSensed"> -<tt class="descname">getSensed</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getSensed" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.setMode"> -<tt class="descname">setMode</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getMode"> -<tt class="descname">getMode</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getMode" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.setTi"> -<tt class="descname">setTi</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTi" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getTi"> -<tt class="descname">getTi</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTi" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.setTd"> -<tt class="descname">setTd</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTd" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getTd"> -<tt class="descname">getTd</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTd" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.setTau"> -<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getTau"> -<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.setGain"> -<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.getGain"> -<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getGain" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.sensedIn"> -<tt class="descname">sensedIn</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.sensedIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) The <cite>VmOut</cite> message of the Compartment object should be connected</p> -</dd></dl> - -</div></blockquote> -<p>here.</p> -<blockquote> -<div><dl class="method"> -<dt id="VClamp.commandIn"> -<tt class="descname">commandIn</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.commandIn" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) The command voltage source should be connected to this.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘process’ call on each time step.</p> -</dd></dl> - -<dl class="method"> -<dt id="VClamp.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VClamp.currentOut"> -<tt class="descname">currentOut</tt><a class="headerlink" href="#VClamp.currentOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Sends out current output of the clamping circuit. This should be connected to the <cite>injectMsg</cite> field of a compartment to voltage clamp it.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VClamp.command"> -<tt class="descname">command</tt><a class="headerlink" href="#VClamp.command" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Command input received by the clamp circuit.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VClamp.current"> -<tt class="descname">current</tt><a class="headerlink" href="#VClamp.current" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) The amount of current injected by the clamp into the membrane.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VClamp.sensed"> -<tt class="descname">sensed</tt><a class="headerlink" href="#VClamp.sensed" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Membrane potential read from compartment.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VClamp.mode"> -<tt class="descname">mode</tt><a class="headerlink" href="#VClamp.mode" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Working mode of the PID controller.</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="docutils"> -<dt>mode = 0, standard PID with proportional, integral and derivative</dt> -<dd>all acting on the error.</dd> -</dl> -<p>mode = 1, derivative action based on command input -mode = 2, proportional action and derivative action are based on -command input.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="ti"> -<tt class="descname">ti</tt><a class="headerlink" href="#ti" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Integration time of the PID controller. Defaults to 1e9, i.e. integral</p> -</dd></dl> - -</div></blockquote> -<p>action is negligibly small.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="td"> -<tt class="descname">td</tt><a class="headerlink" href="#td" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Derivative time of the PID controller. This defaults to 0,</p> -</dd></dl> - -</div></blockquote> -<p>i.e. derivative action is unused.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="tau"> -<tt class="descname">tau</tt><a class="headerlink" href="#tau" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Time constant of the lowpass filter at input of the PID</p> -</dd></dl> - -</div></blockquote> -<p>controller. This smooths out abrupt changes in the input. Set it to -5 * dt or more to avoid overshoots.</p> -<blockquote> -<div><dl class="attribute"> -<dt id="gain"> -<tt class="descname">gain</tt><a class="headerlink" href="#gain" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Proportional gain of the PID controller.</p> -</dd></dl> - -</div></blockquote> -<dl class="class"> -<dt id="VectorTable"> -<em class="property">class </em><tt class="descname">VectorTable</tt><a class="headerlink" href="#VectorTable" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="VectorTable.setXdivs"> -<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getXdivs"> -<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.setXmin"> -<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getXmin"> -<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXmin" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.setXmax"> -<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getXmax"> -<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXmax" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getInvdx"> -<tt class="descname">getInvdx</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getInvdx" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.setTable"> -<tt class="descname">setTable</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setTable" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getTable"> -<tt class="descname">getTable</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getTable" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getLookupvalue"> -<tt class="descname">getLookupvalue</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getLookupvalue" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="VectorTable.getLookupindex"> -<tt class="descname">getLookupindex</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getLookupindex" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.xdivs"> -<tt class="descname">xdivs</tt><a class="headerlink" href="#VectorTable.xdivs" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int (<em>value field</em>) Number of divisions.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.xmin"> -<tt class="descname">xmin</tt><a class="headerlink" href="#VectorTable.xmin" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Minimum value in table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.xmax"> -<tt class="descname">xmax</tt><a class="headerlink" href="#VectorTable.xmax" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value in table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.invdx"> -<tt class="descname">invdx</tt><a class="headerlink" href="#VectorTable.invdx" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximum value in table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.table"> -<tt class="descname">table</tt><a class="headerlink" href="#VectorTable.table" title="Permalink to this definition">¶</a></dt> -<dd><p>vector<double> (<em>value field</em>) The lookup table.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.lookupvalue"> -<tt class="descname">lookupvalue</tt><a class="headerlink" href="#VectorTable.lookupvalue" title="Permalink to this definition">¶</a></dt> -<dd><p>double,double (<em>lookup field</em>) Lookup function that performs interpolation to return a value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="VectorTable.lookupindex"> -<tt class="descname">lookupindex</tt><a class="headerlink" href="#VectorTable.lookupindex" title="Permalink to this definition">¶</a></dt> -<dd><p>unsigned int,double (<em>lookup field</em>) Lookup function that returns value by index.</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="ZombieBufPool"> -<em class="property">class </em><tt class="descname">ZombieBufPool</tt><a class="headerlink" href="#ZombieBufPool" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="ZombieCaConc"> -<em class="property">class </em><tt class="descname">ZombieCaConc</tt><a class="headerlink" href="#ZombieCaConc" title="Permalink to this definition">¶</a></dt> -<dd><dl class="attribute"> -<dt id="ZombieCaConc.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#ZombieCaConc.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setCa"> -<tt class="descname">setCa</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getCa"> -<tt class="descname">getCa</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCa" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setCaBasal"> -<tt class="descname">setCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getCaBasal"> -<tt class="descname">getCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setCa_base"> -<tt class="descname">setCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCa_base" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getCa_base"> -<tt class="descname">getCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCa_base" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setTau"> -<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getTau"> -<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getTau" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setB"> -<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getB"> -<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getB" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setThick"> -<tt class="descname">setThick</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setThick" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getThick"> -<tt class="descname">getThick</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getThick" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setCeiling"> -<tt class="descname">setCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCeiling" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getCeiling"> -<tt class="descname">getCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCeiling" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.setFloor"> -<tt class="descname">setFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setFloor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.getFloor"> -<tt class="descname">getFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getFloor" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.current"> -<tt class="descname">current</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.current" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Calcium Ion current, due to be converted to conc.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.currentFraction"> -<tt class="descname">currentFraction</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.currentFraction" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Fraction of total Ion current, that is carried by Ca2+.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.increase"> -<tt class="descname">increase</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.increase" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Any input current that increases the concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.decrease"> -<tt class="descname">decrease</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.decrease" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Any input current that decreases the concentration.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieCaConc.basal"> -<tt class="descname">basal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.basal" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Synonym for assignment of basal conc.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.concOut"> -<tt class="descname">concOut</tt><a class="headerlink" href="#ZombieCaConc.concOut" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>source message field</em>) Concentration of Ca in pool</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.Ca"> -<tt class="descname">Ca</tt><a class="headerlink" href="#ZombieCaConc.Ca" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Calcium concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.CaBasal"> -<tt class="descname">CaBasal</tt><a class="headerlink" href="#ZombieCaConc.CaBasal" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Basal Calcium concentration.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.Ca_base"> -<tt class="descname">Ca_base</tt><a class="headerlink" href="#ZombieCaConc.Ca_base" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Basal Calcium concentration, synonym for CaBasal</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.tau"> -<tt class="descname">tau</tt><a class="headerlink" href="#ZombieCaConc.tau" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Settling time for Ca concentration</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.B"> -<tt class="descname">B</tt><a class="headerlink" href="#ZombieCaConc.B" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Volume scaling factor</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.thick"> -<tt class="descname">thick</tt><a class="headerlink" href="#ZombieCaConc.thick" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Thickness of Ca shell.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.ceiling"> -<tt class="descname">ceiling</tt><a class="headerlink" href="#ZombieCaConc.ceiling" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieCaConc.floor"> -<tt class="descname">floor</tt><a class="headerlink" href="#ZombieCaConc.floor" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Floor value for Ca concentration. If Ca < floor, Ca = floor</p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="ZombieCompartment"> -<em class="property">class </em><tt class="descname">ZombieCompartment</tt><a class="headerlink" href="#ZombieCompartment" title="Permalink to this definition">¶</a></dt> -<dd><p>Compartment object, for branching neuron models.</p> -</dd></dl> - -<dl class="class"> -<dt id="ZombieEnz"> -<em class="property">class </em><tt class="descname">ZombieEnz</tt><a class="headerlink" href="#ZombieEnz" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="ZombieFuncPool"> -<em class="property">class </em><tt class="descname">ZombieFuncPool</tt><a class="headerlink" href="#ZombieFuncPool" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="ZombieFuncPool.input"> -<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieFuncPool.input" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles input to control value of <a href="#id25"><span class="problematic" id="id26">n_</span></a></p> -</dd></dl> - -</dd></dl> - -<dl class="class"> -<dt id="ZombieHHChannel"> -<em class="property">class </em><tt class="descname">ZombieHHChannel</tt><a class="headerlink" href="#ZombieHHChannel" title="Permalink to this definition">¶</a></dt> -<dd><blockquote> -<div><dl class="attribute"> -<dt id="ZombieHHChannel.proc"> -<tt class="descname">proc</tt><a class="headerlink" href="#ZombieHHChannel.proc" title="Permalink to this definition">¶</a></dt> -<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p> -</dd></dl> - -</div></blockquote> -<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p> -<blockquote> -<div><dl class="method"> -<dt id="ZombieHHChannel.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles process call</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.reinit"> -<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.reinit" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Handles reinit call</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setGbar"> -<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getGbar"> -<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getGbar" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setEk"> -<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getEk"> -<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getEk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setGk"> -<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getGk"> -<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getGk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getIk"> -<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getIk" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setXpower"> -<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getXpower"> -<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getXpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setYpower"> -<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getYpower"> -<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getYpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setZpower"> -<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getZpower"> -<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getZpower" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setInstant"> -<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getInstant"> -<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getInstant" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setX"> -<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getX"> -<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setY"> -<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getY"> -<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setZ"> -<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getZ"> -<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setUseConcentration"> -<tt class="descname">setUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setUseConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns field value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getUseConcentration"> -<tt class="descname">getUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getUseConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.concen"> -<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.concen" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to usein the Z gate calculations</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.createGate"> -<tt class="descname">createGate</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.createGate" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Function to create specified gate.Argument: Gate type [X Y Z]</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setNumGateX"> -<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getNumGateX"> -<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateX" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setNumGateY"> -<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getNumGateY"> -<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateY" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.setNumGateZ"> -<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p> -</dd></dl> - -<dl class="method"> -<dt id="ZombieHHChannel.getNumGateZ"> -<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateZ" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Gbar"> -<tt class="descname">Gbar</tt><a class="headerlink" href="#ZombieHHChannel.Gbar" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Maximal channel conductance</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Ek"> -<tt class="descname">Ek</tt><a class="headerlink" href="#ZombieHHChannel.Ek" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Reversal potential of channel</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Gk"> -<tt class="descname">Gk</tt><a class="headerlink" href="#ZombieHHChannel.Gk" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel conductance variable</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Ik"> -<tt class="descname">Ik</tt><a class="headerlink" href="#ZombieHHChannel.Ik" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Channel current variable</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Xpower"> -<tt class="descname">Xpower</tt><a class="headerlink" href="#ZombieHHChannel.Xpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Ypower"> -<tt class="descname">Ypower</tt><a class="headerlink" href="#ZombieHHChannel.Ypower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Zpower"> -<tt class="descname">Zpower</tt><a class="headerlink" href="#ZombieHHChannel.Zpower" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) Power for Z gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.instant"> -<tt class="descname">instant</tt><a class="headerlink" href="#ZombieHHChannel.instant" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.X"> -<tt class="descname">X</tt><a class="headerlink" href="#ZombieHHChannel.X" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for X gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Y"> -<tt class="descname">Y</tt><a class="headerlink" href="#ZombieHHChannel.Y" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.Z"> -<tt class="descname">Z</tt><a class="headerlink" href="#ZombieHHChannel.Z" title="Permalink to this definition">¶</a></dt> -<dd><p>double (<em>value field</em>) State variable for Y gate</p> -</dd></dl> - -<dl class="attribute"> -<dt id="ZombieHHChannel.useConcentration"> -<tt class="descname">useConcentration</tt><a class="headerlink" href="#ZombieHHChannel.useConcentration" title="Permalink to this definition">¶</a></dt> -<dd><p>int (<em>value field</em>) Flag: when true, use concentration message rather than Vm tocontrol Z gate</p> -</dd></dl> - -</div></blockquote> -</dd></dl> - -<dl class="class"> -<dt id="ZombieMMenz"> -<em class="property">class </em><tt class="descname">ZombieMMenz</tt><a class="headerlink" href="#ZombieMMenz" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="ZombiePool"> -<em class="property">class </em><tt class="descname">ZombiePool</tt><a class="headerlink" href="#ZombiePool" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="ZombieReac"> -<em class="property">class </em><tt class="descname">ZombieReac</tt><a class="headerlink" href="#ZombieReac" title="Permalink to this definition">¶</a></dt> -<dd></dd></dl> - -<dl class="class"> -<dt id="testSched"> -<em class="property">class </em><tt class="descname">testSched</tt><a class="headerlink" href="#testSched" title="Permalink to this definition">¶</a></dt> -<dd><dl class="method"> -<dt id="testSched.process"> -<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#testSched.process" title="Permalink to this definition">¶</a></dt> -<dd><p>(<em>destination message field</em>) handles process call</p> -</dd></dl> - 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Classes","the Multiscale Object-Oriented Simulation Environment","MOOSE Classes","MOOSE Classes","MOOSE = Multiscale Object Oriented Simulation Environment."],objnames:{"0":["py","class","Python class"],"1":["py","attribute","Python attribute"],"2":["py","method","Python method"],"3":["np","class","Python class"],"4":["np","attribute","Python attribute"],"5":["np","method","Python method"]},filenames:["tmp","index","moose_classes","moose_builtins","moose_overview"]}) \ No newline at end of file diff --git a/docs/user/html/pymoose2walkthrough.html b/docs/user/html/pymoose2walkthrough.html deleted file mode 100644 index 7c611cfb6d12cf6c78c0403028a814a3e025ff6e..0000000000000000000000000000000000000000 --- a/docs/user/html/pymoose2walkthrough.html +++ /dev/null @@ -1,282 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <meta name="author" content="Subhasis Ray" /> - <meta name="date" content="2012-12-12" /> - <title>Getting started with python scripting for MOOSE</title> - <style type="text/css">code{white-space: pre;}</style> - <style type="text/css"> -table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode { - margin: 0; padding: 0; vertical-align: baseline; border: none; } -table.sourceCode { width: 100%; line-height: 100%; } -td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; color: #aaaaaa; border-right: 1px solid #aaaaaa; } -td.sourceCode { padding-left: 5px; } -code > span.kw { color: #007020; font-weight: bold; } -code > span.dt { color: #902000; } -code > span.dv { color: #40a070; } -code > span.bn { color: #40a070; } -code > span.fl { color: #40a070; } -code > span.ch { color: #4070a0; } -code > span.st { color: #4070a0; } -code > span.co { color: #60a0b0; font-style: italic; } -code > span.ot { color: #007020; } -code > span.al { color: #ff0000; font-weight: bold; } -code > span.fu { color: #06287e; } -code > span.er { color: #ff0000; font-weight: bold; } - </style> - <link rel="stylesheet" href="css/moosedocs.css" type="text/css" /> -</head> -<body> -<div id="header"> -<h1 class="title">Getting started with python scripting for MOOSE</h1> -<h2 class="author">Subhasis Ray</h2> -<h3 class="date">December 12, 2012</h3> -</div> -<div id="TOC"> -<ul> -<li><a href="#introduction">Introduction</a></li> -<li><a href="#importing-moose-and-accessing-built-in-documentation">Importing MOOSE and accessing built-in documentation</a></li> -<li><a href="#creating-objects-and-traversing-the-object-hierarchy">Creating objects and traversing the object hierarchy</a></li> -<li><a href="#setting-the-properties-of-elements-accessing-fields">Setting the properties of elements: accessing fields</a></li> -<li><a href="#putting-them-together-setting-up-connections">Putting them together: setting up connections</a></li> -<li><a href="#scheduling-and-running-the-simulation">Scheduling and running the simulation</a></li> -<li><a href="#some-more-details">Some more details</a><ul> -<li><a href="#ematrix-melement-and-element"><code>ematrix</code>, <code>melement</code> and <code>element</code></a></li> -<li><a href="#finfos"><code>Finfos</code></a></li> -</ul></li> -<li><a href="#moving-on">Moving on</a></li> -</ul> -</div> -<h1 id="introduction"><a href="#introduction">Introduction</a></h1> -<p>This document describes how to use the <code>moose</code> module in Python scripts or in an interactive Python shell. It aims to give you enough overview to help you start scripting using MOOSE and extract farther information that may be required for advanced work. Knowledge of Python or programming in general will be helpful. If you just want to simulate existing models in one of the supported formats, you can fire the MOOSE GUI and locate the model file using the <code>File</code> menu and load it. The GUI is described <a href="./MooseGuiDocs.html">here</a>. The example code in the boxes can be entered in a Python shell.</p> -<h1 id="importing-moose-and-accessing-built-in-documentation"><a href="#importing-moose-and-accessing-built-in-documentation">Importing MOOSE and accessing built-in documentation</a></h1> -<p>In a python script you import modules to access the functionalities they provide.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="ch">import</span> moose</code></pre> -<p>This makes the <code>moose</code> module available for use in Python. You can use Python's built-in <code>help</code> function to read the top-level documentation for the moose module:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">help</span>(moose)</code></pre> -<p>This will give you an overview of the module. Press <code>q</code> to exit the pager and get back to the interpreter. You can also access the documentation for individual classes and functions this way.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">help</span>(moose.<span class="ot">connect</span>)</code></pre> -<p>To list the available functions and classes you can use <code>dir</code> function<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a>.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">dir</span>(moose)</code></pre> -<p>MOOSE has built-in documentation in the C++-source-code independent of Python. The <code>moose</code> module has a separate <code>doc</code> function to extract this documentation.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(moose.Compartment)</code></pre> -<p>The class level documentation will show whatever the author/maintainer of the class wrote for documentation followed by a list of various kinds of fields and their data types. This can be very useful in an interactive session.</p> -<p>Each field can have its own detailed documentation, too.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(<span class="st">'Compartment.Rm'</span>)</code></pre> -<p>Note that you need to put the class-name followed by dot followed by field-name within quotes. Otherwise, <code>moose.doc</code> will receive the field value as parameter and get confused.</p> -<h1 id="creating-objects-and-traversing-the-object-hierarchy"><a href="#creating-objects-and-traversing-the-object-hierarchy">Creating objects and traversing the object hierarchy</a></h1> -<p>Different types of biological entities like neurons, enzymes, etc are represented by classes and individual instances of those types are objects of those classes. Objects are the building-blocks of models in MOOSE. We call MOOSE objects <code>element</code> and use object and element interchangeably in the context of MOOSE. Elements are conceptually laid out in a tree-like hierarchical structure. If you are familiar with file system hierarchies in common operating systems, this should be simple.</p> -<p>At the top of the object hierarchy sits the <code>Shell</code>, equivalent to the root directory in UNIX-based systems and represented by the path <code>/</code>. You can list the existing objects under <code>/</code> using the <code>le</code> function.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.le()</code></pre> -<p>This shows something like:</p> -<pre class="sourceCode python"><code class="sourceCode python"> Elements under / - /Msgs - /clock - /classes</code></pre> -<p><code>Msgs</code>, <code>clock</code> and <code>classes</code> are predefined objects in MOOSE. And each object can contain other objects inside them. You can see them by passing the path of the parent object to <code>le</code>.</p> -<p>Entering:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.le(<span class="st">'/clock'</span>)</code></pre> -<p>prints:</p> -<pre class="sourceCode python"><code class="sourceCode python"> Elements under /clock - /clock/tick[<span class="dv">0</span>]</code></pre> -<p>Now let us create some objects of our own. This can be done by invoking MOOSE class constructors (just like regular Python classes).</p> -<pre class="sourceCode python"><code class="sourceCode python"> model = moose.Neutral(<span class="st">'/model'</span>)</code></pre> -<p>The above creates a <code>Neutral</code> object named <code>model</code>. <code>Neutral</code> is the most basic class in MOOSE. A <code>Neutral</code> element can act as a container for other elements. We can create something under <code>model</code>:</p> -<pre class="sourceCode python"><code class="sourceCode python"> soma = moose.Compartment(<span class="st">'/model/soma'</span>)</code></pre> -<p>Every element has a unique path. This is a concatenation of the names of all the objects one has to traverse starting with the root to reach that element.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.path</code></pre> -<p>shows you its path:</p> -<pre class="sourceCode python"><code class="sourceCode python"> /model/soma</code></pre> -<p>The name of the element can be printed, too.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.name</code></pre> -<p>shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> soma</code></pre> -<p>The <code>Compartment</code> elements model small portions of a neuron. Some basic experiments can be carried out using a single compartment. Let us create another object to act on the <code>soma</code>. This will be a step current generator to inject a current pulse into the soma.</p> -<pre class="sourceCode python"><code class="sourceCode python"> pulse = moose.PulseGen(<span class="st">'/model/pulse'</span>)</code></pre> -<p>You can use <code>le</code> at any point to see what is there:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.le(<span class="st">'/model'</span>)</code></pre> -<p>will show you:</p> -<pre class="sourceCode python"><code class="sourceCode python"> Elements under /model - /model/soma - /model/pulse</code></pre> -<p>And finally, we can create a <code>Table</code> to record the time series of the soma's membrane potential. It is good practice to organize the data separately from the model. So we do it as below:</p> -<pre class="sourceCode python"><code class="sourceCode python"> data = moose.Neutral(<span class="st">'/data'</span>) - vmtab = moose.Table(<span class="st">'/data/soma_Vm'</span>)</code></pre> -<p>Now that we have the essential elements for a small model, we can go on to set the properties of this model and the experimental protocol.</p> -<h1 id="setting-the-properties-of-elements-accessing-fields"><a href="#setting-the-properties-of-elements-accessing-fields">Setting the properties of elements: accessing fields</a></h1> -<p>Elements have several kinds of fields. The simplest ones are the <code>value fields</code>. These can be accessed like ordinary Python members. You can list the available value fields using <code>getFieldNames</code> function:</p> -<pre class="sourceCode python"><code class="sourceCode python"> soma.getFieldNames(<span class="st">'valueFinfo'</span>)</code></pre> -<p>Here <code>valueFinfo</code> is the type name for value fields. <code>Finfo</code> is short form of <em>field information</em>. For each type of field there is a name ending with <code>-Finfo</code>. The above will display the following list:</p> -<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'this'</span>, - <span class="co">'name'</span>, - <span class="co">'me'</span>, - <span class="co">'parent'</span>, - <span class="co">'children'</span>, - <span class="co">'path'</span>, - <span class="co">'class'</span>, - <span class="co">'linearSize'</span>, - <span class="co">'objectDimensions'</span>, - <span class="co">'lastDimension'</span>, - <span class="co">'localNumField'</span>, - <span class="co">'pathIndices'</span>, - <span class="co">'msgOut'</span>, - <span class="co">'msgIn'</span>, - <span class="co">'Vm'</span>, - <span class="co">'Cm'</span>, - <span class="co">'Em'</span>, - <span class="co">'Im'</span>, - <span class="co">'inject'</span>, - <span class="co">'initVm'</span>, - <span class="co">'Rm'</span>, - <span class="co">'Ra'</span>, - <span class="co">'diameter'</span>, - <span class="co">'length'</span>, - <span class="co">'x0'</span>, - <span class="co">'y0'</span>, - <span class="co">'z0'</span>, - <span class="co">'x'</span>, - <span class="co">'y'</span>, - <span class="co">'z'</span>)</code></pre> -<p>Some of these fields are for internal or advanced use, some give access to the physical properties of the biological entity we are trying to model. Now we are interested in <code>Cm</code>, <code>Rm</code>, <code>Em</code> and <code>initVm</code>. In the most basic form, a neuronal compartment acts like a parallel <code>RC</code> circuit with a battery attached. Here <code>R</code> and <code>C</code> are resistor and capacitor connected in parallel, and the battery with voltage <code>Em</code> is in series with the resistor, as shown below:</p> -<hr /> -<div class="figure"> -<img src="../../images/neuronalcompartment.jpg" alt="Passive neuronal compartment" /><p class="caption"><strong>Passive neuronal compartment</strong></p> -</div> -<hr /> -<p>The fields are populated with some defaults.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm</code></pre> -<p>will give you:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="fl">1.0</span> <span class="fl">1.0</span> -<span class="fl">0.06</span> -<span class="fl">0.06</span> -<span class="fl">0.06</span></code></pre> -<p>You can set the <code>Cm</code> and <code>Rm</code> fields to something realistic using simple assignment (we follow SI unit)<a href="#fn2" class="footnoteRef" id="fnref2"><sup>2</sup></a>.</p> -<pre class="sourceCode python"><code class="sourceCode python"> soma.Cm = <span class="fl">1e-9</span> - soma.Rm = <span class="fl">1e7</span> - soma.initVm = -<span class="fl">0.07</span></code></pre> -<p>Instead of writing print statements for each field, you could use the utility function showfield to see that the changes took effect:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.showfield(soma)</code></pre> -<p>will list most of the fields with their values:</p> -<p><sub><sub><del>{.c} [ /model/soma ] diameter = 0.0 linearSize = 1 localNumField = 0 Ra = 1.0 y0 = 0.0 Rm = 10000000.0 inject = 0.0 Em = -0.06 initVm = -0.07 x = 0.0 path = /model/soma x0 = 0.0 z0 = 0.0 class = Compartment name = soma Cm = 1e-09 Vm = -0.06 length = 0.0 Im = 0.0 y = 0.0 lastDimension = 0 z = 0.0</del></sub></sub>{.python}</p> -<p>Now we can setup the current pulse to be delivered to the soma:</p> -<pre class="sourceCode python"><code class="sourceCode python"> pulse.delay[<span class="dv">0</span>] = <span class="fl">50e-3</span> - pulse.width[<span class="dv">0</span>] = <span class="fl">100e-3</span> - pulse.level[<span class="dv">0</span>] = <span class="fl">1e-9</span> - pulse.delay[<span class="dv">1</span>] = <span class="fl">1e9</span></code></pre> -<p>This tells the pulse generator to create a 100 ms long pulse 50 ms after the start of the simulation. The amplitude of the pulse is set to 1 nA. We set the delay for the next pulse to a very large value (larger than the total simulation time) so that the stimulation stops after the first pulse. Had we set <code>pulse.delay = 0</code> , it would have generated a pulse train at 50 ms intervals.</p> -<h1 id="putting-them-together-setting-up-connections"><a href="#putting-them-together-setting-up-connections">Putting them together: setting up connections</a></h1> -<p>In order for the elements to interact during simulation, we need to connect them via messages. Elements are connected to each other using special source and destination fields. These types are named <code>srcFinfo</code> and <code>destFinfo</code>. You can query the available source and destination fields on an element using <code>getFieldNames</code> as before. This time, let us do it another way: by the class name:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.getFieldNames(<span class="st">'PulseGen'</span>, <span class="st">'srcFinfo'</span>)</code></pre> -<p>This form has the advantage that you can get information about a class without creating elements of that class. The above code shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'childMsg'</span>, <span class="st">'outputOut'</span>)</code></pre> -<p>Here <code>childMsg</code> is a source field that is used by the MOOSE internals to connect child elements to parent elements. The second one is of our interest. Check out the built-in documentation here:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(<span class="st">'PulseGen.outputOut'</span>)</code></pre> -<p>shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> PulseGen.outputOut: double - source field - Current output level.</code></pre> -<p>so this is the output of the pulse generator and this must be injected into the <code>soma</code> to stimulate it. But where in the <code>soma</code> can we send it? Again, MOOSE has some introspection built in.</p> -<pre class="sourceCode python"><code class="sourceCode python"> soma.getFieldNames(<span class="st">'destFinfo'</span>)</code></pre> -<p>shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'parentMsg'</span>, - <span class="co">'set_this'</span>, - <span class="co">'get_this'</span>, - ... - <span class="co">'set_z'</span>, - <span class="co">'get_z'</span>, - <span class="co">'injectMsg'</span>, - <span class="co">'randInject'</span>, - <span class="co">'cable'</span>, - <span class="co">'process'</span>, - <span class="co">'reinit'</span>, - <span class="co">'initProc'</span>, - <span class="co">'initReinit'</span>, - <span class="co">'handleChannel'</span>, - <span class="co">'handleRaxial'</span>, - <span class="co">'handleAxial'</span>)</code></pre> -<p>Now that is a long list. But much of it are fields for internal or special use. Anything that starts with <code>get_</code> or <code>set_</code> are internal <code>destFinfo</code> used for accessing value fields (we shall use one of those when setting up data recording). Among the rest <code>injectMsg</code> seems to be the most likely candidate. Use the <code>connect</code> function to connect the pulse generator output to the soma input:</p> -<pre class="sourceCode python"><code class="sourceCode python"> m = moose.<span class="ot">connect</span>(pulse, <span class="st">'outputOut'</span>, soma, <span class="st">'injectMsg'</span>)</code></pre> -<p><code>connect(source, source_field, dest, dest_field)</code> creates a <code>message</code> from <code>source</code> element's <code>source_field</code> field to <code>dest</code> elements <code>dest_field</code> field and returns that message. Messages are also elements. You can print them to see their identity:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> m</code></pre> -<p>on my system gives:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <moose.SingleMsg: <span class="dt">id</span>=<span class="dv">5</span>, dataId=<span class="dv">733</span>, path=/Msgs/singleMsg[<span class="dv">733</span>]></code></pre> -<p>You can print any element as above and the string representation will show you the class, two numbers(<code>id</code> and <code>dataId</code>) uniquely identifying it among all elements, and its path. You can get some more information about a message:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2</code></pre> -<p>will confirm what you already know:</p> -<pre class="sourceCode python"><code class="sourceCode python"> /model/pulse /model/soma (<span class="st">'outputOut'</span>,) (<span class="st">'injectMsg'</span>,)</code></pre> -<p>A message element has fields <code>e1</code> and <code>e2</code> referring to the elements it connects. For single one-directional messages these are source and destination elements, which are <code>pulse</code> and <code>soma</code> respectively. The next two items are lists of the field names which are connected by this message.</p> -<p>You could also check which elements are connected to a particular field:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.neighbours[<span class="st">'injectMsg'</span>]</code></pre> -<p>shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> [<moose.ematrix: <span class="kw">class</span>=PulseGen, <span class="dt">id</span>=<span class="dv">729</span>,path=/model/pulse>]</code></pre> -<p>Notice that the list contains something called ematrix. We discuss this <a href="#some-more-details">later</a>. Also <code>neighbours</code> is a new kind of field: <code>lookupFinfo</code> which behaves like a dictionary. Next we connect the table to the soma to retrieve its membrane potential <code>Vm</code>. This is where all those <code>destFinfo</code> starting with <code>get_</code> or <code>set_</code> come in use. For each value field <code>X</code>, there is a <code>destFinfo</code> <code>get_{X}</code> to retrieve the value at simulation time. This is used by the table to record the values <code>Vm</code> takes.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.<span class="ot">connect</span>(vmtab, <span class="st">'requestData'</span>, soma, <span class="st">'get_Vm'</span>)</code></pre> -<p>This finishes our model and recording setup. You might be wondering about the source-destination relationship above. It is natural to think that <code>soma</code> is the source of <code>Vm</code> values which should be sent to <code>vmtab</code>. But here <code>requestData</code> is a <code>srcFinfo</code> acting like a reply card. This mode of obtaining data is called <em>pull</em> mode.<a href="#fn3" class="footnoteRef" id="fnref3"><sup>3</sup></a></p> -<h1 id="scheduling-and-running-the-simulation"><a href="#scheduling-and-running-the-simulation">Scheduling and running the simulation</a></h1> -<p>With the model all set up, we have to schedule the simulation. MOOSE has a central clock element (<code>/clock</code>) to manage time. Clock has a set of <code>Tick</code> elements under it that take care of advancing the state of each element with time as the simulation progresses. Every element to be included in a simulation must be assigned a tick. Each tick can have a different ticking interval (<code>dt</code>) that allows different elements to be updated at different rates. We initialize the ticks and set their <code>dt</code> values using the <code>setClock</code> function.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.setClock(<span class="dv">0</span>, <span class="fl">0.025e-3</span>) - moose.setClock(<span class="dv">1</span>, <span class="fl">0.025e-3</span>) - moose.setClock(<span class="dv">2</span>, <span class="fl">0.25e-3</span>)</code></pre> -<p>This will initialize tick #0 and tick #1 with <code>dt = 25</code> μs and tick #2 with <code>dt = 250</code> μs. Thus all the elements scheduled on ticks #0 and 1 will be updated every 25 μs and those on tick #2 every 250 μs. We use the faster clocks for the model components where finer timescale is required for numerical accuracy and the slower clock to sample the values of <code>Vm</code>.</p> -<p>So to assign tick #2 to the table for recording <code>Vm</code>, we pass its whole path to the <code>useClock</code> function.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">2</span>, <span class="st">'/data/soma_Vm'</span>, <span class="st">'process'</span>)</code></pre> -<p>Read this as "use tick # 2 on the element at path <code>/data/soma_Vm</code> to call its <code>process</code> method at every step". Every class that is supposed to update its state or take some action during simulation implements a <code>process</code> method. And in most cases that is the method we want the ticks to call at every time step. A less common method is <code>init</code>, which is implemented in some classes to interleave actions or updates that must be executed in a specific order<a href="#fn4" class="footnoteRef" id="fnref4"><sup>4</sup></a>. The <code>Compartment</code> class is one such case where a neuronal compartment has to know the <code>Vm</code> of its neighboring compartments before it can calculate its <code>Vm</code> for the next step. This is done with:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">0</span>, soma.path, <span class="st">'init'</span>)</code></pre> -<p>Here we used the <code>path</code> field instead of writing the path explicitly.</p> -<p>Next we assign tick #1 to process method of everything under <code>/model</code>.</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">1</span>, <span class="st">'/model/##'</span>, <span class="st">'process'</span>)</code></pre> -<p>Here the second argument is an example of wild-card path. The <code>##</code> matches everything under the path preceding it at any depth. Thus if we had some other objects under <code>/model/soma</code>, <code>process</code> method of those would also have been scheduled on tick #1. This is very useful for complex models where it is tedious to scheduled each element individually. In this case we could have used <code>/model/#</code> as well for the path. This is a single level wild-card which matches only the children of <code>/model</code> but does not go farther down in the hierarchy.</p> -<p>Once the elements are assigned ticks, we can put the model to its initial state using:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.reinit()</code></pre> -<p>You may remember that we had changed initVm from <code>-0.06</code> to <code>-0.07</code>. The reinit call we initialize <code>Vm</code> to that value. You can verify that:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.Vm</code></pre> -<p>gives:</p> -<pre class="sourceCode python"><code class="sourceCode python"> -<span class="fl">0.07</span></code></pre> -<p>Finally, we run the simulation for 300 ms:</p> -<pre class="sourceCode python"><code class="sourceCode python"> moose.start(<span class="fl">300e-3</span>)</code></pre> -<p>The data will be recorded by the <code>soma_vm</code> table, which is referenced by the variable <code>vmtab</code>. The <code>Table</code> class provides a numpy array interface to its content. The field is <code>vec</code>. So you can easily plot the membrane potential using the <a href="http://matplotlib.org/">matplotlib</a> library.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="ch">import</span> pylab - t = pylab.linspace(<span class="dv">0</span>, <span class="fl">300e-3</span>, <span class="dt">len</span>(vmtab.vec)) - pylab.plot(t, vmtab.vec) - pylab.show()</code></pre> -<p>The first line imports the pylab submodule from matplotlib. This useful for interactive plotting. The second line creates the time points to match our simulation time and length of the recorded data. The third line plots the <code>Vm</code> and the fourth line makes it visible. Does the plot match your expectation?</p> -<h1 id="some-more-details"><a href="#some-more-details">Some more details</a></h1> -<h2 id="ematrix-melement-and-element"><a href="#ematrix-melement-and-element"><code>ematrix</code>, <code>melement</code> and <code>element</code></a></h2> -<p>MOOSE elements are instances of the class <code>melement</code>. <code>Compartment</code>, <code>PulseGen</code> and other MOOSE classes are derived classes of <code>melement</code>. All <code>melement</code> instances are contained in array-like structures called <code>ematrix</code>. Each <code>ematrix</code> object has a numerical <code>id_</code> field uniquely identifying it. An <code>ematrix</code> can have one or more elements. You can create an array of elements:</p> -<pre class="sourceCode python"><code class="sourceCode python"> comp_array = moose.ematrix(<span class="st">'/model/comp'</span>, (<span class="dv">3</span>,), <span class="st">'Compartment'</span>)</code></pre> -<p>This tells MOOSE to create an <code>ematrix</code> of 3 <code>Compartment</code> elements with path <code>/model/comp</code>. For <code>ematrix</code> objects with multiple elements, the index in the <code>ematrix</code> is part of the element path.</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> comp_array.path, <span class="dt">type</span>(comp_array)</code></pre> -<p>shows that <code>comp_array</code> is an instance of <code>ematrix</code> class. You can loop through the elements in an <code>ematrix</code> like a Python list:</p> -<pre class="sourceCode python"><code class="sourceCode python"> <span class="kw">for</span> comp in comp_array: - <span class="dt">print</span> comp.path, <span class="dt">type</span>(comp)</code></pre> -<p>shows:</p> -<pre class="sourceCode python"><code class="sourceCode python"> /model/comp[<span class="dv">0</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>> - /model/comp[<span class="dv">1</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>> - /model/comp[<span class="dv">2</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>></code></pre> -<p>Thus elements are instances of class <code>melement</code>. All elements in an <code>ematrix</code> share the <code>id_</code> of the <code>ematrix</code> which can retrieved by <code>melement.getId()</code>.</p> -<p>A frequent use case is that after loading a model from a file one knows the paths of various model components but does not know the appropriate class name for them. For this scenario there is a function called <code>element</code> which converts ("casts" in programming jargon) a path or any moose object to its proper MOOSE class. You can create additional references to <code>soma</code> in the example this way:</p> -<pre class="sourceCode python"><code class="sourceCode python"> x = moose.element(<span class="st">'/model/soma'</span>)</code></pre> -<p>Any MOOSE class can be extended in Python. But any additional attributes added in Python are invisible to MOOSE. So those can be used for functionalities at the Python level only. You can see <code>Demos/squid/squid.py</code> for an example.</p> -<h2 id="finfos"><a href="#finfos"><code>Finfos</code></a></h2> -<p>The following kinds of <code>Finfo</code> are accessible in Python</p> -<ul> -<li><strong><code>valueFinfo</code></strong> : simple values. For each readable <code>valueFinfo</code> <code>XYZ</code> there is a <code>destFinfo</code> <code>get_XYZ</code> that can be used for reading the value at run time. If <code>XYZ</code> is writable then there will also be <code>destFinfo</code> to set it: <code>set_XYZ</code>. Example: <code>Compartment.Rm</code></li> -<li><strong><code>lookupFinfo</code></strong> : lookup tables. These fields act like Python dictionaries but iteration is not supported. Example: <code>Neutral.neighbours</code>.</li> -<li><strong><code>srcFinfo</code></strong> : source of a message. Example: <code>PulseGen.outputOut</code>.</li> -<li><strong><code>destFinfo</code></strong> : destination of a message. Example: <code>Compartment.injectMsg</code>. Apart from being used in setting up messages, these are accessible as functions from Python. <code>HHGate.setupAlpha</code> is an example.</li> -<li><strong><code>sharedFinfo</code></strong> : a composition of source and destination fields. Example: <code>Compartment.channel</code>.</li> -</ul> -<h1 id="moving-on"><a href="#moving-on">Moving on</a></h1> -<p>Now you know the basics of pymoose and how to access the help system. MOOSE is backward compatible with GENESIS and most GENESIS classes have been reimplemented in MOOSE. There is slight change in naming (MOOSE uses CamelCase), and setting up messages are different. But <a href="http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html">GENESIS documentation</a> is still a good source for documentation on classes that have been ported from GENESIS.</p> -<p>In addition, the <code>Demos/snippets</code> directory in your MOOSE installation has small executable python scripts that show usage of specific classes or functionalities. Beyond that you can browse the code in the <code>Demos</code> directory to see some more complex models.</p> -<p>If the built-in MOOSE classes do not satisfy your needs entirely, you are welcome to add new classes to MOOSE. The API documentation will help you get started. Finally you can join the <a href="https://lists.sourceforge.net/lists/listinfo/moose-generic">moose mailing list</a> and request for help.</p> -<div class="footnotes"> -<hr /> -<ol> -<li id="fn1"><p>To list the classes only, use <code>moose.le('/classes')</code><a href="#fnref1">↩</a></p></li> -<li id="fn2"><p>MOOSE is unit agnostic and things should work fine as long as you use values all converted to a consistent unit system.<a href="#fnref2">↩</a></p></li> -<li id="fn3"><p>This apparently convoluted implementation is for performance reason. Can you figure out why? <em>Hint: the table is driven by a slower clock than the compartment.</em><a href="#fnref3">↩</a></p></li> -<li id="fn4"><p>In principle any function available in a MOOSE class can be executed periodically this way as long as that class exposes the function for scheduling following the MOOSE API. So you have to consult the class' documentation for any nonstandard methods that can be scheduled this way.<a href="#fnref4">↩</a></p></li> -</ol> -</div> -</body> -</html> diff --git a/docs/user/index.html b/docs/user/index.html deleted file mode 100644 index bef832ff408fa6bb9c7326f8274c43fcb876c16c..0000000000000000000000000000000000000000 --- a/docs/user/index.html +++ /dev/null @@ -1,27 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <meta name="author" content="Niraj Dudani" /> - <title>User documentation for MOOSE</title> - <style type="text/css">code{white-space: pre;}</style> - <link rel="stylesheet" href="html/css/moosedocs.css" type="text/css" /> -</head> -<body> -<div id="header"> -<h1 class="title">User documentation for MOOSE</h1> -<h2 class="author">Niraj Dudani</h2> -<h3 class="date">January 1, 2013</h3> -</div> -<h2 id="index-for-all-documents">Index for all documents</h2> -<ul> -<li><a href="html/pymoose2walkthrough.html">Getting started with python scripting for MOOSE</a></li> -<li><a href="html/MooseGuiDocs.html">MOOSEGUI: Graphical interface for MOOSE</a></li> -<li><a href="html/Nkit2Documentation.html">Neuronal simulations in MOOSEGUI</a></li> -<li><a href="html/Kkit12Documentation.html">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a></li> -<li><a href="html/moosebuiltindocs.html">Documentation for all MOOSE classes and functions</a></li> -</ul> -</body> -</html> diff --git a/docs/user/markdown/RdesigneurDocumentation.markdown b/docs/user/markdown/RdesigneurDocumentation.markdown index ffc84e23c89b38461823e4c71d3e8e9fb7099d50..fb9b0e3b0bb961e8a877ae35624fc2952ed7c781 100644 --- a/docs/user/markdown/RdesigneurDocumentation.markdown +++ b/docs/user/markdown/RdesigneurDocumentation.markdown @@ -4,7 +4,7 @@ Upi Bhalla -Dec 28 2015. +Aug 26 2016. ----- diff --git a/docs/user/snippets/Makefile b/docs/user/snippets/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..182070907cae692fced766d21141b1ccbc52a887 --- /dev/null +++ b/docs/user/snippets/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. 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The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. 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When it is not found, a full rebuild will be done. +config: 601daa5d29254955369b4905c1672965 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/user/snippets/_build/html/_modules/convert_Genesis2Sbml.html b/docs/user/snippets/_build/html/_modules/convert_Genesis2Sbml.html new file mode 100644 index 0000000000000000000000000000000000000000..81bbf1b62edadd547a1136e23f1443829ea8b792 --- /dev/null +++ b/docs/user/snippets/_build/html/_modules/convert_Genesis2Sbml.html @@ -0,0 +1,257 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>convert_Genesis2Sbml — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="../index.html"/> + <link rel="up" title="Module code" href="index.html"/> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="../_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="../snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="../index.html">Docs</a> »</li> + + <li><a href="index.html">Module code</a> »</li> + + <li>convert_Genesis2Sbml</li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <h1>Source code for convert_Genesis2Sbml</h1><div class="highlight"><pre> +<span class="c"># convert_Genesis2Sbml.py --- </span> +<span class="c"># </span> +<span class="c"># Filename: convert_Genesis2Sbml.py</span> +<span class="c"># Description: </span> +<span class="c"># Author:Harsha Rani </span> +<span class="c"># Maintainer: </span> +<span class="c"># Created: Mon Jan 19 09:16:58 2015 (+0530)</span> +<span class="c"># Version: </span> +<span class="c"># Last-Updated: Mon Nov 7 15:155:38 2012 (+0530)</span> +<span class="c"># By: Harsha Rani</span> +<span class="c"># Update #: </span> +<span class="c"># URL: </span> +<span class="c"># Keywords: </span> +<span class="c"># Compatibility: </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Commentary: </span> +<span class="c"># </span> +<span class="c"># The script demonstates to convert Chemical (Genesis) file to SBML file using moose</span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Change log:</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># This program is free software; you can redistribute it and/or</span> +<span class="c"># modify it under the terms of the GNU General Public License as</span> +<span class="c"># published by the Free Software Foundation; either version 3, or</span> +<span class="c"># (at your option) any later version.</span> +<span class="c"># </span> +<span class="c"># This program is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span> +<span class="c"># General Public License for more details.</span> +<span class="c"># </span> +<span class="c"># You should have received a copy of the GNU General Public License</span> +<span class="c"># along with this program; see the file COPYING. If not, write to</span> +<span class="c"># the Free Software Foundation, Inc., 51 Franklin Street, Fifth</span> +<span class="c"># Floor, Boston, MA 02110-1301, USA.</span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Code:</span> + +<span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">from</span> <span class="nn">moose.SBML</span> <span class="kn">import</span> <span class="o">*</span> +<div class="viewcode-block" id="main"><a class="viewcode-back" href="../snippet.html#convert_Genesis2Sbml.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">"""This example illustrates loading a kinetic model defined in Genesis format</span> +<span class="sd"> into Moose using loadModel function and using writeSBML function</span> +<span class="sd"> one can save the model into SBML format. \n</span> +<span class="sd"> Moose needs to be compiled with libsbml</span> +<span class="sd">"""</span> + <span class="c">#This command loads the file into the path '/Kholodenko'</span> + <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span><span class="s">'../genesis/Kholodenko.g'</span><span class="p">,</span><span class="s">'/Kholodenko'</span><span class="p">)</span> + + <span class="c">#Writes model to xml file</span> + <span class="n">written</span> <span class="o">=</span> <span class="n">mooseWriteSBML</span><span class="p">(</span><span class="s">'/Kholodenko'</span><span class="p">,</span><span class="s">'../genesis/Kholodenko_tosbml.xml'</span><span class="p">)</span> + <span class="k">print</span> <span class="n">written</span> +</div> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'../', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/_modules/index.html b/docs/user/snippets/_build/html/_modules/index.html new file mode 100644 index 0000000000000000000000000000000000000000..0db8718a0078e05f9eba1741d70d13ecabb0a0ef --- /dev/null +++ b/docs/user/snippets/_build/html/_modules/index.html @@ -0,0 +1,194 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>Overview: module code — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="../index.html"/> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="../_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="../snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="../index.html">Docs</a> »</li> + + <li>Overview: module code</li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <h1>All modules for which code is available</h1> +<ul><li><a href="convert_Genesis2Sbml.html">convert_Genesis2Sbml</a></li> +<li><a href="loadCspaceModel.html">loadCspaceModel</a></li> +<li><a href="loadKineticModel.html">loadKineticModel</a></li> +<li><a href="loadSbmlmodel.html">loadSbmlmodel</a></li> +</ul> + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'../', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/_modules/loadCspaceModel.html b/docs/user/snippets/_build/html/_modules/loadCspaceModel.html new file mode 100644 index 0000000000000000000000000000000000000000..027415dfa7d12f3bbeef1ad69af9df507069cc41 --- /dev/null +++ b/docs/user/snippets/_build/html/_modules/loadCspaceModel.html @@ -0,0 +1,267 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>loadCspaceModel — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="../index.html"/> + <link rel="up" title="Module code" href="index.html"/> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="../_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="../snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="../index.html">Docs</a> »</li> + + <li><a href="index.html">Module code</a> »</li> + + <li>loadCspaceModel</li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <h1>Source code for loadCspaceModel</h1><div class="highlight"><pre> +<span class="c"># loadCspaceModel.py --- </span> +<span class="c"># </span> +<span class="c"># Filename: loadCspaceModel.py</span> +<span class="c"># Description: </span> +<span class="c"># Author: Upi Bhalla </span> +<span class="c"># Maintainer: </span> +<span class="c"># Created: Sat Oct 04 10:14:15 2014 (+0530)</span> +<span class="c"># Version: </span> +<span class="c"># Last-Updated: </span> +<span class="c"># By: </span> +<span class="c"># Update #: 0</span> +<span class="c"># URL: </span> +<span class="c"># Keywords: </span> +<span class="c"># Compatibility: </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Commentary: </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Change log:</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># This program is free software; you can redistribute it and/or</span> +<span class="c"># modify it under the terms of the GNU General Public License as</span> +<span class="c"># published by the Free Software Foundation; either version 3, or</span> +<span class="c"># (at your option) any later version.</span> +<span class="c"># </span> +<span class="c"># This program is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span> +<span class="c"># General Public License for more details.</span> +<span class="c"># </span> +<span class="c"># You should have received a copy of the GNU General Public License</span> +<span class="c"># along with this program; see the file COPYING. If not, write to</span> +<span class="c"># the Free Software Foundation, Inc., 51 Franklin Street, Fifth</span> +<span class="c"># Floor, Boston, MA 02110-1301, USA.</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># Code:</span> + +<span class="kn">import</span> <span class="nn">math</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">moose</span> +<div class="viewcode-block" id="main"><a class="viewcode-back" href="../snippet.html#loadCspaceModel.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates loading and running, a kinetic model </span> +<span class="sd"> defined in cspace format. We use the gsl solver here. The model already</span> +<span class="sd"> defines a couple of plots and sets the runtime to 3000 seconds. </span> +<span class="sd"> """</span> + <span class="c"># This command loads the file into the path '/model', and tells</span> + <span class="c"># the system to use the gsl solver.</span> + <span class="n">modelId</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="s">'Osc.cspace'</span><span class="p">,</span> <span class="s">'model'</span><span class="p">,</span> <span class="s">'gsl'</span> <span class="p">)</span> + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">3000.0</span> <span class="p">)</span> <span class="c"># Run the model for 300 seconds.</span> + + <span class="c"># display all plots</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/graphs/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="c"># moose.saveModel( modelId, 'saveReaction.g' )</span> + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span></div> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'../', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/_modules/loadKineticModel.html b/docs/user/snippets/_build/html/_modules/loadKineticModel.html new file mode 100644 index 0000000000000000000000000000000000000000..14cb66db55a432453580d6e46159442ccc1bb48a --- /dev/null +++ b/docs/user/snippets/_build/html/_modules/loadKineticModel.html @@ -0,0 +1,290 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>loadKineticModel — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="../index.html"/> + <link rel="up" title="Module code" href="index.html"/> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="../_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="../snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="../index.html">Docs</a> »</li> + + <li><a href="index.html">Module code</a> »</li> + + <li>loadKineticModel</li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <h1>Source code for loadKineticModel</h1><div class="highlight"><pre> +<span class="c"># loadKineticModel.py --- </span> +<span class="c"># </span> +<span class="c"># Filename: loadKineticModel.py</span> +<span class="c"># Description: </span> +<span class="c"># Author: Upi Bhalla </span> +<span class="c"># Maintainer: </span> +<span class="c"># Created: Sat Oct 04 12:14:15 2014 (+0530)</span> +<span class="c"># Version: </span> +<span class="c"># Last-Updated: </span> +<span class="c"># By: </span> +<span class="c"># Update #: 0</span> +<span class="c"># URL: </span> +<span class="c"># Keywords: </span> +<span class="c"># Compatibility: </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Commentary: </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Change log:</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># This program is free software; you can redistribute it and/or</span> +<span class="c"># modify it under the terms of the GNU General Public License as</span> +<span class="c"># published by the Free Software Foundation; either version 3, or</span> +<span class="c"># (at your option) any later version.</span> +<span class="c"># </span> +<span class="c"># This program is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span> +<span class="c"># General Public License for more details.</span> +<span class="c"># </span> +<span class="c"># You should have received a copy of the GNU General Public License</span> +<span class="c"># along with this program; see the file COPYING. If not, write to</span> +<span class="c"># the Free Software Foundation, Inc., 51 Franklin Street, Fifth</span> +<span class="c"># Floor, Boston, MA 02110-1301, USA.</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># Code:</span> + +<span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">sys</span> + +<div class="viewcode-block" id="main"><a class="viewcode-back" href="../snippet.html#loadKineticModel.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates loading, running, and saving a kinetic model </span> +<span class="sd"> defined in kkit format. It uses a default kkit model but you can specify another using the command line ``python filename runtime solver``. We use the gsl solver here. The model already defines a couple of plots and sets the runtime to 20 seconds.</span> +<span class="sd"> """</span> + <span class="n">solver</span> <span class="o">=</span> <span class="s">"gsl"</span> <span class="c"># Pick any of gsl, gssa, ee..</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="s">'../genesis/kkit_objects_example.g'</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="mf">20.0</span> + <span class="k">if</span> <span class="p">(</span> <span class="nb">len</span><span class="p">(</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span> <span class="p">)</span> <span class="o">>=</span> <span class="mi">3</span> <span class="p">):</span> + <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'/'</span><span class="p">:</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="s">'../genesis/'</span> <span class="o">+</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="p">)</span> + <span class="k">if</span> <span class="p">(</span> <span class="nb">len</span><span class="p">(</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span> <span class="p">)</span> <span class="o">==</span> <span class="mi">4</span> <span class="p">):</span> + <span class="n">solver</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> + <span class="n">modelId</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="n">mfile</span><span class="p">,</span> <span class="s">'model'</span><span class="p">,</span> <span class="n">solver</span> <span class="p">)</span> + <span class="c"># Increase volume so that the stochastic solver gssa </span> + <span class="c"># gives an interesting output</span> + <span class="c">#compt = moose.element( '/model/kinetics' )</span> + <span class="c">#compt.volume = 1e-19 </span> + + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="n">runtime</span> <span class="p">)</span> + + <span class="c"># Report parameters</span> + <span class="sd">'''</span> +<span class="sd"> for x in moose.wildcardFind( '/model/kinetics/##[ISA=PoolBase]' ):</span> +<span class="sd"> print x.name, x.nInit, x.concInit</span> +<span class="sd"> for x in moose.wildcardFind( '/model/kinetics/##[ISA=ReacBase]' ):</span> +<span class="sd"> print x.name, 'num: (', x.numKf, ', ', x.numKb, '), conc: (', x.Kf, ', ', x.Kb, ')'</span> +<span class="sd"> for x in moose.wildcardFind('/model/kinetics/##[ISA=EnzBase]'):</span> +<span class="sd"> print x.name, '(', x.Km, ', ', x.numKm, ', ', x.kcat, ')'</span> +<span class="sd"> '''</span> + + <span class="c"># Display all plots.</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/#graphs/conc#/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="o">.</span><span class="n">dt</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span></div> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'../', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/_modules/loadSbmlmodel.html b/docs/user/snippets/_build/html/_modules/loadSbmlmodel.html new file mode 100644 index 0000000000000000000000000000000000000000..d9f15ddddd2321a4bbda606ff21fddb47bbf0f89 --- /dev/null +++ b/docs/user/snippets/_build/html/_modules/loadSbmlmodel.html @@ -0,0 +1,303 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>loadSbmlmodel — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="../index.html"/> + <link rel="up" title="Module code" href="index.html"/> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="../_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="../snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="../index.html">Docs</a> »</li> + + <li><a href="index.html">Module code</a> »</li> + + <li>loadSbmlmodel</li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <h1>Source code for loadSbmlmodel</h1><div class="highlight"><pre> +<span class="c"># -*- coding: utf-8 -*-</span> +<span class="c"># Filename: loadSbmlmodel.py</span> +<span class="c"># Description: </span> +<span class="c"># Author: Harsha rani </span> +<span class="c"># Maintainer: </span> +<span class="c"># Created: Fri Jan 29 11:43:15 2016 (+0530)</span> +<span class="c"># Version: </span> +<span class="c"># Last-Updated: </span> +<span class="c"># By: </span> +<span class="c"># Update #: 0</span> +<span class="c"># URL: </span> +<span class="c"># Keywords: </span> +<span class="c"># Compatibility: </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Commentary: </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> + +<span class="c"># Change log:</span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># </span> +<span class="c"># This program is free software; you can redistribute it and/or</span> +<span class="c"># modify it under the terms of the GNU General Public License as</span> +<span class="c"># published by the Free Software Foundation; either version 3, or</span> +<span class="c"># (at your option) any later version.</span> +<span class="c"># </span> +<span class="c"># This program is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span> +<span class="c"># General Public License for more details.</span> +<span class="c"># </span> + +<span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">matplotlib</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> +<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span> +<span class="kn">import</span> <span class="nn">sys</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">from</span> <span class="nn">moose.SBML</span> <span class="kn">import</span> <span class="o">*</span> +<span class="kn">import</span> <span class="nn">os.path</span> + +<div class="viewcode-block" id="main"><a class="viewcode-back" href="../snippet.html#loadSbmlmodel.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates loading, running of an SBML model defined in XML format.\n</span> +<span class="sd"> The model 00001-sbml-l3v1.xml is taken from l3v1 SBML testcase.\n</span> +<span class="sd"> Plots are setup.\n</span> +<span class="sd"> Model is run for 20sec.\n</span> +<span class="sd"> As a general rule we created model under '/path/model' and plots under '/path/graphs'.\n</span> +<span class="sd"> """</span> + + <span class="n">mfile</span> <span class="o">=</span> <span class="s">"../genesis/00001-sbml-l3v1.xml"</span> + <span class="k">try</span><span class="p">:</span> + <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="k">except</span><span class="p">:</span> + <span class="k">pass</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + + <span class="k">try</span><span class="p">:</span> + <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="k">except</span><span class="p">:</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="mf">20.0</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> + + <span class="c"># Loading the sbml file into MOOSE, models are loaded in path/model</span> + <span class="n">sbmlId</span> <span class="o">=</span> <span class="n">mooseReadSBML</span><span class="p">(</span><span class="n">mfile</span><span class="p">,</span><span class="s">'/sbml'</span><span class="p">)</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sbmlId</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span> + <span class="k">print</span> <span class="n">sbmlId</span> + <span class="k">elif</span> <span class="n">sbmlId</span><span class="o">.</span><span class="n">path</span> <span class="o">!=</span> <span class="s">'/'</span><span class="p">:</span> + + <span class="n">s1</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span><span class="s">'/sbml/model/compartment/S1'</span><span class="p">)</span> + <span class="n">s2</span><span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span><span class="s">'/sbml/model/compartment/S2'</span><span class="p">)</span> + + <span class="c"># Creating MOOSE Table, Table2 is for the chemical model</span> + <span class="n">graphs</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'/sbml/graphs'</span> <span class="p">)</span> + <span class="n">outputs1</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/sbml/graphs/concS1'</span><span class="p">)</span> + <span class="n">outputs2</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/sbml/graphs/concS2'</span><span class="p">)</span> + + <span class="c"># connect up the tables</span> + <span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputs1</span><span class="p">,</span><span class="s">'requestOut'</span><span class="p">,</span> <span class="n">s1</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span> + <span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputs2</span><span class="p">,</span><span class="s">'requestOut'</span><span class="p">,</span> <span class="n">s2</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span> + + + <span class="c"># Reset and Run</span> + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="n">runtime</span><span class="p">)</span> + <span class="k">return</span> <span class="n">sbmlId</span><span class="p">,</span><span class="bp">True</span> + <span class="k">return</span> <span class="n">sbmlId</span><span class="p">,</span><span class="bp">False</span> +</div> +<span class="k">def</span> <span class="nf">displayPlots</span><span class="p">():</span> + <span class="c"># Display all plots.</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/sbml/graphs/#[TYPE=Table2]'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span> + <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> +<span class="k">if</span> <span class="n">__name__</span><span class="o">==</span><span class="s">'__main__'</span><span class="p">:</span> + + <span class="n">modelPath</span><span class="p">,</span> <span class="n">modelpathexist</span> <span class="o">=</span> <span class="n">main</span><span class="p">()</span> + <span class="k">if</span> <span class="n">modelpathexist</span> <span class="o">==</span> <span class="bp">True</span><span class="p">:</span> + <span class="n">displayPlots</span><span class="p">()</span> +</pre></div> + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'../', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/_sources/index.txt b/docs/user/snippets/_build/html/_sources/index.txt new file mode 100644 index 0000000000000000000000000000000000000000..e91f8041fb5e5bde93c3a92d48ef2533fcf25f41 --- /dev/null +++ b/docs/user/snippets/_build/html/_sources/index.txt @@ -0,0 +1,15 @@ +.. MOOSE documentation master file, created by + sphinx-quickstart on Tue Feb 2 14:05:47 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Snippets of MOOSE +================================== +A diverse collection of snippets: (mostly) short code examples illustrating different features of MOOSE + +.. toctree:: + :maxdepth: 2 + :numbered: + + + snippet diff --git a/docs/user/snippets/_build/html/_sources/snippet.txt b/docs/user/snippets/_build/html/_sources/snippet.txt new file mode 100644 index 0000000000000000000000000000000000000000..fff4d674d06b85384ed81dada2a03a1b7a804fb9 --- /dev/null +++ b/docs/user/snippets/_build/html/_sources/snippet.txt @@ -0,0 +1,66 @@ +.. A snippets for MOOSE +.. Lists all the snippets in moose-examples/snippets directory + +MOOSE Snippet +============== + +The MOOSE Snippet contains examples showing you how to do specific +tasks in MOOSE. + +Scripting Parser +---------------- + +Class features +-------------- + +Network Models +-------------- + +Single Neuron Models +--------------------- +Some salient properties of neuronal building blocks in MOOSE are described below. + +Signaling Pathways +------------------ +This section show some of the chemical signaling pathways related settings + +Define a kinetic model using the scripting in moose +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: scriptKineticModel + :members: + +Set up of kinetic solver +^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: scriptKineticSolver + :members: + +Multi scale models +------------------- + +3-D graphics +------------- + +Load-Run-Saving pre-existing model files +---------------------------------------- +This section of the documentation explains how to load-run-save predefined models in MOOSE. + +Load Kinetics Models +^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: loadKineticModel + :members: + +Load SBML Models +^^^^^^^^^^^^^^^^^ +.. automodule:: loadSbmlmodel + :members: + +Load Cspace Models +^^^^^^^^^^^^^^^^^^^ +.. automodule:: loadCspaceModel + :members: + +Save Models to Sbml format +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: convert_Genesis2Sbml + :members: + diff --git a/docs/user/html/pymoose/_static/ajax-loader.gif b/docs/user/snippets/_build/html/_static/ajax-loader.gif similarity index 100% rename from docs/user/html/pymoose/_static/ajax-loader.gif rename to docs/user/snippets/_build/html/_static/ajax-loader.gif diff --git a/docs/user/html/pymoose/_static/basic.css b/docs/user/snippets/_build/html/_static/basic.css similarity index 86% rename from docs/user/html/pymoose/_static/basic.css rename to docs/user/snippets/_build/html/_static/basic.css index 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jQuery JavaScript Library v1.11.1 + * http://jquery.com/ + * + * Includes Sizzle.js + * http://sizzlejs.com/ + * + * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors + * Released under the MIT license + * http://jquery.org/license + * + * Date: 2014-05-01T17:42Z + */ + +(function( global, factory ) { + + if ( typeof module === "object" && typeof module.exports === "object" ) { + // For CommonJS and CommonJS-like environments where a proper window is present, + // execute the factory and get jQuery + // For environments that do not inherently posses a window with a document + // (such as Node.js), expose a jQuery-making factory as module.exports + // This accentuates the need for the creation of a real window + // e.g. var jQuery = require("jquery")(window); + // See ticket #14549 for more info + module.exports = global.document ? + factory( global, true ) : + function( w ) { + if ( !w.document ) { + throw new Error( "jQuery requires a window with a document" ); + } + return factory( w ); + }; + } else { + factory( global ); + } + +// Pass this if window is not defined yet +}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) { + +// Can't do this because several apps including ASP.NET trace +// the stack via arguments.caller.callee and Firefox dies if +// you try to trace through "use strict" call chains. (#13335) +// Support: Firefox 18+ +// + +var deletedIds = []; + +var slice = deletedIds.slice; + +var concat = deletedIds.concat; + +var push = deletedIds.push; + +var indexOf = deletedIds.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var support = {}; + + + +var + version = "1.11.1", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }, + + // Support: Android<4.1, IE<9 + // Make sure we trim BOM and NBSP + rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, + + // Matches dashed string for camelizing + rmsPrefix = /^-ms-/, + rdashAlpha = /-([\da-z])/gi, + + // Used by jQuery.camelCase as callback to replace() + fcamelCase = function( all, letter ) { + return letter.toUpperCase(); + }; + +jQuery.fn = jQuery.prototype = { + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // Start with an empty selector + selector: "", + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + return num != null ? + + // Return just the one element from the set + ( num < 0 ? this[ num + this.length ] : this[ num ] ) : + + // Return all the elements in a clean array + slice.call( this ); + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + ret.context = this.context; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + // (You can seed the arguments with an array of args, but this is + // only used internally.) + each: function( callback, args ) { + return jQuery.each( this, callback, args ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map(this, function( elem, i ) { + return callback.call( elem, i, elem ); + })); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(null); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: deletedIds.sort, + splice: deletedIds.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var src, copyIsArray, copy, name, options, clone, + target = arguments[0] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !jQuery.isFunction(target) ) { + target = {}; + } + + // extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + // Only deal with non-null/undefined values + if ( (options = arguments[ i ]) != null ) { + // Extend the base object + for ( name in options ) { + src = target[ name ]; + copy = options[ name ]; + + // Prevent never-ending loop + if ( target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) { + if ( copyIsArray ) { + copyIsArray = false; + clone = src && jQuery.isArray(src) ? src : []; + + } else { + clone = src && jQuery.isPlainObject(src) ? src : {}; + } + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend({ + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + // See test/unit/core.js for details concerning isFunction. + // Since version 1.3, DOM methods and functions like alert + // aren't supported. They return false on IE (#2968). + isFunction: function( obj ) { + return jQuery.type(obj) === "function"; + }, + + isArray: Array.isArray || function( obj ) { + return jQuery.type(obj) === "array"; + }, + + isWindow: function( obj ) { + /* jshint eqeqeq: false */ + return obj != null && obj == obj.window; + }, + + isNumeric: function( obj ) { + // parseFloat NaNs numeric-cast false positives (null|true|false|"") + // ...but misinterprets leading-number strings, particularly hex literals ("0x...") + // subtraction forces infinities to NaN + return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0; + }, + + isEmptyObject: function( obj ) { + var name; + for ( name in obj ) { + return false; + } + return true; + }, + + isPlainObject: function( obj ) { + var key; + + // Must be an Object. + // Because of IE, we also have to check the presence of the constructor property. + // Make sure that DOM nodes and window objects don't pass through, as well + if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) { + return false; + } + + try { + // Not own constructor property must be Object + if ( obj.constructor && + !hasOwn.call(obj, "constructor") && + !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) { + return false; + } + } catch ( e ) { + // IE8,9 Will throw exceptions on certain host objects #9897 + return false; + } + + // Support: IE<9 + // Handle iteration over inherited properties before own properties. + if ( support.ownLast ) { + for ( key in obj ) { + return hasOwn.call( obj, key ); + } + } + + // Own properties are enumerated firstly, so to speed up, + // if last one is own, then all properties are own. + for ( key in obj ) {} + + return key === undefined || hasOwn.call( obj, key ); + }, + + type: function( obj ) { + if ( obj == null ) { + return obj + ""; + } + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call(obj) ] || "object" : + typeof obj; + }, + + // Evaluates a script in a global context + // Workarounds based on findings by Jim Driscoll + // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context + globalEval: function( data ) { + if ( data && jQuery.trim( data ) ) { + // We use execScript on Internet Explorer + // We use an anonymous function so that context is window + // rather than jQuery in Firefox + ( window.execScript || function( data ) { + window[ "eval" ].call( window, data ); + } )( data ); + } + }, + + // Convert dashed to camelCase; used by the css and data modules + // Microsoft forgot to hump their vendor prefix (#9572) + camelCase: function( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); + }, + + nodeName: function( elem, name ) { + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + }, + + // args is for internal usage only + each: function( obj, callback, args ) { + var value, + i = 0, + length = obj.length, + isArray = isArraylike( obj ); + + if ( args ) { + if ( isArray ) { + for ( ; i < length; i++ ) { + value = callback.apply( obj[ i ], args ); + + if ( value === false ) { + break; + } + } + } else { + for ( i in obj ) { + value = callback.apply( obj[ i ], args ); + + if ( value === false ) { + break; + } + } + } + + // A special, fast, case for the most common use of each + } else { + if ( isArray ) { + for ( ; i < length; i++ ) { + value = callback.call( obj[ i ], i, obj[ i ] ); + + if ( value === false ) { + break; + } + } + } else { + for ( i in obj ) { + value = callback.call( obj[ i ], i, obj[ i ] ); + + if ( value === false ) { + break; + } + } + } + } + + return obj; + }, + + // Support: Android<4.1, IE<9 + trim: function( text ) { + return text == null ? + "" : + ( text + "" ).replace( rtrim, "" ); + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArraylike( Object(arr) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + var len; + + if ( arr ) { + if ( indexOf ) { + return indexOf.call( arr, elem, i ); + } + + len = arr.length; + i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0; + + for ( ; i < len; i++ ) { + // Skip accessing in sparse arrays + if ( i in arr && arr[ i ] === elem ) { + return i; + } + } + } + + return -1; + }, + + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + while ( j < len ) { + first[ i++ ] = second[ j++ ]; + } + + // Support: IE<9 + // Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists) + if ( len !== len ) { + while ( second[j] !== undefined ) { + first[ i++ ] = second[ j++ ]; + } + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var value, + i = 0, + length = elems.length, + isArray = isArraylike( elems ), + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArray ) { + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return concat.apply( [], ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // Bind a function to a context, optionally partially applying any + // arguments. + proxy: function( fn, context ) { + var args, proxy, tmp; + + if ( typeof context === "string" ) { + tmp = fn[ context ]; + context = fn; + fn = tmp; + } + + // Quick check to determine if target is callable, in the spec + // this throws a TypeError, but we will just return undefined. + if ( !jQuery.isFunction( fn ) ) { + return undefined; + } + + // Simulated bind + args = slice.call( arguments, 2 ); + proxy = function() { + return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); + }; + + // Set the guid of unique handler to the same of original handler, so it can be removed + proxy.guid = fn.guid = fn.guid || jQuery.guid++; + + return proxy; + }, + + now: function() { + return +( new Date() ); + }, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +}); + +// Populate the class2type map +jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); +}); + +function isArraylike( obj ) { + var length = obj.length, + type = jQuery.type( obj ); + + if ( type === "function" || jQuery.isWindow( obj ) ) { + return false; + } + + if ( obj.nodeType === 1 && length ) { + return true; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v1.10.19 + * http://sizzlejs.com/ + * + * Copyright 2013 jQuery Foundation, Inc. and other contributors + * Released under the MIT license + * http://jquery.org/license + * + * Date: 2014-04-18 + */ +(function( window ) { + +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + -(new Date()), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // General-purpose constants + strundefined = typeof undefined, + MAX_NEGATIVE = 1 << 31, + + // Instance methods + hasOwn = ({}).hasOwnProperty, + arr = [], + pop = arr.pop, + push_native = arr.push, + push = arr.push, + slice = arr.slice, + // Use a stripped-down indexOf if we can't use a native one + indexOf = arr.indexOf || function( elem ) { + var i = 0, + len = this.length; + for ( ; i < len; i++ ) { + if ( this[i] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + // http://www.w3.org/TR/css3-syntax/#characters + characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+", + + // Loosely modeled on CSS identifier characters + // An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors + // Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier + identifier = characterEncoding.replace( "w", "w#" ), + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + + "*\\]", + + pseudos = ":(" + characterEncoding + ")(?:\\((" + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), + + rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + characterEncoding + ")" ), + "CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ), + "TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + + whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + rescape = /'|\\/g, + + // CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), + funescape = function( _, escaped, escapedWhitespace ) { + var high = "0x" + escaped - 0x10000; + // NaN means non-codepoint + // Support: Firefox<24 + // Workaround erroneous numeric interpretation of +"0x" + return high !== high || escapedWhitespace ? + escaped : + high < 0 ? + // BMP codepoint + String.fromCharCode( high + 0x10000 ) : + // Supplemental Plane codepoint (surrogate pair) + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }; + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + (arr = slice.call( preferredDoc.childNodes )), + preferredDoc.childNodes + ); + // Support: Android<4.0 + // Detect silently failing push.apply + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + push_native.apply( target, slice.call(els) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + // Can't trust NodeList.length + while ( (target[j++] = els[i++]) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var match, elem, m, nodeType, + // QSA vars + i, groups, old, nid, newContext, newSelector; + + if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { + setDocument( context ); + } + + context = context || document; + results = results || []; + + if ( !selector || typeof selector !== "string" ) { + return results; + } + + if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) { + return []; + } + + if ( documentIsHTML && !seed ) { + + // Shortcuts + if ( (match = rquickExpr.exec( selector )) ) { + // Speed-up: Sizzle("#ID") + if ( (m = match[1]) ) { + if ( nodeType === 9 ) { + elem = context.getElementById( m ); + // Check parentNode to catch when Blackberry 4.6 returns + // nodes that are no longer in the document (jQuery #6963) + if ( elem && elem.parentNode ) { + // Handle the case where IE, Opera, and Webkit return items + // by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + } else { + // Context is not a document + if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) && + contains( context, elem ) && elem.id === m ) { + results.push( elem ); + return results; + } + } + + // Speed-up: Sizzle("TAG") + } else if ( match[2] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Speed-up: Sizzle(".CLASS") + } else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) { + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // QSA path + if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { + nid = old = expando; + newContext = context; + newSelector = nodeType === 9 && selector; + + // qSA works strangely on Element-rooted queries + // We can work around this by specifying an extra ID on the root + // and working up from there (Thanks to Andrew Dupont for the technique) + // IE 8 doesn't work on object elements + if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) { + groups = tokenize( selector ); + + if ( (old = context.getAttribute("id")) ) { + nid = old.replace( rescape, "\\$&" ); + } else { + context.setAttribute( "id", nid ); + } + nid = "[id='" + nid + "'] "; + + i = groups.length; + while ( i-- ) { + groups[i] = nid + toSelector( groups[i] ); + } + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context; + newSelector = groups.join(","); + } + + if ( newSelector ) { + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch(qsaError) { + } finally { + if ( !old ) { + context.removeAttribute("id"); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {Function(string, Object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return (cache[ key + " " ] = value); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created div and expects a boolean result + */ +function assert( fn ) { + var div = document.createElement("div"); + + try { + return !!fn( div ); + } catch (e) { + return false; + } finally { + // Remove from its parent by default + if ( div.parentNode ) { + div.parentNode.removeChild( div ); + } + // release memory in IE + div = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split("|"), + i = attrs.length; + + while ( i-- ) { + Expr.attrHandle[ arr[i] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + ( ~b.sourceIndex || MAX_NEGATIVE ) - + ( ~a.sourceIndex || MAX_NEGATIVE ); + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( (cur = cur.nextSibling) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return (name === "input" || name === "button") && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction(function( argument ) { + argument = +argument; + return markFunction(function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ (j = matchIndexes[i]) ] ) { + seed[j] = !(matches[j] = seed[j]); + } + } + }); + }); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== strundefined && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + // documentElement is verified for cases where it doesn't yet exist + // (such as loading iframes in IE - #4833) + var documentElement = elem && (elem.ownerDocument || elem).documentElement; + return documentElement ? documentElement.nodeName !== "HTML" : false; +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, + doc = node ? node.ownerDocument || node : preferredDoc, + parent = doc.defaultView; + + // If no document and documentElement is available, return + if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Set our document + document = doc; + docElem = doc.documentElement; + + // Support tests + documentIsHTML = !isXML( doc ); + + // Support: IE>8 + // If iframe document is assigned to "document" variable and if iframe has been reloaded, + // IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936 + // IE6-8 do not support the defaultView property so parent will be undefined + if ( parent && parent !== parent.top ) { + // IE11 does not have attachEvent, so all must suffer + if ( parent.addEventListener ) { + parent.addEventListener( "unload", function() { + setDocument(); + }, false ); + } else if ( parent.attachEvent ) { + parent.attachEvent( "onunload", function() { + setDocument(); + }); + } + } + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans) + support.attributes = assert(function( div ) { + div.className = "i"; + return !div.getAttribute("className"); + }); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert(function( div ) { + div.appendChild( doc.createComment("") ); + return !div.getElementsByTagName("*").length; + }); + + // Check if getElementsByClassName can be trusted + support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) { + div.innerHTML = "<div class='a'></div><div class='a i'></div>"; + + // Support: Safari<4 + // Catch class over-caching + div.firstChild.className = "i"; + // Support: Opera<10 + // Catch gEBCN failure to find non-leading classes + return div.getElementsByClassName("i").length === 2; + }); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert(function( div ) { + docElem.appendChild( div ).id = expando; + return !doc.getElementsByName || !doc.getElementsByName( expando ).length; + }); + + // ID find and filter + if ( support.getById ) { + Expr.find["ID"] = function( id, context ) { + if ( typeof context.getElementById !== strundefined && documentIsHTML ) { + var m = context.getElementById( id ); + // Check parentNode to catch when Blackberry 4.6 returns + // nodes that are no longer in the document #6963 + return m && m.parentNode ? [ m ] : []; + } + }; + Expr.filter["ID"] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute("id") === attrId; + }; + }; + } else { + // Support: IE6/7 + // getElementById is not reliable as a find shortcut + delete Expr.find["ID"]; + + Expr.filter["ID"] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id"); + return node && node.value === attrId; + }; + }; + } + + // Tag + Expr.find["TAG"] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== strundefined ) { + return context.getElementsByTagName( tag ); + } + } : + function( tag, context ) { + var elem, + tmp = [], + i = 0, + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( (elem = results[i++]) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See http://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) { + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert(function( div ) { + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // http://bugs.jquery.com/ticket/12359 + div.innerHTML = "<select msallowclip=''><option selected=''></option></select>"; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( div.querySelectorAll("[msallowclip^='']").length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !div.querySelectorAll("[selected]").length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !div.querySelectorAll(":checked").length ) { + rbuggyQSA.push(":checked"); + } + }); + + assert(function( div ) { + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = doc.createElement("input"); + input.setAttribute( "type", "hidden" ); + div.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( div.querySelectorAll("[name=d]").length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( !div.querySelectorAll(":enabled").length ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Opera 10-11 does not throw on post-comma invalid pseudos + div.querySelectorAll("*,:x"); + rbuggyQSA.push(",.*:"); + }); + } + + if ( (support.matchesSelector = rnative.test( (matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector) )) ) { + + assert(function( div ) { + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( div, "div" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( div, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + }); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully does not implement inclusive descendent + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + )); + } : + function( a, b ) { + if ( b ) { + while ( (b = b.parentNode) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) { + + // Choose the first element that is related to our preferred document + if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) { + return -1; + } + if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + return a === doc ? -1 : + b === doc ? 1 : + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( (cur = cur.parentNode) ) { + ap.unshift( cur ); + } + cur = b; + while ( (cur = cur.parentNode) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[i] === bp[i] ) { + i++; + } + + return i ? + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[i], bp[i] ) : + + // Otherwise nodes in our document sort first + ap[i] === preferredDoc ? -1 : + bp[i] === preferredDoc ? 1 : + 0; + }; + + return doc; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + // Set document vars if needed + if ( ( elem.ownerDocument || elem ) !== document ) { + setDocument( elem ); + } + + // Make sure that attribute selectors are quoted + expr = expr.replace( rattributeQuotes, "='$1']" ); + + if ( support.matchesSelector && documentIsHTML && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch(e) {} + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + // Set document vars if needed + if ( ( context.ownerDocument || context ) !== document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + // Set document vars if needed + if ( ( elem.ownerDocument || elem ) !== document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + (val = elem.getAttributeNode(name)) && val.specified ? + val.value : + null; +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( (elem = results[i++]) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + // If no nodeType, this is expected to be an array + while ( (node = elem[i++]) ) { + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[1] = match[1].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape ); + + if ( match[2] === "~=" ) { + match[3] = " " + match[3] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[1] = match[1].toLowerCase(); + + if ( match[1].slice( 0, 3 ) === "nth" ) { + // nth-* requires argument + if ( !match[3] ) { + Sizzle.error( match[0] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) ); + match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" ); + + // other types prohibit arguments + } else if ( match[3] ) { + Sizzle.error( match[0] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[6] && match[2]; + + if ( matchExpr["CHILD"].test( match[0] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[3] ) { + match[2] = match[4] || match[5] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + // Get excess from tokenize (recursively) + (excess = tokenize( unquoted, true )) && + // advance to the next closing parenthesis + (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) { + + // excess is a negative index + match[0] = match[0].slice( 0, excess ); + match[2] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { return true; } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && + classCache( className, function( elem ) { + return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" ); + }); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + }; + }, + + "CHILD": function( type, what, argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, context, xml ) { + var cache, outerCache, node, diff, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( (node = node[ dir ]) ) { + if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) { + return false; + } + } + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + // Seek `elem` from a previously-cached index + outerCache = parent[ expando ] || (parent[ expando ] = {}); + cache = outerCache[ type ] || []; + nodeIndex = cache[0] === dirruns && cache[1]; + diff = cache[0] === dirruns && cache[2]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( (node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + (diff = nodeIndex = 0) || start.pop()) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + outerCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + // Use previously-cached element index if available + } else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) { + diff = cache[1]; + + // xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...) + } else { + // Use the same loop as above to seek `elem` from the start + while ( (node = ++nodeIndex && node && node[ dir ] || + (diff = nodeIndex = 0) || start.pop()) ) { + + if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) { + // Cache the index of each encountered element + if ( useCache ) { + (node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction(function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf.call( seed, matched[i] ); + seed[ idx ] = !( matches[ idx ] = matched[i] ); + } + }) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + // Potentially complex pseudos + "not": markFunction(function( selector ) { + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction(function( seed, matches, context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( (elem = unmatched[i]) ) { + seed[i] = !(matches[i] = elem); + } + } + }) : + function( elem, context, xml ) { + input[0] = elem; + matcher( input, null, xml, results ); + return !results.pop(); + }; + }), + + "has": markFunction(function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + }), + + "contains": markFunction(function( text ) { + return function( elem ) { + return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; + }; + }), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + // lang value must be a valid identifier + if ( !ridentifier.test(lang || "") ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( (elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( (elem = elem.parentNode) && elem.nodeType === 1 ); + return false; + }; + }), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex); + }, + + // Boolean properties + "enabled": function( elem ) { + return elem.disabled === false; + }, + + "disabled": function( elem ) { + return elem.disabled === true; + }, + + "checked": function( elem ) { + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected); + }, + + "selected": function( elem ) { + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos["empty"]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo(function() { + return [ 0 ]; + }), + + "last": createPositionalPseudo(function( matchIndexes, length ) { + return [ length - 1 ]; + }), + + "eq": createPositionalPseudo(function( matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + }), + + "even": createPositionalPseudo(function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "odd": createPositionalPseudo(function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "lt": createPositionalPseudo(function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "gt": createPositionalPseudo(function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + }) + } +}; + +Expr.pseudos["nth"] = Expr.pseudos["eq"]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || (match = rcomma.exec( soFar )) ) { + if ( match ) { + // Don't consume trailing commas as valid + soFar = soFar.slice( match[0].length ) || soFar; + } + groups.push( (tokens = []) ); + } + + matched = false; + + // Combinators + if ( (match = rcombinators.exec( soFar )) ) { + matched = match.shift(); + tokens.push({ + value: matched, + // Cast descendant combinators to space + type: match[0].replace( rtrim, " " ) + }); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] || + (match = preFilters[ type ]( match ))) ) { + matched = match.shift(); + tokens.push({ + value: matched, + type: type, + matches: match + }); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[i].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + checkNonElements = base && dir === "parentNode", + doneName = done++; + + return combinator.first ? + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from dir caching + if ( xml ) { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || (elem[ expando ] = {}); + if ( (oldCache = outerCache[ dir ]) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return (newCache[ 2 ] = oldCache[ 2 ]); + } else { + // Reuse newcache so results back-propagate to previous elements + outerCache[ dir ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) { + return true; + } + } + } + } + } + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[i]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[0]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[i], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( (elem = unmatched[i]) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction(function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( (elem = temp[i]) ) { + matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( (elem = matcherOut[i]) ) { + // Restore matcherIn since elem is not yet a final match + temp.push( (matcherIn[i] = elem) ); + } + } + postFinder( null, (matcherOut = []), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( (elem = matcherOut[i]) && + (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) { + + seed[temp] = !(results[temp] = elem); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + }); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[0].type ], + implicitRelative = leadingRelative || Expr.relative[" "], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf.call( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + return ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + (checkContext = context).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + } ]; + + for ( ; i < len; i++ ) { + if ( (matcher = Expr.relative[ tokens[i].type ]) ) { + matchers = [ addCombinator(elementMatcher( matchers ), matcher) ]; + } else { + matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[j].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" }) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( (tokens = tokens.slice( j )) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find["TAG"]( "*", outermost ), + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1), + len = elems.length; + + if ( outermost ) { + outermostContext = context !== document && context; + } + + // Add elements passing elementMatchers directly to results + // Keep `i` a string if there are no elements so `matchedCount` will be "00" below + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id + for ( ; i !== len && (elem = elems[i]) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + while ( (matcher = elementMatchers[j++]) ) { + if ( matcher( elem, context, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + // They will have gone through all possible matchers + if ( (elem = !matcher && elem) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // Apply set filters to unmatched elements + matchedCount += i; + if ( bySet && i !== matchedCount ) { + j = 0; + while ( (matcher = setMatchers[j++]) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !(unmatched[i] || setMatched[i]) ) { + setMatched[i] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[i] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( (selector = compiled.selector || selector) ); + + results = results || []; + + // Try to minimize operations if there is no seed and only one group + if ( match.length === 1 ) { + + // Take a shortcut and set the context if the root selector is an ID + tokens = match[0] = match[0].slice( 0 ); + if ( tokens.length > 2 && (token = tokens[0]).type === "ID" && + support.getById && context.nodeType === 9 && documentIsHTML && + Expr.relative[ tokens[1].type ] ) { + + context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[i]; + + // Abort if we hit a combinator + if ( Expr.relative[ (type = token.type) ] ) { + break; + } + if ( (find = Expr.find[ type ]) ) { + // Search, expanding context for leading sibling combinators + if ( (seed = find( + token.matches[0].replace( runescape, funescape ), + rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context + )) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; + +// Support: Chrome<14 +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert(function( div1 ) { + // Should return 1, but returns 4 (following) + return div1.compareDocumentPosition( document.createElement("div") ) & 1; +}); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert(function( div ) { + div.innerHTML = "<a href='#'></a>"; + return div.firstChild.getAttribute("href") === "#" ; +}) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + }); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert(function( div ) { + div.innerHTML = "<input/>"; + div.firstChild.setAttribute( "value", "" ); + return div.firstChild.getAttribute( "value" ) === ""; +}) ) { + addHandle( "value", function( elem, name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + }); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert(function( div ) { + return div.getAttribute("disabled") == null; +}) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + (val = elem.getAttributeNode( name )) && val.specified ? + val.value : + null; + } + }); +} + +return Sizzle; + +})( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; +jQuery.expr[":"] = jQuery.expr.pseudos; +jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; + + + +var rneedsContext = jQuery.expr.match.needsContext; + +var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/); + + + +var risSimple = /^.[^:#\[\.,]*$/; + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( jQuery.isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + /* jshint -W018 */ + return !!qualifier.call( elem, i, elem ) !== not; + }); + + } + + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + }); + + } + + if ( typeof qualifier === "string" ) { + if ( risSimple.test( qualifier ) ) { + return jQuery.filter( qualifier, elements, not ); + } + + qualifier = jQuery.filter( qualifier, elements ); + } + + return jQuery.grep( elements, function( elem ) { + return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not; + }); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + return elems.length === 1 && elem.nodeType === 1 ? + jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] : + jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + })); +}; + +jQuery.fn.extend({ + find: function( selector ) { + var i, + ret = [], + self = this, + len = self.length; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter(function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + }) ); + } + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + // Needed because $( selector, context ) becomes $( context ).find( selector ) + ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret ); + ret.selector = this.selector ? this.selector + " " + selector : selector; + return ret; + }, + filter: function( selector ) { + return this.pushStack( winnow(this, selector || [], false) ); + }, + not: function( selector ) { + return this.pushStack( winnow(this, selector || [], true) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +}); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // Use the correct document accordingly with window argument (sandbox) + document = window.document, + + // A simple way to check for HTML strings + // Prioritize #id over <tag> to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/, + + init = jQuery.fn.init = function( selector, context ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) { + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && (match[1] || !context) ) { + + // HANDLE: $(html) -> $(array) + if ( match[1] ) { + context = context instanceof jQuery ? context[0] : context; + + // scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[1], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + // Properties of context are called as methods if possible + if ( jQuery.isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[2] ); + + // Check parentNode to catch when Blackberry 4.6 returns + // nodes that are no longer in the document #6963 + if ( elem && elem.parentNode ) { + // Handle the case where IE and Opera return items + // by name instead of ID + if ( elem.id !== match[2] ) { + return rootjQuery.find( selector ); + } + + // Otherwise, we inject the element directly into the jQuery object + this.length = 1; + this[0] = elem; + } + + this.context = document; + this.selector = selector; + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || rootjQuery ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this.context = this[0] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( jQuery.isFunction( selector ) ) { + return typeof rootjQuery.ready !== "undefined" ? + rootjQuery.ready( selector ) : + // Execute immediately if ready is not present + selector( jQuery ); + } + + if ( selector.selector !== undefined ) { + this.selector = selector.selector; + this.context = selector.context; + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + // methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.extend({ + dir: function( elem, dir, until ) { + var matched = [], + cur = elem[ dir ]; + + while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) { + if ( cur.nodeType === 1 ) { + matched.push( cur ); + } + cur = cur[dir]; + } + return matched; + }, + + sibling: function( n, elem ) { + var r = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + r.push( n ); + } + } + + return r; + } +}); + +jQuery.fn.extend({ + has: function( target ) { + var i, + targets = jQuery( target, this ), + len = targets.length; + + return this.filter(function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( this, targets[i] ) ) { + return true; + } + } + }); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ? + jQuery( selectors, context || this.context ) : + 0; + + for ( ; i < l; i++ ) { + for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) { + // Always skip document fragments + if ( cur.nodeType < 11 && (pos ? + pos.index(cur) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector(cur, selectors)) ) { + + matched.push( cur ); + break; + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched ); + }, + + // Determine the position of an element within + // the matched set of elements + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1; + } + + // index in selector + if ( typeof elem === "string" ) { + return jQuery.inArray( this[0], jQuery( elem ) ); + } + + // Locate the position of the desired element + return jQuery.inArray( + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[0] : elem, this ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.unique( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter(selector) + ); + } +}); + +function sibling( cur, dir ) { + do { + cur = cur[ dir ]; + } while ( cur && cur.nodeType !== 1 ); + + return cur; +} + +jQuery.each({ + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return jQuery.dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, i, until ) { + return jQuery.dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return jQuery.dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return jQuery.dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, i, until ) { + return jQuery.dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, i, until ) { + return jQuery.dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return jQuery.sibling( elem.firstChild ); + }, + contents: function( elem ) { + return jQuery.nodeName( elem, "iframe" ) ? + elem.contentDocument || elem.contentWindow.document : + jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var ret = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + ret = jQuery.filter( selector, ret ); + } + + if ( this.length > 1 ) { + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + ret = jQuery.unique( ret ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + ret = ret.reverse(); + } + } + + return this.pushStack( ret ); + }; +}); +var rnotwhite = (/\S+/g); + + + +// String to Object options format cache +var optionsCache = {}; + +// Convert String-formatted options into Object-formatted ones and store in cache +function createOptions( options ) { + var object = optionsCache[ options ] = {}; + jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) { + object[ flag ] = true; + }); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + ( optionsCache[ options ] || createOptions( options ) ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + // Last fire value (for non-forgettable lists) + memory, + // Flag to know if list was already fired + fired, + // End of the loop when firing + firingLength, + // Index of currently firing callback (modified by remove if needed) + firingIndex, + // First callback to fire (used internally by add and fireWith) + firingStart, + // Actual callback list + list = [], + // Stack of fire calls for repeatable lists + stack = !options.once && [], + // Fire callbacks + fire = function( data ) { + memory = options.memory && data; + fired = true; + firingIndex = firingStart || 0; + firingStart = 0; + firingLength = list.length; + firing = true; + for ( ; list && firingIndex < firingLength; firingIndex++ ) { + if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) { + memory = false; // To prevent further calls using add + break; + } + } + firing = false; + if ( list ) { + if ( stack ) { + if ( stack.length ) { + fire( stack.shift() ); + } + } else if ( memory ) { + list = []; + } else { + self.disable(); + } + } + }, + // Actual Callbacks object + self = { + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + // First, we save the current length + var start = list.length; + (function add( args ) { + jQuery.each( args, function( _, arg ) { + var type = jQuery.type( arg ); + if ( type === "function" ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && type !== "string" ) { + // Inspect recursively + add( arg ); + } + }); + })( arguments ); + // Do we need to add the callbacks to the + // current firing batch? + if ( firing ) { + firingLength = list.length; + // With memory, if we're not firing then + // we should call right away + } else if ( memory ) { + firingStart = start; + fire( memory ); + } + } + return this; + }, + // Remove a callback from the list + remove: function() { + if ( list ) { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + // Handle firing indexes + if ( firing ) { + if ( index <= firingLength ) { + firingLength--; + } + if ( index <= firingIndex ) { + firingIndex--; + } + } + } + }); + } + return this; + }, + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length ); + }, + // Remove all callbacks from the list + empty: function() { + list = []; + firingLength = 0; + return this; + }, + // Have the list do nothing anymore + disable: function() { + list = stack = memory = undefined; + return this; + }, + // Is it disabled? + disabled: function() { + return !list; + }, + // Lock the list in its current state + lock: function() { + stack = undefined; + if ( !memory ) { + self.disable(); + } + return this; + }, + // Is it locked? + locked: function() { + return !stack; + }, + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( list && ( !fired || stack ) ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + if ( firing ) { + stack.push( args ); + } else { + fire( args ); + } + } + return this; + }, + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +jQuery.extend({ + + Deferred: function( func ) { + var tuples = [ + // action, add listener, listener list, final state + [ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ], + [ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ], + [ "notify", "progress", jQuery.Callbacks("memory") ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + then: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + return jQuery.Deferred(function( newDefer ) { + jQuery.each( tuples, function( i, tuple ) { + var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ]; + // deferred[ done | fail | progress ] for forwarding actions to newDefer + deferred[ tuple[1] ](function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && jQuery.isFunction( returned.promise ) ) { + returned.promise() + .done( newDefer.resolve ) + .fail( newDefer.reject ) + .progress( newDefer.notify ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments ); + } + }); + }); + fns = null; + }).promise(); + }, + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Keep pipe for back-compat + promise.pipe = promise.then; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 3 ]; + + // promise[ done | fail | progress ] = list.add + promise[ tuple[1] ] = list.add; + + // Handle state + if ( stateString ) { + list.add(function() { + // state = [ resolved | rejected ] + state = stateString; + + // [ reject_list | resolve_list ].disable; progress_list.lock + }, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock ); + } + + // deferred[ resolve | reject | notify ] + deferred[ tuple[0] ] = function() { + deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments ); + return this; + }; + deferred[ tuple[0] + "With" ] = list.fireWith; + }); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( subordinate /* , ..., subordinateN */ ) { + var i = 0, + resolveValues = slice.call( arguments ), + length = resolveValues.length, + + // the count of uncompleted subordinates + remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0, + + // the master Deferred. If resolveValues consist of only a single Deferred, just use that. + deferred = remaining === 1 ? subordinate : jQuery.Deferred(), + + // Update function for both resolve and progress values + updateFunc = function( i, contexts, values ) { + return function( value ) { + contexts[ i ] = this; + values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( values === progressValues ) { + deferred.notifyWith( contexts, values ); + + } else if ( !(--remaining) ) { + deferred.resolveWith( contexts, values ); + } + }; + }, + + progressValues, progressContexts, resolveContexts; + + // add listeners to Deferred subordinates; treat others as resolved + if ( length > 1 ) { + progressValues = new Array( length ); + progressContexts = new Array( length ); + resolveContexts = new Array( length ); + for ( ; i < length; i++ ) { + if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) { + resolveValues[ i ].promise() + .done( updateFunc( i, resolveContexts, resolveValues ) ) + .fail( deferred.reject ) + .progress( updateFunc( i, progressContexts, progressValues ) ); + } else { + --remaining; + } + } + } + + // if we're not waiting on anything, resolve the master + if ( !remaining ) { + deferred.resolveWith( resolveContexts, resolveValues ); + } + + return deferred.promise(); + } +}); + + +// The deferred used on DOM ready +var readyList; + +jQuery.fn.ready = function( fn ) { + // Add the callback + jQuery.ready.promise().done( fn ); + + return this; +}; + +jQuery.extend({ + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Hold (or release) the ready event + holdReady: function( hold ) { + if ( hold ) { + jQuery.readyWait++; + } else { + jQuery.ready( true ); + } + }, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). + if ( !document.body ) { + return setTimeout( jQuery.ready ); + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + + // Trigger any bound ready events + if ( jQuery.fn.triggerHandler ) { + jQuery( document ).triggerHandler( "ready" ); + jQuery( document ).off( "ready" ); + } + } +}); + +/** + * Clean-up method for dom ready events + */ +function detach() { + if ( document.addEventListener ) { + document.removeEventListener( "DOMContentLoaded", completed, false ); + window.removeEventListener( "load", completed, false ); + + } else { + document.detachEvent( "onreadystatechange", completed ); + window.detachEvent( "onload", completed ); + } +} + +/** + * The ready event handler and self cleanup method + */ +function completed() { + // readyState === "complete" is good enough for us to call the dom ready in oldIE + if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) { + detach(); + jQuery.ready(); + } +} + +jQuery.ready.promise = function( obj ) { + if ( !readyList ) { + + readyList = jQuery.Deferred(); + + // Catch cases where $(document).ready() is called after the browser event has already occurred. + // we once tried to use readyState "interactive" here, but it caused issues like the one + // discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15 + if ( document.readyState === "complete" ) { + // Handle it asynchronously to allow scripts the opportunity to delay ready + setTimeout( jQuery.ready ); + + // Standards-based browsers support DOMContentLoaded + } else if ( document.addEventListener ) { + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed, false ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed, false ); + + // If IE event model is used + } else { + // Ensure firing before onload, maybe late but safe also for iframes + document.attachEvent( "onreadystatechange", completed ); + + // A fallback to window.onload, that will always work + window.attachEvent( "onload", completed ); + + // If IE and not a frame + // continually check to see if the document is ready + var top = false; + + try { + top = window.frameElement == null && document.documentElement; + } catch(e) {} + + if ( top && top.doScroll ) { + (function doScrollCheck() { + if ( !jQuery.isReady ) { + + try { + // Use the trick by Diego Perini + // http://javascript.nwbox.com/IEContentLoaded/ + top.doScroll("left"); + } catch(e) { + return setTimeout( doScrollCheck, 50 ); + } + + // detach all dom ready events + detach(); + + // and execute any waiting functions + jQuery.ready(); + } + })(); + } + } + } + return readyList.promise( obj ); +}; + + +var strundefined = typeof undefined; + + + +// Support: IE<9 +// Iteration over object's inherited properties before its own +var i; +for ( i in jQuery( support ) ) { + break; +} +support.ownLast = i !== "0"; + +// Note: most support tests are defined in their respective modules. +// false until the test is run +support.inlineBlockNeedsLayout = false; + +// Execute ASAP in case we need to set body.style.zoom +jQuery(function() { + // Minified: var a,b,c,d + var val, div, body, container; + + body = document.getElementsByTagName( "body" )[ 0 ]; + if ( !body || !body.style ) { + // Return for frameset docs that don't have a body + return; + } + + // Setup + div = document.createElement( "div" ); + container = document.createElement( "div" ); + container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px"; + body.appendChild( container ).appendChild( div ); + + if ( typeof div.style.zoom !== strundefined ) { + // Support: IE<8 + // Check if natively block-level elements act like inline-block + // elements when setting their display to 'inline' and giving + // them layout + div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1"; + + support.inlineBlockNeedsLayout = val = div.offsetWidth === 3; + if ( val ) { + // Prevent IE 6 from affecting layout for positioned elements #11048 + // Prevent IE from shrinking the body in IE 7 mode #12869 + // Support: IE<8 + body.style.zoom = 1; + } + } + + body.removeChild( container ); +}); + + + + +(function() { + var div = document.createElement( "div" ); + + // Execute the test only if not already executed in another module. + if (support.deleteExpando == null) { + // Support: IE<9 + support.deleteExpando = true; + try { + delete div.test; + } catch( e ) { + support.deleteExpando = false; + } + } + + // Null elements to avoid leaks in IE. + div = null; +})(); + + +/** + * Determines whether an object can have data + */ +jQuery.acceptData = function( elem ) { + var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ], + nodeType = +elem.nodeType || 1; + + // Do not set data on non-element DOM nodes because it will not be cleared (#8335). + return nodeType !== 1 && nodeType !== 9 ? + false : + + // Nodes accept data unless otherwise specified; rejection can be conditional + !noData || noData !== true && elem.getAttribute("classid") === noData; +}; + + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /([A-Z])/g; + +function dataAttr( elem, key, data ) { + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + + var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase(); + + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = data === "true" ? true : + data === "false" ? false : + data === "null" ? null : + // Only convert to a number if it doesn't change the string + +data + "" === data ? +data : + rbrace.test( data ) ? jQuery.parseJSON( data ) : + data; + } catch( e ) {} + + // Make sure we set the data so it isn't changed later + jQuery.data( elem, key, data ); + + } else { + data = undefined; + } + } + + return data; +} + +// checks a cache object for emptiness +function isEmptyDataObject( obj ) { + var name; + for ( name in obj ) { + + // if the public data object is empty, the private is still empty + if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) { + continue; + } + if ( name !== "toJSON" ) { + return false; + } + } + + return true; +} + +function internalData( elem, name, data, pvt /* Internal Use Only */ ) { + if ( !jQuery.acceptData( elem ) ) { + return; + } + + var ret, thisCache, + internalKey = jQuery.expando, + + // We have to handle DOM nodes and JS objects differently because IE6-7 + // can't GC object references properly across the DOM-JS boundary + isNode = elem.nodeType, + + // Only DOM nodes need the global jQuery cache; JS object data is + // attached directly to the object so GC can occur automatically + cache = isNode ? jQuery.cache : elem, + + // Only defining an ID for JS objects if its cache already exists allows + // the code to shortcut on the same path as a DOM node with no cache + id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey; + + // Avoid doing any more work than we need to when trying to get data on an + // object that has no data at all + if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) { + return; + } + + if ( !id ) { + // Only DOM nodes need a new unique ID for each element since their data + // ends up in the global cache + if ( isNode ) { + id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++; + } else { + id = internalKey; + } + } + + if ( !cache[ id ] ) { + // Avoid exposing jQuery metadata on plain JS objects when the object + // is serialized using JSON.stringify + cache[ id ] = isNode ? {} : { toJSON: jQuery.noop }; + } + + // An object can be passed to jQuery.data instead of a key/value pair; this gets + // shallow copied over onto the existing cache + if ( typeof name === "object" || typeof name === "function" ) { + if ( pvt ) { + cache[ id ] = jQuery.extend( cache[ id ], name ); + } else { + cache[ id ].data = jQuery.extend( cache[ id ].data, name ); + } + } + + thisCache = cache[ id ]; + + // jQuery data() is stored in a separate object inside the object's internal data + // cache in order to avoid key collisions between internal data and user-defined + // data. + if ( !pvt ) { + if ( !thisCache.data ) { + thisCache.data = {}; + } + + thisCache = thisCache.data; + } + + if ( data !== undefined ) { + thisCache[ jQuery.camelCase( name ) ] = data; + } + + // Check for both converted-to-camel and non-converted data property names + // If a data property was specified + if ( typeof name === "string" ) { + + // First Try to find as-is property data + ret = thisCache[ name ]; + + // Test for null|undefined property data + if ( ret == null ) { + + // Try to find the camelCased property + ret = thisCache[ jQuery.camelCase( name ) ]; + } + } else { + ret = thisCache; + } + + return ret; +} + +function internalRemoveData( elem, name, pvt ) { + if ( !jQuery.acceptData( elem ) ) { + return; + } + + var thisCache, i, + isNode = elem.nodeType, + + // See jQuery.data for more information + cache = isNode ? jQuery.cache : elem, + id = isNode ? elem[ jQuery.expando ] : jQuery.expando; + + // If there is already no cache entry for this object, there is no + // purpose in continuing + if ( !cache[ id ] ) { + return; + } + + if ( name ) { + + thisCache = pvt ? cache[ id ] : cache[ id ].data; + + if ( thisCache ) { + + // Support array or space separated string names for data keys + if ( !jQuery.isArray( name ) ) { + + // try the string as a key before any manipulation + if ( name in thisCache ) { + name = [ name ]; + } else { + + // split the camel cased version by spaces unless a key with the spaces exists + name = jQuery.camelCase( name ); + if ( name in thisCache ) { + name = [ name ]; + } else { + name = name.split(" "); + } + } + } else { + // If "name" is an array of keys... + // When data is initially created, via ("key", "val") signature, + // keys will be converted to camelCase. + // Since there is no way to tell _how_ a key was added, remove + // both plain key and camelCase key. #12786 + // This will only penalize the array argument path. + name = name.concat( jQuery.map( name, jQuery.camelCase ) ); + } + + i = name.length; + while ( i-- ) { + delete thisCache[ name[i] ]; + } + + // If there is no data left in the cache, we want to continue + // and let the cache object itself get destroyed + if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) { + return; + } + } + } + + // See jQuery.data for more information + if ( !pvt ) { + delete cache[ id ].data; + + // Don't destroy the parent cache unless the internal data object + // had been the only thing left in it + if ( !isEmptyDataObject( cache[ id ] ) ) { + return; + } + } + + // Destroy the cache + if ( isNode ) { + jQuery.cleanData( [ elem ], true ); + + // Use delete when supported for expandos or `cache` is not a window per isWindow (#10080) + /* jshint eqeqeq: false */ + } else if ( support.deleteExpando || cache != cache.window ) { + /* jshint eqeqeq: true */ + delete cache[ id ]; + + // When all else fails, null + } else { + cache[ id ] = null; + } +} + +jQuery.extend({ + cache: {}, + + // The following elements (space-suffixed to avoid Object.prototype collisions) + // throw uncatchable exceptions if you attempt to set expando properties + noData: { + "applet ": true, + "embed ": true, + // ...but Flash objects (which have this classid) *can* handle expandos + "object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" + }, + + hasData: function( elem ) { + elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ]; + return !!elem && !isEmptyDataObject( elem ); + }, + + data: function( elem, name, data ) { + return internalData( elem, name, data ); + }, + + removeData: function( elem, name ) { + return internalRemoveData( elem, name ); + }, + + // For internal use only. + _data: function( elem, name, data ) { + return internalData( elem, name, data, true ); + }, + + _removeData: function( elem, name ) { + return internalRemoveData( elem, name, true ); + } +}); + +jQuery.fn.extend({ + data: function( key, value ) { + var i, name, data, + elem = this[0], + attrs = elem && elem.attributes; + + // Special expections of .data basically thwart jQuery.access, + // so implement the relevant behavior ourselves + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = jQuery.data( elem ); + + if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE11+ + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = jQuery.camelCase( name.slice(5) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + jQuery._data( elem, "parsedAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each(function() { + jQuery.data( this, key ); + }); + } + + return arguments.length > 1 ? + + // Sets one value + this.each(function() { + jQuery.data( this, key, value ); + }) : + + // Gets one value + // Try to fetch any internally stored data first + elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined; + }, + + removeData: function( key ) { + return this.each(function() { + jQuery.removeData( this, key ); + }); + } +}); + + +jQuery.extend({ + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = jQuery._data( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || jQuery.isArray(data) ) { + queue = jQuery._data( elem, type, jQuery.makeArray(data) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // not intended for public consumption - generates a queueHooks object, or returns the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return jQuery._data( elem, key ) || jQuery._data( elem, key, { + empty: jQuery.Callbacks("once memory").add(function() { + jQuery._removeData( elem, type + "queue" ); + jQuery._removeData( elem, key ); + }) + }); + } +}); + +jQuery.fn.extend({ + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[0], type ); + } + + return data === undefined ? + this : + this.each(function() { + var queue = jQuery.queue( this, type, data ); + + // ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[0] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + }); + }, + dequeue: function( type ) { + return this.each(function() { + jQuery.dequeue( this, type ); + }); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = jQuery._data( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +}); +var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source; + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var isHidden = function( elem, el ) { + // isHidden might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem ); + }; + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + length = elems.length, + bulk = key == null; + + // Sets many values + if ( jQuery.type( key ) === "object" ) { + chainable = true; + for ( i in key ) { + jQuery.access( elems, fn, i, key[i], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !jQuery.isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < length; i++ ) { + fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) ); + } + } + } + + return chainable ? + elems : + + // Gets + bulk ? + fn.call( elems ) : + length ? fn( elems[0], key ) : emptyGet; +}; +var rcheckableType = (/^(?:checkbox|radio)$/i); + + + +(function() { + // Minified: var a,b,c + var input = document.createElement( "input" ), + div = document.createElement( "div" ), + fragment = document.createDocumentFragment(); + + // Setup + div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>"; + + // IE strips leading whitespace when .innerHTML is used + support.leadingWhitespace = div.firstChild.nodeType === 3; + + // Make sure that tbody elements aren't automatically inserted + // IE will insert them into empty tables + support.tbody = !div.getElementsByTagName( "tbody" ).length; + + // Make sure that link elements get serialized correctly by innerHTML + // This requires a wrapper element in IE + support.htmlSerialize = !!div.getElementsByTagName( "link" ).length; + + // Makes sure cloning an html5 element does not cause problems + // Where outerHTML is undefined, this still works + support.html5Clone = + document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>"; + + // Check if a disconnected checkbox will retain its checked + // value of true after appended to the DOM (IE6/7) + input.type = "checkbox"; + input.checked = true; + fragment.appendChild( input ); + support.appendChecked = input.checked; + + // Make sure textarea (and checkbox) defaultValue is properly cloned + // Support: IE6-IE11+ + div.innerHTML = "<textarea>x</textarea>"; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // #11217 - WebKit loses check when the name is after the checked attribute + fragment.appendChild( div ); + div.innerHTML = "<input type='radio' checked='checked' name='t'/>"; + + // Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3 + // old WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE<9 + // Opera does not clone events (and typeof div.attachEvent === undefined). + // IE9-10 clones events bound via attachEvent, but they don't trigger with .click() + support.noCloneEvent = true; + if ( div.attachEvent ) { + div.attachEvent( "onclick", function() { + support.noCloneEvent = false; + }); + + div.cloneNode( true ).click(); + } + + // Execute the test only if not already executed in another module. + if (support.deleteExpando == null) { + // Support: IE<9 + support.deleteExpando = true; + try { + delete div.test; + } catch( e ) { + support.deleteExpando = false; + } + } +})(); + + +(function() { + var i, eventName, + div = document.createElement( "div" ); + + // Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event) + for ( i in { submit: true, change: true, focusin: true }) { + eventName = "on" + i; + + if ( !(support[ i + "Bubbles" ] = eventName in window) ) { + // Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP) + div.setAttribute( eventName, "t" ); + support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false; + } + } + + // Null elements to avoid leaks in IE. + div = null; +})(); + + +var rformElems = /^(?:input|select|textarea)$/i, + rkeyEvent = /^key/, + rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/, + rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + rtypenamespace = /^([^.]*)(?:\.(.+)|)$/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + var tmp, events, t, handleObjIn, + special, eventHandle, handleObj, + handlers, type, namespaces, origType, + elemData = jQuery._data( elem ); + + // Don't attach events to noData or text/comment nodes (but allow plain objects) + if ( !elemData ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !(events = elemData.events) ) { + events = elemData.events = {}; + } + if ( !(eventHandle = elemData.handle) ) { + eventHandle = elemData.handle = function( e ) { + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ? + jQuery.event.dispatch.apply( eventHandle.elem, arguments ) : + undefined; + }; + // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events + eventHandle.elem = elem; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnotwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[t] ) || []; + type = origType = tmp[1]; + namespaces = ( tmp[2] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend({ + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join(".") + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !(handlers = events[ type ]) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener/attachEvent if the special events handler returns false + if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + // Bind the global event handler to the element + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle, false ); + + } else if ( elem.attachEvent ) { + elem.attachEvent( "on" + type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + // Nullify elem to prevent memory leaks in IE + elem = null; + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + var j, handleObj, tmp, + origCount, t, events, + special, handlers, type, + namespaces, origType, + elemData = jQuery.hasData( elem ) && jQuery._data( elem ); + + if ( !elemData || !(events = elemData.events) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnotwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[t] ) || []; + type = origType = tmp[1]; + namespaces = ( tmp[2] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + delete elemData.handle; + + // removeData also checks for emptiness and clears the expando if empty + // so use it instead of delete + jQuery._removeData( elem, "events" ); + } + }, + + trigger: function( event, data, elem, onlyHandlers ) { + var handle, ontype, cur, + bubbleType, special, tmp, i, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : []; + + cur = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf(".") >= 0 ) { + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split("."); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf(":") < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join("."); + event.namespace_re = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === (elem.ownerDocument || document) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) { + + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && jQuery.acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) && + jQuery.acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name name as the event. + // Can't use an .isFunction() check here because IE6/7 fails that test. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + try { + elem[ type ](); + } catch ( e ) { + // IE<9 dies on focus/blur to hidden element (#1486,#12518) + // only reproducible on winXP IE8 native, not IE9 in IE8 mode + } + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + dispatch: function( event ) { + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( event ); + + var i, ret, handleObj, matched, j, + handlerQueue = [], + args = slice.call( arguments ), + handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[0] = event; + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) { + + // Triggered event must either 1) have no namespace, or + // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace). + if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler ) + .apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( (event.result = ret) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var sel, handleObj, matches, i, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + // Black-hole SVG <use> instance trees (#13180) + // Avoid non-left-click bubbling in Firefox (#3861) + if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) { + + /* jshint eqeqeq: false */ + for ( ; cur != this; cur = cur.parentNode || this ) { + /* jshint eqeqeq: true */ + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) { + matches = []; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matches[ sel ] === undefined ) { + matches[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) >= 0 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matches[ sel ] ) { + matches.push( handleObj ); + } + } + if ( matches.length ) { + handlerQueue.push({ elem: cur, handlers: matches }); + } + } + } + } + + // Add the remaining (directly-bound) handlers + if ( delegateCount < handlers.length ) { + handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) }); + } + + return handlerQueue; + }, + + fix: function( event ) { + if ( event[ jQuery.expando ] ) { + return event; + } + + // Create a writable copy of the event object and normalize some properties + var i, prop, copy, + type = event.type, + originalEvent = event, + fixHook = this.fixHooks[ type ]; + + if ( !fixHook ) { + this.fixHooks[ type ] = fixHook = + rmouseEvent.test( type ) ? this.mouseHooks : + rkeyEvent.test( type ) ? this.keyHooks : + {}; + } + copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props; + + event = new jQuery.Event( originalEvent ); + + i = copy.length; + while ( i-- ) { + prop = copy[ i ]; + event[ prop ] = originalEvent[ prop ]; + } + + // Support: IE<9 + // Fix target property (#1925) + if ( !event.target ) { + event.target = originalEvent.srcElement || document; + } + + // Support: Chrome 23+, Safari? + // Target should not be a text node (#504, #13143) + if ( event.target.nodeType === 3 ) { + event.target = event.target.parentNode; + } + + // Support: IE<9 + // For mouse/key events, metaKey==false if it's undefined (#3368, #11328) + event.metaKey = !!event.metaKey; + + return fixHook.filter ? fixHook.filter( event, originalEvent ) : event; + }, + + // Includes some event props shared by KeyEvent and MouseEvent + props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "), + + fixHooks: {}, + + keyHooks: { + props: "char charCode key keyCode".split(" "), + filter: function( event, original ) { + + // Add which for key events + if ( event.which == null ) { + event.which = original.charCode != null ? original.charCode : original.keyCode; + } + + return event; + } + }, + + mouseHooks: { + props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "), + filter: function( event, original ) { + var body, eventDoc, doc, + button = original.button, + fromElement = original.fromElement; + + // Calculate pageX/Y if missing and clientX/Y available + if ( event.pageX == null && original.clientX != null ) { + eventDoc = event.target.ownerDocument || document; + doc = eventDoc.documentElement; + body = eventDoc.body; + + event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 ); + event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 ); + } + + // Add relatedTarget, if necessary + if ( !event.relatedTarget && fromElement ) { + event.relatedTarget = fromElement === event.target ? original.toElement : fromElement; + } + + // Add which for click: 1 === left; 2 === middle; 3 === right + // Note: button is not normalized, so don't use it + if ( !event.which && button !== undefined ) { + event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) ); + } + + return event; + } + }, + + special: { + load: { + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + focus: { + // Fire native event if possible so blur/focus sequence is correct + trigger: function() { + if ( this !== safeActiveElement() && this.focus ) { + try { + this.focus(); + return false; + } catch ( e ) { + // Support: IE<9 + // If we error on focus to hidden element (#1486, #12518), + // let .trigger() run the handlers + } + } + }, + delegateType: "focusin" + }, + blur: { + trigger: function() { + if ( this === safeActiveElement() && this.blur ) { + this.blur(); + return false; + } + }, + delegateType: "focusout" + }, + click: { + // For checkbox, fire native event so checked state will be right + trigger: function() { + if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) { + this.click(); + return false; + } + }, + + // For cross-browser consistency, don't fire native .click() on links + _default: function( event ) { + return jQuery.nodeName( event.target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + }, + + simulate: function( type, elem, event, bubble ) { + // Piggyback on a donor event to simulate a different one. + // Fake originalEvent to avoid donor's stopPropagation, but if the + // simulated event prevents default then we do the same on the donor. + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true, + originalEvent: {} + } + ); + if ( bubble ) { + jQuery.event.trigger( e, null, elem ); + } else { + jQuery.event.dispatch.call( elem, e ); + } + if ( e.isDefaultPrevented() ) { + event.preventDefault(); + } + } +}; + +jQuery.removeEvent = document.removeEventListener ? + function( elem, type, handle ) { + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle, false ); + } + } : + function( elem, type, handle ) { + var name = "on" + type; + + if ( elem.detachEvent ) { + + // #8545, #7054, preventing memory leaks for custom events in IE6-8 + // detachEvent needed property on element, by name of that event, to properly expose it to GC + if ( typeof elem[ name ] === strundefined ) { + elem[ name ] = null; + } + + elem.detachEvent( name, handle ); + } + }; + +jQuery.Event = function( src, props ) { + // Allow instantiation without the 'new' keyword + if ( !(this instanceof jQuery.Event) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + // Support: IE < 9, Android < 4.0 + src.returnValue === false ? + returnTrue : + returnFalse; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || jQuery.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + if ( !e ) { + return; + } + + // If preventDefault exists, run it on the original event + if ( e.preventDefault ) { + e.preventDefault(); + + // Support: IE + // Otherwise set the returnValue property of the original event to false + } else { + e.returnValue = false; + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + if ( !e ) { + return; + } + // If stopPropagation exists, run it on the original event + if ( e.stopPropagation ) { + e.stopPropagation(); + } + + // Support: IE + // Set the cancelBubble property of the original event to true + e.cancelBubble = true; + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && e.stopImmediatePropagation ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Create mouseenter/leave events using mouseover/out and event-time checks +jQuery.each({ + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mousenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || (related !== target && !jQuery.contains( target, related )) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +}); + +// IE submit delegation +if ( !support.submitBubbles ) { + + jQuery.event.special.submit = { + setup: function() { + // Only need this for delegated form submit events + if ( jQuery.nodeName( this, "form" ) ) { + return false; + } + + // Lazy-add a submit handler when a descendant form may potentially be submitted + jQuery.event.add( this, "click._submit keypress._submit", function( e ) { + // Node name check avoids a VML-related crash in IE (#9807) + var elem = e.target, + form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined; + if ( form && !jQuery._data( form, "submitBubbles" ) ) { + jQuery.event.add( form, "submit._submit", function( event ) { + event._submit_bubble = true; + }); + jQuery._data( form, "submitBubbles", true ); + } + }); + // return undefined since we don't need an event listener + }, + + postDispatch: function( event ) { + // If form was submitted by the user, bubble the event up the tree + if ( event._submit_bubble ) { + delete event._submit_bubble; + if ( this.parentNode && !event.isTrigger ) { + jQuery.event.simulate( "submit", this.parentNode, event, true ); + } + } + }, + + teardown: function() { + // Only need this for delegated form submit events + if ( jQuery.nodeName( this, "form" ) ) { + return false; + } + + // Remove delegated handlers; cleanData eventually reaps submit handlers attached above + jQuery.event.remove( this, "._submit" ); + } + }; +} + +// IE change delegation and checkbox/radio fix +if ( !support.changeBubbles ) { + + jQuery.event.special.change = { + + setup: function() { + + if ( rformElems.test( this.nodeName ) ) { + // IE doesn't fire change on a check/radio until blur; trigger it on click + // after a propertychange. Eat the blur-change in special.change.handle. + // This still fires onchange a second time for check/radio after blur. + if ( this.type === "checkbox" || this.type === "radio" ) { + jQuery.event.add( this, "propertychange._change", function( event ) { + if ( event.originalEvent.propertyName === "checked" ) { + this._just_changed = true; + } + }); + jQuery.event.add( this, "click._change", function( event ) { + if ( this._just_changed && !event.isTrigger ) { + this._just_changed = false; + } + // Allow triggered, simulated change events (#11500) + jQuery.event.simulate( "change", this, event, true ); + }); + } + return false; + } + // Delegated event; lazy-add a change handler on descendant inputs + jQuery.event.add( this, "beforeactivate._change", function( e ) { + var elem = e.target; + + if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) { + jQuery.event.add( elem, "change._change", function( event ) { + if ( this.parentNode && !event.isSimulated && !event.isTrigger ) { + jQuery.event.simulate( "change", this.parentNode, event, true ); + } + }); + jQuery._data( elem, "changeBubbles", true ); + } + }); + }, + + handle: function( event ) { + var elem = event.target; + + // Swallow native change events from checkbox/radio, we already triggered them above + if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) { + return event.handleObj.handler.apply( this, arguments ); + } + }, + + teardown: function() { + jQuery.event.remove( this, "._change" ); + + return !rformElems.test( this.nodeName ); + } + }; +} + +// Create "bubbling" focus and blur events +if ( !support.focusinBubbles ) { + jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + var doc = this.ownerDocument || this, + attaches = jQuery._data( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + jQuery._data( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this, + attaches = jQuery._data( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + jQuery._removeData( doc, fix ); + } else { + jQuery._data( doc, fix, attaches ); + } + } + }; + }); +} + +jQuery.fn.extend({ + + on: function( types, selector, data, fn, /*INTERNAL*/ one ) { + var type, origFn; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + this.on( type, selector, data, types[ type ], one ); + } + return this; + } + + if ( data == null && fn == null ) { + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return this; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return this.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + }); + }, + one: function( types, selector, data, fn ) { + return this.on( types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each(function() { + jQuery.event.remove( this, types, fn, selector ); + }); + }, + + trigger: function( type, data ) { + return this.each(function() { + jQuery.event.trigger( type, data, this ); + }); + }, + triggerHandler: function( type, data ) { + var elem = this[0]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +}); + + +function createSafeFragment( document ) { + var list = nodeNames.split( "|" ), + safeFrag = document.createDocumentFragment(); + + if ( safeFrag.createElement ) { + while ( list.length ) { + safeFrag.createElement( + list.pop() + ); + } + } + return safeFrag; +} + +var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" + + "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video", + rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g, + rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"), + rleadingWhitespace = /^\s+/, + rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi, + rtagName = /<([\w:]+)/, + rtbody = /<tbody/i, + rhtml = /<|&#?\w+;/, + rnoInnerhtml = /<(?:script|style|link)/i, + // checked="checked" or checked + rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, + rscriptType = /^$|\/(?:java|ecma)script/i, + rscriptTypeMasked = /^true\/(.*)/, + rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g, + + // We have to close these tags to support XHTML (#13200) + wrapMap = { + option: [ 1, "<select multiple='multiple'>", "</select>" ], + legend: [ 1, "<fieldset>", "</fieldset>" ], + area: [ 1, "<map>", "</map>" ], + param: [ 1, "<object>", "</object>" ], + thead: [ 1, "<table>", "</table>" ], + tr: [ 2, "<table><tbody>", "</tbody></table>" ], + col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ], + td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ], + + // IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags, + // unless wrapped in a div with non-breaking characters in front of it. + _default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>" ] + }, + safeFragment = createSafeFragment( document ), + fragmentDiv = safeFragment.appendChild( document.createElement("div") ); + +wrapMap.optgroup = wrapMap.option; +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +function getAll( context, tag ) { + var elems, elem, + i = 0, + found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) : + typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) : + undefined; + + if ( !found ) { + for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) { + if ( !tag || jQuery.nodeName( elem, tag ) ) { + found.push( elem ); + } else { + jQuery.merge( found, getAll( elem, tag ) ); + } + } + } + + return tag === undefined || tag && jQuery.nodeName( context, tag ) ? + jQuery.merge( [ context ], found ) : + found; +} + +// Used in buildFragment, fixes the defaultChecked property +function fixDefaultChecked( elem ) { + if ( rcheckableType.test( elem.type ) ) { + elem.defaultChecked = elem.checked; + } +} + +// Support: IE<8 +// Manipulating tables requires a tbody +function manipulationTarget( elem, content ) { + return jQuery.nodeName( elem, "table" ) && + jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ? + + elem.getElementsByTagName("tbody")[0] || + elem.appendChild( elem.ownerDocument.createElement("tbody") ) : + elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + var match = rscriptTypeMasked.exec( elem.type ); + if ( match ) { + elem.type = match[1]; + } else { + elem.removeAttribute("type"); + } + return elem; +} + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var elem, + i = 0; + for ( ; (elem = elems[i]) != null; i++ ) { + jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) ); + } +} + +function cloneCopyEvent( src, dest ) { + + if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) { + return; + } + + var type, i, l, + oldData = jQuery._data( src ), + curData = jQuery._data( dest, oldData ), + events = oldData.events; + + if ( events ) { + delete curData.handle; + curData.events = {}; + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + + // make the cloned public data object a copy from the original + if ( curData.data ) { + curData.data = jQuery.extend( {}, curData.data ); + } +} + +function fixCloneNodeIssues( src, dest ) { + var nodeName, e, data; + + // We do not need to do anything for non-Elements + if ( dest.nodeType !== 1 ) { + return; + } + + nodeName = dest.nodeName.toLowerCase(); + + // IE6-8 copies events bound via attachEvent when using cloneNode. + if ( !support.noCloneEvent && dest[ jQuery.expando ] ) { + data = jQuery._data( dest ); + + for ( e in data.events ) { + jQuery.removeEvent( dest, e, data.handle ); + } + + // Event data gets referenced instead of copied if the expando gets copied too + dest.removeAttribute( jQuery.expando ); + } + + // IE blanks contents when cloning scripts, and tries to evaluate newly-set text + if ( nodeName === "script" && dest.text !== src.text ) { + disableScript( dest ).text = src.text; + restoreScript( dest ); + + // IE6-10 improperly clones children of object elements using classid. + // IE10 throws NoModificationAllowedError if parent is null, #12132. + } else if ( nodeName === "object" ) { + if ( dest.parentNode ) { + dest.outerHTML = src.outerHTML; + } + + // This path appears unavoidable for IE9. When cloning an object + // element in IE9, the outerHTML strategy above is not sufficient. + // If the src has innerHTML and the destination does not, + // copy the src.innerHTML into the dest.innerHTML. #10324 + if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) { + dest.innerHTML = src.innerHTML; + } + + } else if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + // IE6-8 fails to persist the checked state of a cloned checkbox + // or radio button. Worse, IE6-7 fail to give the cloned element + // a checked appearance if the defaultChecked value isn't also set + + dest.defaultChecked = dest.checked = src.checked; + + // IE6-7 get confused and end up setting the value of a cloned + // checkbox/radio button to an empty string instead of "on" + if ( dest.value !== src.value ) { + dest.value = src.value; + } + + // IE6-8 fails to return the selected option to the default selected + // state when cloning options + } else if ( nodeName === "option" ) { + dest.defaultSelected = dest.selected = src.defaultSelected; + + // IE6-8 fails to set the defaultValue to the correct value when + // cloning other types of input fields + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +jQuery.extend({ + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var destElements, node, clone, i, srcElements, + inPage = jQuery.contains( elem.ownerDocument, elem ); + + if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) { + clone = elem.cloneNode( true ); + + // IE<=8 does not properly clone detached, unknown element nodes + } else { + fragmentDiv.innerHTML = elem.outerHTML; + fragmentDiv.removeChild( clone = fragmentDiv.firstChild ); + } + + if ( (!support.noCloneEvent || !support.noCloneChecked) && + (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) { + + // We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + // Fix all IE cloning issues + for ( i = 0; (node = srcElements[i]) != null; ++i ) { + // Ensure that the destination node is not null; Fixes #9587 + if ( destElements[i] ) { + fixCloneNodeIssues( node, destElements[i] ); + } + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0; (node = srcElements[i]) != null; i++ ) { + cloneCopyEvent( node, destElements[i] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + destElements = srcElements = node = null; + + // Return the cloned set + return clone; + }, + + buildFragment: function( elems, context, scripts, selection ) { + var j, elem, contains, + tmp, tag, tbody, wrap, + l = elems.length, + + // Ensure a safe fragment + safe = createSafeFragment( context ), + + nodes = [], + i = 0; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( jQuery.type( elem ) === "object" ) { + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || safe.appendChild( context.createElement("div") ); + + // Deserialize a standard representation + tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + + tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2]; + + // Descend through wrappers to the right content + j = wrap[0]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Manually add leading whitespace removed by IE + if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) { + nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) ); + } + + // Remove IE's autoinserted <tbody> from table fragments + if ( !support.tbody ) { + + // String was a <table>, *may* have spurious <tbody> + elem = tag === "table" && !rtbody.test( elem ) ? + tmp.firstChild : + + // String was a bare <thead> or <tfoot> + wrap[1] === "<table>" && !rtbody.test( elem ) ? + tmp : + 0; + + j = elem && elem.childNodes.length; + while ( j-- ) { + if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) { + elem.removeChild( tbody ); + } + } + } + + jQuery.merge( nodes, tmp.childNodes ); + + // Fix #12392 for WebKit and IE > 9 + tmp.textContent = ""; + + // Fix #12392 for oldIE + while ( tmp.firstChild ) { + tmp.removeChild( tmp.firstChild ); + } + + // Remember the top-level container for proper cleanup + tmp = safe.lastChild; + } + } + } + + // Fix #11356: Clear elements from fragment + if ( tmp ) { + safe.removeChild( tmp ); + } + + // Reset defaultChecked for any radios and checkboxes + // about to be appended to the DOM in IE 6/7 (#8060) + if ( !support.appendChecked ) { + jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked ); + } + + i = 0; + while ( (elem = nodes[ i++ ]) ) { + + // #4087 - If origin and destination elements are the same, and this is + // that element, do not do anything + if ( selection && jQuery.inArray( elem, selection ) !== -1 ) { + continue; + } + + contains = jQuery.contains( elem.ownerDocument, elem ); + + // Append to fragment + tmp = getAll( safe.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( contains ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( (elem = tmp[ j++ ]) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + tmp = null; + + return safe; + }, + + cleanData: function( elems, /* internal */ acceptData ) { + var elem, type, id, data, + i = 0, + internalKey = jQuery.expando, + cache = jQuery.cache, + deleteExpando = support.deleteExpando, + special = jQuery.event.special; + + for ( ; (elem = elems[i]) != null; i++ ) { + if ( acceptData || jQuery.acceptData( elem ) ) { + + id = elem[ internalKey ]; + data = id && cache[ id ]; + + if ( data ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Remove cache only if it was not already removed by jQuery.event.remove + if ( cache[ id ] ) { + + delete cache[ id ]; + + // IE does not allow us to delete expando properties from nodes, + // nor does it have a removeAttribute function on Document nodes; + // we must handle all of these cases + if ( deleteExpando ) { + delete elem[ internalKey ]; + + } else if ( typeof elem.removeAttribute !== strundefined ) { + elem.removeAttribute( internalKey ); + + } else { + elem[ internalKey ] = null; + } + + deletedIds.push( id ); + } + } + } + } + } +}); + +jQuery.fn.extend({ + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) ); + }, null, value, arguments.length ); + }, + + append: function() { + return this.domManip( arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + }); + }, + + prepend: function() { + return this.domManip( arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + }); + }, + + before: function() { + return this.domManip( arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + }); + }, + + after: function() { + return this.domManip( arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + }); + }, + + remove: function( selector, keepData /* Internal Use Only */ ) { + var elem, + elems = selector ? jQuery.filter( selector, this ) : this, + i = 0; + + for ( ; (elem = elems[i]) != null; i++ ) { + + if ( !keepData && elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem ) ); + } + + if ( elem.parentNode ) { + if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) { + setGlobalEval( getAll( elem, "script" ) ); + } + elem.parentNode.removeChild( elem ); + } + } + + return this; + }, + + empty: function() { + var elem, + i = 0; + + for ( ; (elem = this[i]) != null; i++ ) { + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + } + + // Remove any remaining nodes + while ( elem.firstChild ) { + elem.removeChild( elem.firstChild ); + } + + // If this is a select, ensure that it displays empty (#12336) + // Support: IE<9 + if ( elem.options && jQuery.nodeName( elem, "select" ) ) { + elem.options.length = 0; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map(function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + }); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined ) { + return elem.nodeType === 1 ? + elem.innerHTML.replace( rinlinejQuery, "" ) : + undefined; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + ( support.htmlSerialize || !rnoshimcache.test( value ) ) && + ( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) && + !wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) { + + value = value.replace( rxhtmlTag, "<$1></$2>" ); + + try { + for (; i < l; i++ ) { + // Remove element nodes and prevent memory leaks + elem = this[i] || {}; + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch(e) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var arg = arguments[ 0 ]; + + // Make the changes, replacing each context element with the new content + this.domManip( arguments, function( elem ) { + arg = this.parentNode; + + jQuery.cleanData( getAll( this ) ); + + if ( arg ) { + arg.replaceChild( elem, this ); + } + }); + + // Force removal if there was no new content (e.g., from empty arguments) + return arg && (arg.length || arg.nodeType) ? this : this.remove(); + }, + + detach: function( selector ) { + return this.remove( selector, true ); + }, + + domManip: function( args, callback ) { + + // Flatten any nested arrays + args = concat.apply( [], args ); + + var first, node, hasScripts, + scripts, doc, fragment, + i = 0, + l = this.length, + set = this, + iNoClone = l - 1, + value = args[0], + isFunction = jQuery.isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( isFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return this.each(function( index ) { + var self = set.eq( index ); + if ( isFunction ) { + args[0] = value.call( this, index, self.html() ); + } + self.domManip( args, callback ); + }); + } + + if ( l ) { + fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + if ( first ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( this[i], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) { + + if ( node.src ) { + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl ) { + jQuery._evalUrl( node.src ); + } + } else { + jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) ); + } + } + } + } + + // Fix #11809: Avoid leaking memory + fragment = first = null; + } + } + + return this; + } +}); + +jQuery.each({ + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + i = 0, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone(true); + jQuery( insert[i] )[ original ]( elems ); + + // Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get() + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +}); + + +var iframe, + elemdisplay = {}; + +/** + * Retrieve the actual display of a element + * @param {String} name nodeName of the element + * @param {Object} doc Document object + */ +// Called only from within defaultDisplay +function actualDisplay( name, doc ) { + var style, + elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ), + + // getDefaultComputedStyle might be reliably used only on attached element + display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ? + + // Use of this method is a temporary fix (more like optmization) until something better comes along, + // since it was removed from specification and supported only in FF + style.display : jQuery.css( elem[ 0 ], "display" ); + + // We don't have any data stored on the element, + // so use "detach" method as fast way to get rid of the element + elem.detach(); + + return display; +} + +/** + * Try to determine the default display value of an element + * @param {String} nodeName + */ +function defaultDisplay( nodeName ) { + var doc = document, + display = elemdisplay[ nodeName ]; + + if ( !display ) { + display = actualDisplay( nodeName, doc ); + + // If the simple way fails, read from inside an iframe + if ( display === "none" || !display ) { + + // Use the already-created iframe if possible + iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement ); + + // Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse + doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document; + + // Support: IE + doc.write(); + doc.close(); + + display = actualDisplay( nodeName, doc ); + iframe.detach(); + } + + // Store the correct default display + elemdisplay[ nodeName ] = display; + } + + return display; +} + + +(function() { + var shrinkWrapBlocksVal; + + support.shrinkWrapBlocks = function() { + if ( shrinkWrapBlocksVal != null ) { + return shrinkWrapBlocksVal; + } + + // Will be changed later if needed. + shrinkWrapBlocksVal = false; + + // Minified: var b,c,d + var div, body, container; + + body = document.getElementsByTagName( "body" )[ 0 ]; + if ( !body || !body.style ) { + // Test fired too early or in an unsupported environment, exit. + return; + } + + // Setup + div = document.createElement( "div" ); + container = document.createElement( "div" ); + container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px"; + body.appendChild( container ).appendChild( div ); + + // Support: IE6 + // Check if elements with layout shrink-wrap their children + if ( typeof div.style.zoom !== strundefined ) { + // Reset CSS: box-sizing; display; margin; border + div.style.cssText = + // Support: Firefox<29, Android 2.3 + // Vendor-prefix box-sizing + "-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" + + "box-sizing:content-box;display:block;margin:0;border:0;" + + "padding:1px;width:1px;zoom:1"; + div.appendChild( document.createElement( "div" ) ).style.width = "5px"; + shrinkWrapBlocksVal = div.offsetWidth !== 3; + } + + body.removeChild( container ); + + return shrinkWrapBlocksVal; + }; + +})(); +var rmargin = (/^margin/); + +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + + + +var getStyles, curCSS, + rposition = /^(top|right|bottom|left)$/; + +if ( window.getComputedStyle ) { + getStyles = function( elem ) { + return elem.ownerDocument.defaultView.getComputedStyle( elem, null ); + }; + + curCSS = function( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is only needed for .css('filter') in IE9, see #12537 + ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined; + + if ( computed ) { + + if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right + // Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels + // this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values + if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + // Support: IE + // IE returns zIndex value as an integer. + return ret === undefined ? + ret : + ret + ""; + }; +} else if ( document.documentElement.currentStyle ) { + getStyles = function( elem ) { + return elem.currentStyle; + }; + + curCSS = function( elem, name, computed ) { + var left, rs, rsLeft, ret, + style = elem.style; + + computed = computed || getStyles( elem ); + ret = computed ? computed[ name ] : undefined; + + // Avoid setting ret to empty string here + // so we don't default to auto + if ( ret == null && style && style[ name ] ) { + ret = style[ name ]; + } + + // From the awesome hack by Dean Edwards + // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291 + + // If we're not dealing with a regular pixel number + // but a number that has a weird ending, we need to convert it to pixels + // but not position css attributes, as those are proportional to the parent element instead + // and we can't measure the parent instead because it might trigger a "stacking dolls" problem + if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) { + + // Remember the original values + left = style.left; + rs = elem.runtimeStyle; + rsLeft = rs && rs.left; + + // Put in the new values to get a computed value out + if ( rsLeft ) { + rs.left = elem.currentStyle.left; + } + style.left = name === "fontSize" ? "1em" : ret; + ret = style.pixelLeft + "px"; + + // Revert the changed values + style.left = left; + if ( rsLeft ) { + rs.left = rsLeft; + } + } + + // Support: IE + // IE returns zIndex value as an integer. + return ret === undefined ? + ret : + ret + "" || "auto"; + }; +} + + + + +function addGetHookIf( conditionFn, hookFn ) { + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + var condition = conditionFn(); + + if ( condition == null ) { + // The test was not ready at this point; screw the hook this time + // but check again when needed next time. + return; + } + + if ( condition ) { + // Hook not needed (or it's not possible to use it due to missing dependency), + // remove it. + // Since there are no other hooks for marginRight, remove the whole object. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + + return (this.get = hookFn).apply( this, arguments ); + } + }; +} + + +(function() { + // Minified: var b,c,d,e,f,g, h,i + var div, style, a, pixelPositionVal, boxSizingReliableVal, + reliableHiddenOffsetsVal, reliableMarginRightVal; + + // Setup + div = document.createElement( "div" ); + div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>"; + a = div.getElementsByTagName( "a" )[ 0 ]; + style = a && a.style; + + // Finish early in limited (non-browser) environments + if ( !style ) { + return; + } + + style.cssText = "float:left;opacity:.5"; + + // Support: IE<9 + // Make sure that element opacity exists (as opposed to filter) + support.opacity = style.opacity === "0.5"; + + // Verify style float existence + // (IE uses styleFloat instead of cssFloat) + support.cssFloat = !!style.cssFloat; + + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + // Support: Firefox<29, Android 2.3 + // Vendor-prefix box-sizing + support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" || + style.WebkitBoxSizing === ""; + + jQuery.extend(support, { + reliableHiddenOffsets: function() { + if ( reliableHiddenOffsetsVal == null ) { + computeStyleTests(); + } + return reliableHiddenOffsetsVal; + }, + + boxSizingReliable: function() { + if ( boxSizingReliableVal == null ) { + computeStyleTests(); + } + return boxSizingReliableVal; + }, + + pixelPosition: function() { + if ( pixelPositionVal == null ) { + computeStyleTests(); + } + return pixelPositionVal; + }, + + // Support: Android 2.3 + reliableMarginRight: function() { + if ( reliableMarginRightVal == null ) { + computeStyleTests(); + } + return reliableMarginRightVal; + } + }); + + function computeStyleTests() { + // Minified: var b,c,d,j + var div, body, container, contents; + + body = document.getElementsByTagName( "body" )[ 0 ]; + if ( !body || !body.style ) { + // Test fired too early or in an unsupported environment, exit. + return; + } + + // Setup + div = document.createElement( "div" ); + container = document.createElement( "div" ); + container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px"; + body.appendChild( container ).appendChild( div ); + + div.style.cssText = + // Support: Firefox<29, Android 2.3 + // Vendor-prefix box-sizing + "-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" + + "box-sizing:border-box;display:block;margin-top:1%;top:1%;" + + "border:1px;padding:1px;width:4px;position:absolute"; + + // Support: IE<9 + // Assume reasonable values in the absence of getComputedStyle + pixelPositionVal = boxSizingReliableVal = false; + reliableMarginRightVal = true; + + // Check for getComputedStyle so that this code is not run in IE<9. + if ( window.getComputedStyle ) { + pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%"; + boxSizingReliableVal = + ( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px"; + + // Support: Android 2.3 + // Div with explicit width and no margin-right incorrectly + // gets computed margin-right based on width of container (#3333) + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + contents = div.appendChild( document.createElement( "div" ) ); + + // Reset CSS: box-sizing; display; margin; border; padding + contents.style.cssText = div.style.cssText = + // Support: Firefox<29, Android 2.3 + // Vendor-prefix box-sizing + "-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" + + "box-sizing:content-box;display:block;margin:0;border:0;padding:0"; + contents.style.marginRight = contents.style.width = "0"; + div.style.width = "1px"; + + reliableMarginRightVal = + !parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight ); + } + + // Support: IE8 + // Check if table cells still have offsetWidth/Height when they are set + // to display:none and there are still other visible table cells in a + // table row; if so, offsetWidth/Height are not reliable for use when + // determining if an element has been hidden directly using + // display:none (it is still safe to use offsets if a parent element is + // hidden; don safety goggles and see bug #4512 for more information). + div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>"; + contents = div.getElementsByTagName( "td" ); + contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none"; + reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0; + if ( reliableHiddenOffsetsVal ) { + contents[ 0 ].style.display = ""; + contents[ 1 ].style.display = "none"; + reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0; + } + + body.removeChild( container ); + } + +})(); + + +// A method for quickly swapping in/out CSS properties to get correct calculations. +jQuery.swap = function( elem, options, callback, args ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.apply( elem, args || [] ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var + ralpha = /alpha\([^)]*\)/i, + ropacity = /opacity\s*=\s*([^)]*)/, + + // swappable if display is none or starts with table except "table", "table-cell", or "table-caption" + // see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ), + rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ), + + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }, + + cssPrefixes = [ "Webkit", "O", "Moz", "ms" ]; + + +// return a css property mapped to a potentially vendor prefixed property +function vendorPropName( style, name ) { + + // shortcut for names that are not vendor prefixed + if ( name in style ) { + return name; + } + + // check for vendor prefixed names + var capName = name.charAt(0).toUpperCase() + name.slice(1), + origName = name, + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in style ) { + return name; + } + } + + return origName; +} + +function showHide( elements, show ) { + var display, elem, hidden, + values = [], + index = 0, + length = elements.length; + + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + values[ index ] = jQuery._data( elem, "olddisplay" ); + display = elem.style.display; + if ( show ) { + // Reset the inline display of this element to learn if it is + // being hidden by cascaded rules or not + if ( !values[ index ] && display === "none" ) { + elem.style.display = ""; + } + + // Set elements which have been overridden with display: none + // in a stylesheet to whatever the default browser style is + // for such an element + if ( elem.style.display === "" && isHidden( elem ) ) { + values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) ); + } + } else { + hidden = isHidden( elem ); + + if ( display && display !== "none" || !hidden ) { + jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) ); + } + } + } + + // Set the display of most of the elements in a second loop + // to avoid the constant reflow + for ( index = 0; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + if ( !show || elem.style.display === "none" || elem.style.display === "" ) { + elem.style.display = show ? values[ index ] || "" : "none"; + } + } + + return elements; +} + +function setPositiveNumber( elem, value, subtract ) { + var matches = rnumsplit.exec( value ); + return matches ? + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) : + value; +} + +function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) { + var i = extra === ( isBorderBox ? "border" : "content" ) ? + // If we already have the right measurement, avoid augmentation + 4 : + // Otherwise initialize for horizontal or vertical properties + name === "width" ? 1 : 0, + + val = 0; + + for ( ; i < 4; i += 2 ) { + // both box models exclude margin, so add it if we want it + if ( extra === "margin" ) { + val += jQuery.css( elem, extra + cssExpand[ i ], true, styles ); + } + + if ( isBorderBox ) { + // border-box includes padding, so remove it if we want content + if ( extra === "content" ) { + val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // at this point, extra isn't border nor margin, so remove border + if ( extra !== "margin" ) { + val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } else { + // at this point, extra isn't content, so add padding + val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // at this point, extra isn't content nor padding, so add border + if ( extra !== "padding" ) { + val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + return val; +} + +function getWidthOrHeight( elem, name, extra ) { + + // Start with offset property, which is equivalent to the border-box value + var valueIsBorderBox = true, + val = name === "width" ? elem.offsetWidth : elem.offsetHeight, + styles = getStyles( elem ), + isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // some non-html elements return undefined for offsetWidth, so check for null/undefined + // svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285 + // MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668 + if ( val <= 0 || val == null ) { + // Fall back to computed then uncomputed css if necessary + val = curCSS( elem, name, styles ); + if ( val < 0 || val == null ) { + val = elem.style[ name ]; + } + + // Computed unit is not pixels. Stop here and return. + if ( rnumnonpx.test(val) ) { + return val; + } + + // we need the check for style in case a browser which returns unreliable values + // for getComputedStyle silently falls back to the reliable elem.style + valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] ); + + // Normalize "", auto, and prepare for extra + val = parseFloat( val ) || 0; + } + + // use the active box-sizing model to add/subtract irrelevant styles + return ( val + + augmentWidthOrHeight( + elem, + name, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles + ) + ) + "px"; +} + +jQuery.extend({ + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: { + // normalize float css property + "float": support.cssFloat ? "cssFloat" : "styleFloat" + }, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = jQuery.camelCase( name ), + style = elem.style; + + name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) ); + + // gets hook for the prefixed version + // followed by the unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // convert relative number strings (+= or -=) to relative numbers. #7345 + if ( type === "string" && (ret = rrelNum.exec( value )) ) { + value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) ); + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set. See: #7116 + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add 'px' to the (except for certain CSS properties) + if ( type === "number" && !jQuery.cssNumber[ origName ] ) { + value += "px"; + } + + // Fixes #8908, it can be done more correctly by specifing setters in cssHooks, + // but it would mean to define eight (for every problematic property) identical functions + if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) { + + // Support: IE + // Swallow errors from 'invalid' CSS values (#5509) + try { + style[ name ] = value; + } catch(e) {} + } + + } else { + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) { + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var num, val, hooks, + origName = jQuery.camelCase( name ); + + // Make sure that we're working with the right name + name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) ); + + // gets hook for the prefixed version + // followed by the unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + //convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Return, converting to number if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || jQuery.isNumeric( num ) ? num || 0 : val; + } + return val; + } +}); + +jQuery.each([ "height", "width" ], function( i, name ) { + jQuery.cssHooks[ name ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + // certain elements can have dimension info if we invisibly show them + // however, it must have a current display style that would benefit from this + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ? + jQuery.swap( elem, cssShow, function() { + return getWidthOrHeight( elem, name, extra ); + }) : + getWidthOrHeight( elem, name, extra ); + } + }, + + set: function( elem, value, extra ) { + var styles = extra && getStyles( elem ); + return setPositiveNumber( elem, value, extra ? + augmentWidthOrHeight( + elem, + name, + extra, + support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + styles + ) : 0 + ); + } + }; +}); + +if ( !support.opacity ) { + jQuery.cssHooks.opacity = { + get: function( elem, computed ) { + // IE uses filters for opacity + return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ? + ( 0.01 * parseFloat( RegExp.$1 ) ) + "" : + computed ? "1" : ""; + }, + + set: function( elem, value ) { + var style = elem.style, + currentStyle = elem.currentStyle, + opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "", + filter = currentStyle && currentStyle.filter || style.filter || ""; + + // IE has trouble with opacity if it does not have layout + // Force it by setting the zoom level + style.zoom = 1; + + // if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652 + // if value === "", then remove inline opacity #12685 + if ( ( value >= 1 || value === "" ) && + jQuery.trim( filter.replace( ralpha, "" ) ) === "" && + style.removeAttribute ) { + + // Setting style.filter to null, "" & " " still leave "filter:" in the cssText + // if "filter:" is present at all, clearType is disabled, we want to avoid this + // style.removeAttribute is IE Only, but so apparently is this code path... + style.removeAttribute( "filter" ); + + // if there is no filter style applied in a css rule or unset inline opacity, we are done + if ( value === "" || currentStyle && !currentStyle.filter ) { + return; + } + } + + // otherwise, set new filter values + style.filter = ralpha.test( filter ) ? + filter.replace( ralpha, opacity ) : + filter + " " + opacity; + } + }; +} + +jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight, + function( elem, computed ) { + if ( computed ) { + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + // Work around by temporarily setting element display to inline-block + return jQuery.swap( elem, { "display": "inline-block" }, + curCSS, [ elem, "marginRight" ] ); + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each({ + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // assumes a single number if not a string + parts = typeof value === "string" ? value.split(" ") : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( !rmargin.test( prefix ) ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +}); + +jQuery.fn.extend({ + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( jQuery.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + }, + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each(function() { + if ( isHidden( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + }); + } +}); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || "swing"; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + if ( tween.elem[ tween.prop ] != null && + (!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) { + return tween.elem[ tween.prop ]; + } + + // passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails + // so, simple values such as "10px" are parsed to Float. + // complex values such as "rotate(1rad)" are returned as is. + result = jQuery.css( tween.elem, tween.prop, "" ); + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + // use step hook for back compat - use cssHook if its there - use .style if its + // available and use plain properties where available + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 +// Panic based approach to setting things on disconnected nodes + +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + } +}; + +jQuery.fx = Tween.prototype.init; + +// Back Compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, timerId, + rfxtypes = /^(?:toggle|show|hide)$/, + rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ), + rrun = /queueHooks$/, + animationPrefilters = [ defaultPrefilter ], + tweeners = { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ), + target = tween.cur(), + parts = rfxnum.exec( value ), + unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) && + rfxnum.exec( jQuery.css( tween.elem, prop ) ), + scale = 1, + maxIterations = 20; + + if ( start && start[ 3 ] !== unit ) { + // Trust units reported by jQuery.css + unit = unit || start[ 3 ]; + + // Make sure we update the tween properties later on + parts = parts || []; + + // Iteratively approximate from a nonzero starting point + start = +target || 1; + + do { + // If previous iteration zeroed out, double until we get *something* + // Use a string for doubling factor so we don't accidentally see scale as unchanged below + scale = scale || ".5"; + + // Adjust and apply + start = start / scale; + jQuery.style( tween.elem, prop, start + unit ); + + // Update scale, tolerating zero or NaN from tween.cur() + // And breaking the loop if scale is unchanged or perfect, or if we've just had enough + } while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations ); + } + + // Update tween properties + if ( parts ) { + start = tween.start = +start || +target || 0; + tween.unit = unit; + // If a +=/-= token was provided, we're doing a relative animation + tween.end = parts[ 1 ] ? + start + ( parts[ 1 ] + 1 ) * parts[ 2 ] : + +parts[ 2 ]; + } + + return tween; + } ] + }; + +// Animations created synchronously will run synchronously +function createFxNow() { + setTimeout(function() { + fxNow = undefined; + }); + return ( fxNow = jQuery.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + attrs = { height: type }, + i = 0; + + // if we include width, step value is 1 to do all cssExpand values, + // if we don't include width, step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4 ; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( (tween = collection[ index ].call( animation, prop, value )) ) { + + // we're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + /* jshint validthis: true */ + var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHidden( elem ), + dataShow = jQuery._data( elem, "fxshow" ); + + // handle queue: false promises + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always(function() { + // doing this makes sure that the complete handler will be called + // before this completes + anim.always(function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + }); + }); + } + + // height/width overflow pass + if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) { + // Make sure that nothing sneaks out + // Record all 3 overflow attributes because IE does not + // change the overflow attribute when overflowX and + // overflowY are set to the same value + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Set display property to inline-block for height/width + // animations on inline elements that are having width/height animated + display = jQuery.css( elem, "display" ); + + // Test default display if display is currently "none" + checkDisplay = display === "none" ? + jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display; + + if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) { + + // inline-level elements accept inline-block; + // block-level elements need to be inline with layout + if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) { + style.display = "inline-block"; + } else { + style.zoom = 1; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + if ( !support.shrinkWrapBlocks() ) { + anim.always(function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + }); + } + } + + // show/hide pass + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.exec( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + + // Any non-fx value stops us from restoring the original display value + } else { + display = undefined; + } + } + + if ( !jQuery.isEmptyObject( orig ) ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = jQuery._data( elem, "fxshow", {} ); + } + + // store state if its toggle - enables .stop().toggle() to "reverse" + if ( toggle ) { + dataShow.hidden = !hidden; + } + if ( hidden ) { + jQuery( elem ).show(); + } else { + anim.done(function() { + jQuery( elem ).hide(); + }); + } + anim.done(function() { + var prop; + jQuery._removeData( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + }); + for ( prop in orig ) { + tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = tween.start; + if ( hidden ) { + tween.end = tween.start; + tween.start = prop === "width" || prop === "height" ? 1 : 0; + } + } + } + + // If this is a noop like .hide().hide(), restore an overwritten display value + } else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) { + style.display = display; + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = jQuery.camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( jQuery.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // not quite $.extend, this wont overwrite keys already present. + // also - reusing 'index' from above because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = animationPrefilters.length, + deferred = jQuery.Deferred().always( function() { + // don't match elem in the :animated selector + delete tick.elem; + }), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + // archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length ; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ]); + + if ( percent < 1 && length ) { + return remaining; + } else { + deferred.resolveWith( elem, [ animation ] ); + return false; + } + }, + animation = deferred.promise({ + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { specialEasing: {} }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + // if we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length ; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // resolve when we played the last frame + // otherwise, reject + if ( gotoEnd ) { + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + }), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length ; index++ ) { + result = animationPrefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( jQuery.isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + }) + ); + + // attach callbacks from options + return animation.progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); +} + +jQuery.Animation = jQuery.extend( Animation, { + tweener: function( props, callback ) { + if ( jQuery.isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.split(" "); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length ; index++ ) { + prop = props[ index ]; + tweeners[ prop ] = tweeners[ prop ] || []; + tweeners[ prop ].unshift( callback ); + } + }, + + prefilter: function( callback, prepend ) { + if ( prepend ) { + animationPrefilters.unshift( callback ); + } else { + animationPrefilters.push( callback ); + } + } +}); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + jQuery.isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing + }; + + opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration : + opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default; + + // normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( jQuery.isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend({ + fadeTo: function( speed, to, easing, callback ) { + + // show any hidden elements after setting opacity to 0 + return this.filter( isHidden ).css( "opacity", 0 ).show() + + // animate to the value specified + .end().animate({ opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || jQuery._data( this, "finish" ) ) { + anim.stop( true ); + } + }; + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue && type !== false ) { + this.queue( type || "fx", [] ); + } + + return this.each(function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = jQuery._data( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) { + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // start the next in the queue if the last step wasn't forced + // timers currently will call their complete callbacks, which will dequeue + // but only if they were gotoEnd + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + }); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each(function() { + var index, + data = jQuery._data( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // enable finishing flag on private data + data.finish = true; + + // empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // turn off finishing flag + delete data.finish; + }); + } +}); + +jQuery.each([ "toggle", "show", "hide" ], function( i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +}); + +// Generate shortcuts for custom animations +jQuery.each({ + slideDown: genFx("show"), + slideUp: genFx("hide"), + slideToggle: genFx("toggle"), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +}); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + timers = jQuery.timers, + i = 0; + + fxNow = jQuery.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + // Checks the timer has not already been removed + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + if ( timer() ) { + jQuery.fx.start(); + } else { + jQuery.timers.pop(); + } +}; + +jQuery.fx.interval = 13; + +jQuery.fx.start = function() { + if ( !timerId ) { + timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval ); + } +}; + +jQuery.fx.stop = function() { + clearInterval( timerId ); + timerId = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = setTimeout( next, time ); + hooks.stop = function() { + clearTimeout( timeout ); + }; + }); +}; + + +(function() { + // Minified: var a,b,c,d,e + var input, div, select, a, opt; + + // Setup + div = document.createElement( "div" ); + div.setAttribute( "className", "t" ); + div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>"; + a = div.getElementsByTagName("a")[ 0 ]; + + // First batch of tests. + select = document.createElement("select"); + opt = select.appendChild( document.createElement("option") ); + input = div.getElementsByTagName("input")[ 0 ]; + + a.style.cssText = "top:1px"; + + // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7) + support.getSetAttribute = div.className !== "t"; + + // Get the style information from getAttribute + // (IE uses .cssText instead) + support.style = /top/.test( a.getAttribute("style") ); + + // Make sure that URLs aren't manipulated + // (IE normalizes it by default) + support.hrefNormalized = a.getAttribute("href") === "/a"; + + // Check the default checkbox/radio value ("" on WebKit; "on" elsewhere) + support.checkOn = !!input.value; + + // Make sure that a selected-by-default option has a working selected property. + // (WebKit defaults to false instead of true, IE too, if it's in an optgroup) + support.optSelected = opt.selected; + + // Tests for enctype support on a form (#6743) + support.enctype = !!document.createElement("form").enctype; + + // Make sure that the options inside disabled selects aren't marked as disabled + // (WebKit marks them as disabled) + select.disabled = true; + support.optDisabled = !opt.disabled; + + // Support: IE8 only + // Check if we can trust getAttribute("value") + input = document.createElement( "input" ); + input.setAttribute( "value", "" ); + support.input = input.getAttribute( "value" ) === ""; + + // Check if an input maintains its value after becoming a radio + input.value = "t"; + input.setAttribute( "type", "radio" ); + support.radioValue = input.value === "t"; +})(); + + +var rreturn = /\r/g; + +jQuery.fn.extend({ + val: function( value ) { + var hooks, ret, isFunction, + elem = this[0]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) { + return ret; + } + + ret = elem.value; + + return typeof ret === "string" ? + // handle most common string cases + ret.replace(rreturn, "") : + // handle cases where value is null/undef or number + ret == null ? "" : ret; + } + + return; + } + + isFunction = jQuery.isFunction( value ); + + return this.each(function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( isFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + } else if ( typeof val === "number" ) { + val += ""; + } else if ( jQuery.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + }); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + }); + } +}); + +jQuery.extend({ + valHooks: { + option: { + get: function( elem ) { + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + // Support: IE10-11+ + // option.text throws exceptions (#14686, #14858) + jQuery.trim( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one" || index < 0, + values = one ? null : [], + max = one ? index + 1 : options.length, + i = index < 0 ? + max : + one ? index : 0; + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // oldIE doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + // Don't return options that are disabled or in a disabled optgroup + ( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) && + ( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) { + + // Support: IE6 + // When new option element is added to select box we need to + // force reflow of newly added node in order to workaround delay + // of initialization properties + try { + option.selected = optionSet = true; + + } catch ( _ ) { + + // Will be executed only in IE6 + option.scrollHeight; + } + + } else { + option.selected = false; + } + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + + return options; + } + } + } +}); + +// Radios and checkboxes getter/setter +jQuery.each([ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( jQuery.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + // Support: Webkit + // "" is returned instead of "on" if a value isn't specified + return elem.getAttribute("value") === null ? "on" : elem.value; + }; + } +}); + + + + +var nodeHook, boolHook, + attrHandle = jQuery.expr.attrHandle, + ruseDefault = /^(?:checked|selected)$/i, + getSetAttribute = support.getSetAttribute, + getSetInput = support.input; + +jQuery.fn.extend({ + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each(function() { + jQuery.removeAttr( this, name ); + }); + } +}); + +jQuery.extend({ + attr: function( elem, name, value ) { + var hooks, ret, + nType = elem.nodeType; + + // don't get/set attributes on text, comment and attribute nodes + if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === strundefined ) { + return jQuery.prop( elem, name, value ); + } + + // All attributes are lowercase + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + name = name.toLowerCase(); + hooks = jQuery.attrHooks[ name ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook ); + } + + if ( value !== undefined ) { + + if ( value === null ) { + jQuery.removeAttr( elem, name ); + + } else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) { + return ret; + + } else { + elem.setAttribute( name, value + "" ); + return value; + } + + } else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) { + return ret; + + } else { + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? + undefined : + ret; + } + }, + + removeAttr: function( elem, value ) { + var name, propName, + i = 0, + attrNames = value && value.match( rnotwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( (name = attrNames[i++]) ) { + propName = jQuery.propFix[ name ] || name; + + // Boolean attributes get special treatment (#10870) + if ( jQuery.expr.match.bool.test( name ) ) { + // Set corresponding property to false + if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) { + elem[ propName ] = false; + // Support: IE<9 + // Also clear defaultChecked/defaultSelected (if appropriate) + } else { + elem[ jQuery.camelCase( "default-" + name ) ] = + elem[ propName ] = false; + } + + // See #9699 for explanation of this approach (setting first, then removal) + } else { + jQuery.attr( elem, name, "" ); + } + + elem.removeAttribute( getSetAttribute ? name : propName ); + } + } + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) { + // Setting the type on a radio button after the value resets the value in IE6-9 + // Reset value to default in case type is set after value during creation + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + } +}); + +// Hook for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) { + // IE<8 needs the *property* name + elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name ); + + // Use defaultChecked and defaultSelected for oldIE + } else { + elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true; + } + + return name; + } +}; + +// Retrieve booleans specially +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) { + + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ? + function( elem, name, isXML ) { + var ret, handle; + if ( !isXML ) { + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ name ]; + attrHandle[ name ] = ret; + ret = getter( elem, name, isXML ) != null ? + name.toLowerCase() : + null; + attrHandle[ name ] = handle; + } + return ret; + } : + function( elem, name, isXML ) { + if ( !isXML ) { + return elem[ jQuery.camelCase( "default-" + name ) ] ? + name.toLowerCase() : + null; + } + }; +}); + +// fix oldIE attroperties +if ( !getSetInput || !getSetAttribute ) { + jQuery.attrHooks.value = { + set: function( elem, value, name ) { + if ( jQuery.nodeName( elem, "input" ) ) { + // Does not return so that setAttribute is also used + elem.defaultValue = value; + } else { + // Use nodeHook if defined (#1954); otherwise setAttribute is fine + return nodeHook && nodeHook.set( elem, value, name ); + } + } + }; +} + +// IE6/7 do not support getting/setting some attributes with get/setAttribute +if ( !getSetAttribute ) { + + // Use this for any attribute in IE6/7 + // This fixes almost every IE6/7 issue + nodeHook = { + set: function( elem, value, name ) { + // Set the existing or create a new attribute node + var ret = elem.getAttributeNode( name ); + if ( !ret ) { + elem.setAttributeNode( + (ret = elem.ownerDocument.createAttribute( name )) + ); + } + + ret.value = value += ""; + + // Break association with cloned elements by also using setAttribute (#9646) + if ( name === "value" || value === elem.getAttribute( name ) ) { + return value; + } + } + }; + + // Some attributes are constructed with empty-string values when not defined + attrHandle.id = attrHandle.name = attrHandle.coords = + function( elem, name, isXML ) { + var ret; + if ( !isXML ) { + return (ret = elem.getAttributeNode( name )) && ret.value !== "" ? + ret.value : + null; + } + }; + + // Fixing value retrieval on a button requires this module + jQuery.valHooks.button = { + get: function( elem, name ) { + var ret = elem.getAttributeNode( name ); + if ( ret && ret.specified ) { + return ret.value; + } + }, + set: nodeHook.set + }; + + // Set contenteditable to false on removals(#10429) + // Setting to empty string throws an error as an invalid value + jQuery.attrHooks.contenteditable = { + set: function( elem, value, name ) { + nodeHook.set( elem, value === "" ? false : value, name ); + } + }; + + // Set width and height to auto instead of 0 on empty string( Bug #8150 ) + // This is for removals + jQuery.each([ "width", "height" ], function( i, name ) { + jQuery.attrHooks[ name ] = { + set: function( elem, value ) { + if ( value === "" ) { + elem.setAttribute( name, "auto" ); + return value; + } + } + }; + }); +} + +if ( !support.style ) { + jQuery.attrHooks.style = { + get: function( elem ) { + // Return undefined in the case of empty string + // Note: IE uppercases css property names, but if we were to .toLowerCase() + // .cssText, that would destroy case senstitivity in URL's, like in "background" + return elem.style.cssText || undefined; + }, + set: function( elem, value ) { + return ( elem.style.cssText = value + "" ); + } + }; +} + + + + +var rfocusable = /^(?:input|select|textarea|button|object)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend({ + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + name = jQuery.propFix[ name ] || name; + return this.each(function() { + // try/catch handles cases where IE balks (such as removing a property on window) + try { + this[ name ] = undefined; + delete this[ name ]; + } catch( e ) {} + }); + } +}); + +jQuery.extend({ + propFix: { + "for": "htmlFor", + "class": "className" + }, + + prop: function( elem, name, value ) { + var ret, hooks, notxml, + nType = elem.nodeType; + + // don't get/set properties on text, comment and attribute nodes + if ( !elem || nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + notxml = nType !== 1 || !jQuery.isXMLDoc( elem ); + + if ( notxml ) { + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ? + ret : + ( elem[ name ] = value ); + + } else { + return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ? + ret : + elem[ name ]; + } + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set + // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + return tabindex ? + parseInt( tabindex, 10 ) : + rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ? + 0 : + -1; + } + } + } +}); + +// Some attributes require a special call on IE +// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !support.hrefNormalized ) { + // href/src property should get the full normalized URL (#10299/#12915) + jQuery.each([ "href", "src" ], function( i, name ) { + jQuery.propHooks[ name ] = { + get: function( elem ) { + return elem.getAttribute( name, 4 ); + } + }; + }); +} + +// Support: Safari, IE9+ +// mis-reports the default selected property of an option +// Accessing the parent's selectedIndex property fixes it +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + var parent = elem.parentNode; + + if ( parent ) { + parent.selectedIndex; + + // Make sure that it also works with optgroups, see #5701 + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + return null; + } + }; +} + +jQuery.each([ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +}); + +// IE6/7 call enctype encoding +if ( !support.enctype ) { + jQuery.propFix.enctype = "encoding"; +} + + + + +var rclass = /[\t\r\n\f]/g; + +jQuery.fn.extend({ + addClass: function( value ) { + var classes, elem, cur, clazz, j, finalValue, + i = 0, + len = this.length, + proceed = typeof value === "string" && value; + + if ( jQuery.isFunction( value ) ) { + return this.each(function( j ) { + jQuery( this ).addClass( value.call( this, j, this.className ) ); + }); + } + + if ( proceed ) { + // The disjunction here is for better compressibility (see removeClass) + classes = ( value || "" ).match( rnotwhite ) || []; + + for ( ; i < len; i++ ) { + elem = this[ i ]; + cur = elem.nodeType === 1 && ( elem.className ? + ( " " + elem.className + " " ).replace( rclass, " " ) : + " " + ); + + if ( cur ) { + j = 0; + while ( (clazz = classes[j++]) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // only assign if different to avoid unneeded rendering. + finalValue = jQuery.trim( cur ); + if ( elem.className !== finalValue ) { + elem.className = finalValue; + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, clazz, j, finalValue, + i = 0, + len = this.length, + proceed = arguments.length === 0 || typeof value === "string" && value; + + if ( jQuery.isFunction( value ) ) { + return this.each(function( j ) { + jQuery( this ).removeClass( value.call( this, j, this.className ) ); + }); + } + if ( proceed ) { + classes = ( value || "" ).match( rnotwhite ) || []; + + for ( ; i < len; i++ ) { + elem = this[ i ]; + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( elem.className ? + ( " " + elem.className + " " ).replace( rclass, " " ) : + "" + ); + + if ( cur ) { + j = 0; + while ( (clazz = classes[j++]) ) { + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) >= 0 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // only assign if different to avoid unneeded rendering. + finalValue = value ? jQuery.trim( cur ) : ""; + if ( elem.className !== finalValue ) { + elem.className = finalValue; + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value; + + if ( typeof stateVal === "boolean" && type === "string" ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( jQuery.isFunction( value ) ) { + return this.each(function( i ) { + jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal ); + }); + } + + return this.each(function() { + if ( type === "string" ) { + // toggle individual class names + var className, + i = 0, + self = jQuery( this ), + classNames = value.match( rnotwhite ) || []; + + while ( (className = classNames[ i++ ]) ) { + // check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( type === strundefined || type === "boolean" ) { + if ( this.className ) { + // store className if set + jQuery._data( this, "__className__", this.className ); + } + + // If the element has a class name or if we're passed "false", + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || ""; + } + }); + }, + + hasClass: function( selector ) { + var className = " " + selector + " ", + i = 0, + l = this.length; + for ( ; i < l; i++ ) { + if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) { + return true; + } + } + + return false; + } +}); + + + + +// Return jQuery for attributes-only inclusion + + +jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " + + "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + + "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) { + + // Handle event binding + jQuery.fn[ name ] = function( data, fn ) { + return arguments.length > 0 ? + this.on( name, null, data, fn ) : + this.trigger( name ); + }; +}); + +jQuery.fn.extend({ + hover: function( fnOver, fnOut ) { + return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); + }, + + bind: function( types, data, fn ) { + return this.on( types, null, data, fn ); + }, + unbind: function( types, fn ) { + return this.off( types, null, fn ); + }, + + delegate: function( selector, types, data, fn ) { + return this.on( types, selector, data, fn ); + }, + undelegate: function( selector, types, fn ) { + // ( namespace ) or ( selector, types [, fn] ) + return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn ); + } +}); + + +var nonce = jQuery.now(); + +var rquery = (/\?/); + + + +var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g; + +jQuery.parseJSON = function( data ) { + // Attempt to parse using the native JSON parser first + if ( window.JSON && window.JSON.parse ) { + // Support: Android 2.3 + // Workaround failure to string-cast null input + return window.JSON.parse( data + "" ); + } + + var requireNonComma, + depth = null, + str = jQuery.trim( data + "" ); + + // Guard against invalid (and possibly dangerous) input by ensuring that nothing remains + // after removing valid tokens + return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) { + + // Force termination if we see a misplaced comma + if ( requireNonComma && comma ) { + depth = 0; + } + + // Perform no more replacements after returning to outermost depth + if ( depth === 0 ) { + return token; + } + + // Commas must not follow "[", "{", or "," + requireNonComma = open || comma; + + // Determine new depth + // array/object open ("[" or "{"): depth += true - false (increment) + // array/object close ("]" or "}"): depth += false - true (decrement) + // other cases ("," or primitive): depth += true - true (numeric cast) + depth += !close - !open; + + // Remove this token + return ""; + }) ) ? + ( Function( "return " + str ) )() : + jQuery.error( "Invalid JSON: " + data ); +}; + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml, tmp; + if ( !data || typeof data !== "string" ) { + return null; + } + try { + if ( window.DOMParser ) { // Standard + tmp = new DOMParser(); + xml = tmp.parseFromString( data, "text/xml" ); + } else { // IE + xml = new ActiveXObject( "Microsoft.XMLDOM" ); + xml.async = "false"; + xml.loadXML( data ); + } + } catch( e ) { + xml = undefined; + } + if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) { + jQuery.error( "Invalid XML: " + data ); + } + return xml; +}; + + +var + // Document location + ajaxLocParts, + ajaxLocation, + + rhash = /#.*$/, + rts = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat("*"); + +// #8138, IE may throw an exception when accessing +// a field from window.location if document.domain has been set +try { + ajaxLocation = location.href; +} catch( e ) { + // Use the href attribute of an A element + // since IE will modify it given document.location + ajaxLocation = document.createElement( "a" ); + ajaxLocation.href = ""; + ajaxLocation = ajaxLocation.href; +} + +// Segment location into parts +ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || []; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || []; + + if ( jQuery.isFunction( func ) ) { + // For each dataType in the dataTypeExpression + while ( (dataType = dataTypes[i++]) ) { + // Prepend if requested + if ( dataType.charAt( 0 ) === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + (structure[ dataType ] = structure[ dataType ] || []).unshift( func ); + + // Otherwise append + } else { + (structure[ dataType ] = structure[ dataType ] || []).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + }); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var deep, key, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + var firstDataType, ct, finalDataType, type, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader("Content-Type"); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s[ "throws" ] ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend({ + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: ajaxLocation, + type: "GET", + isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /xml/, + html: /html/, + json: /json/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": jQuery.parseJSON, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var // Cross-domain detection vars + parts, + // Loop variable + i, + // URL without anti-cache param + cacheURL, + // Response headers as string + responseHeadersString, + // timeout handle + timeoutTimer, + + // To know if global events are to be dispatched + fireGlobals, + + transport, + // Response headers + responseHeaders, + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + // Callbacks context + callbackContext = s.context || s, + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks("once memory"), + // Status-dependent callbacks + statusCode = s.statusCode || {}, + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + // The jqXHR state + state = 0, + // Default abort message + strAbort = "canceled", + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( state === 2 ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( (match = rheaders.exec( responseHeadersString )) ) { + responseHeaders[ match[1].toLowerCase() ] = match[ 2 ]; + } + } + match = responseHeaders[ key.toLowerCase() ]; + } + return match == null ? null : match; + }, + + // Raw string + getAllResponseHeaders: function() { + return state === 2 ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + var lname = name.toLowerCase(); + if ( !state ) { + name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( !state ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( state < 2 ) { + for ( code in map ) { + // Lazy-add the new callback in a way that preserves old ones + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } else { + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ).complete = completeDeferred.add; + jqXHR.success = jqXHR.done; + jqXHR.error = jqXHR.fail; + + // Remove hash character (#7531: and string promotion) + // Add protocol if not provided (#5866: IE7 issue with protocol-less urls) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ]; + + // A cross-domain request is in order when we have a protocol:host:port mismatch + if ( s.crossDomain == null ) { + parts = rurl.exec( s.url.toLowerCase() ); + s.crossDomain = !!( parts && + ( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] || + ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !== + ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) ) + ); + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( state === 2 ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + fireGlobals = s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger("ajaxStart"); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + cacheURL = s.url; + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // If data is available, append data to url + if ( s.data ) { + cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data ); + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add anti-cache in url if needed + if ( s.cache === false ) { + s.url = rts.test( cacheURL ) ? + + // If there is already a '_' parameter, set its value + cacheURL.replace( rts, "$1_=" + nonce++ ) : + + // Otherwise add one to the end + cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++; + } + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ? + s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) { + // Abort if not done already and return + return jqXHR.abort(); + } + + // aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + for ( i in { success: 1, error: 1, complete: 1 } ) { + jqXHR[ i ]( s[ i ] ); + } + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = setTimeout(function() { + jqXHR.abort("timeout"); + }, s.timeout ); + } + + try { + state = 1; + transport.send( requestHeaders, done ); + } catch ( e ) { + // Propagate exception as error if not done + if ( state < 2 ) { + done( -1, e ); + // Simply rethrow otherwise + } else { + throw e; + } + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Called once + if ( state === 2 ) { + return; + } + + // State is "done" now + state = 2; + + // Clear timeout if it exists + if ( timeoutTimer ) { + clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader("Last-Modified"); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader("etag"); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + // We extract error from statusText + // then normalize statusText and status for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger("ajaxStop"); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +}); + +jQuery.each( [ "get", "post" ], function( i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + // shift arguments if data argument was omitted + if ( jQuery.isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + return jQuery.ajax({ + url: url, + type: method, + dataType: type, + data: data, + success: callback + }); + }; +}); + +// Attach a bunch of functions for handling common AJAX events +jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) { + jQuery.fn[ type ] = function( fn ) { + return this.on( type, fn ); + }; +}); + + +jQuery._evalUrl = function( url ) { + return jQuery.ajax({ + url: url, + type: "GET", + dataType: "script", + async: false, + global: false, + "throws": true + }); +}; + + +jQuery.fn.extend({ + wrapAll: function( html ) { + if ( jQuery.isFunction( html ) ) { + return this.each(function(i) { + jQuery(this).wrapAll( html.call(this, i) ); + }); + } + + if ( this[0] ) { + // The elements to wrap the target around + var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true); + + if ( this[0].parentNode ) { + wrap.insertBefore( this[0] ); + } + + wrap.map(function() { + var elem = this; + + while ( elem.firstChild && elem.firstChild.nodeType === 1 ) { + elem = elem.firstChild; + } + + return elem; + }).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( jQuery.isFunction( html ) ) { + return this.each(function(i) { + jQuery(this).wrapInner( html.call(this, i) ); + }); + } + + return this.each(function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + }); + }, + + wrap: function( html ) { + var isFunction = jQuery.isFunction( html ); + + return this.each(function(i) { + jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html ); + }); + }, + + unwrap: function() { + return this.parent().each(function() { + if ( !jQuery.nodeName( this, "body" ) ) { + jQuery( this ).replaceWith( this.childNodes ); + } + }).end(); + } +}); + + +jQuery.expr.filters.hidden = function( elem ) { + // Support: Opera <= 12.12 + // Opera reports offsetWidths and offsetHeights less than zero on some elements + return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 || + (!support.reliableHiddenOffsets() && + ((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none"); +}; + +jQuery.expr.filters.visible = function( elem ) { + return !jQuery.expr.filters.hidden( elem ); +}; + + + + +var r20 = /%20/g, + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( jQuery.isArray( obj ) ) { + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + // Item is non-scalar (array or object), encode its numeric index. + buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add ); + } + }); + + } else if ( !traditional && jQuery.type( obj ) === "object" ) { + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, value ) { + // If value is a function, invoke it and return its value + value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value ); + s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value ); + }; + + // Set traditional to true for jQuery <= 1.3.2 behavior. + if ( traditional === undefined ) { + traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + }); + + } else { + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ).replace( r20, "+" ); +}; + +jQuery.fn.extend({ + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map(function() { + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + }) + .filter(function() { + var type = this.type; + // Use .is(":disabled") so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + }) + .map(function( i, elem ) { + var val = jQuery( this ).val(); + + return val == null ? + null : + jQuery.isArray( val ) ? + jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + }) : + { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + }).get(); + } +}); + + +// Create the request object +// (This is still attached to ajaxSettings for backward compatibility) +jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ? + // Support: IE6+ + function() { + + // XHR cannot access local files, always use ActiveX for that case + return !this.isLocal && + + // Support: IE7-8 + // oldIE XHR does not support non-RFC2616 methods (#13240) + // See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx + // and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9 + // Although this check for six methods instead of eight + // since IE also does not support "trace" and "connect" + /^(get|post|head|put|delete|options)$/i.test( this.type ) && + + createStandardXHR() || createActiveXHR(); + } : + // For all other browsers, use the standard XMLHttpRequest object + createStandardXHR; + +var xhrId = 0, + xhrCallbacks = {}, + xhrSupported = jQuery.ajaxSettings.xhr(); + +// Support: IE<10 +// Open requests must be manually aborted on unload (#5280) +if ( window.ActiveXObject ) { + jQuery( window ).on( "unload", function() { + for ( var key in xhrCallbacks ) { + xhrCallbacks[ key ]( undefined, true ); + } + }); +} + +// Determine support properties +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +xhrSupported = support.ajax = !!xhrSupported; + +// Create transport if the browser can provide an xhr +if ( xhrSupported ) { + + jQuery.ajaxTransport(function( options ) { + // Cross domain only allowed if supported through XMLHttpRequest + if ( !options.crossDomain || support.cors ) { + + var callback; + + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(), + id = ++xhrId; + + // Open the socket + xhr.open( options.type, options.url, options.async, options.username, options.password ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers["X-Requested-With"] ) { + headers["X-Requested-With"] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + // Support: IE<9 + // IE's ActiveXObject throws a 'Type Mismatch' exception when setting + // request header to a null-value. + // + // To keep consistent with other XHR implementations, cast the value + // to string and ignore `undefined`. + if ( headers[ i ] !== undefined ) { + xhr.setRequestHeader( i, headers[ i ] + "" ); + } + } + + // Do send the request + // This may raise an exception which is actually + // handled in jQuery.ajax (so no try/catch here) + xhr.send( ( options.hasContent && options.data ) || null ); + + // Listener + callback = function( _, isAbort ) { + var status, statusText, responses; + + // Was never called and is aborted or complete + if ( callback && ( isAbort || xhr.readyState === 4 ) ) { + // Clean up + delete xhrCallbacks[ id ]; + callback = undefined; + xhr.onreadystatechange = jQuery.noop; + + // Abort manually if needed + if ( isAbort ) { + if ( xhr.readyState !== 4 ) { + xhr.abort(); + } + } else { + responses = {}; + status = xhr.status; + + // Support: IE<10 + // Accessing binary-data responseText throws an exception + // (#11426) + if ( typeof xhr.responseText === "string" ) { + responses.text = xhr.responseText; + } + + // Firefox throws an exception when accessing + // statusText for faulty cross-domain requests + try { + statusText = xhr.statusText; + } catch( e ) { + // We normalize with Webkit giving an empty statusText + statusText = ""; + } + + // Filter status for non standard behaviors + + // If the request is local and we have data: assume a success + // (success with no data won't get notified, that's the best we + // can do given current implementations) + if ( !status && options.isLocal && !options.crossDomain ) { + status = responses.text ? 200 : 404; + // IE - #1450: sometimes returns 1223 when it should be 204 + } else if ( status === 1223 ) { + status = 204; + } + } + } + + // Call complete if needed + if ( responses ) { + complete( status, statusText, responses, xhr.getAllResponseHeaders() ); + } + }; + + if ( !options.async ) { + // if we're in sync mode we fire the callback + callback(); + } else if ( xhr.readyState === 4 ) { + // (IE6 & IE7) if it's in cache and has been + // retrieved directly we need to fire the callback + setTimeout( callback ); + } else { + // Add to the list of active xhr callbacks + xhr.onreadystatechange = xhrCallbacks[ id ] = callback; + } + }, + + abort: function() { + if ( callback ) { + callback( undefined, true ); + } + } + }; + } + }); +} + +// Functions to create xhrs +function createStandardXHR() { + try { + return new window.XMLHttpRequest(); + } catch( e ) {} +} + +function createActiveXHR() { + try { + return new window.ActiveXObject( "Microsoft.XMLHTTP" ); + } catch( e ) {} +} + + + + +// Install script dataType +jQuery.ajaxSetup({ + accepts: { + script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /(?:java|ecma)script/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +}); + +// Handle cache's special case and global +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + s.global = false; + } +}); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function(s) { + + // This transport only deals with cross domain requests + if ( s.crossDomain ) { + + var script, + head = document.head || jQuery("head")[0] || document.documentElement; + + return { + + send: function( _, callback ) { + + script = document.createElement("script"); + + script.async = true; + + if ( s.scriptCharset ) { + script.charset = s.scriptCharset; + } + + script.src = s.url; + + // Attach handlers for all browsers + script.onload = script.onreadystatechange = function( _, isAbort ) { + + if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) { + + // Handle memory leak in IE + script.onload = script.onreadystatechange = null; + + // Remove the script + if ( script.parentNode ) { + script.parentNode.removeChild( script ); + } + + // Dereference the script + script = null; + + // Callback if not abort + if ( !isAbort ) { + callback( 200, "success" ); + } + } + }; + + // Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending + // Use native DOM manipulation to avoid our domManip AJAX trickery + head.insertBefore( script, head.firstChild ); + }, + + abort: function() { + if ( script ) { + script.onload( undefined, true ); + } + } + }; + } +}); + + + + +var oldCallbacks = [], + rjsonp = /(=)\?(?=&|$)|\?\?/; + +// Default jsonp settings +jQuery.ajaxSetup({ + jsonp: "callback", + jsonpCallback: function() { + var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) ); + this[ callback ] = true; + return callback; + } +}); + +// Detect, normalize options and install callbacks for jsonp requests +jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) { + + var callbackName, overwritten, responseContainer, + jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ? + "url" : + typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data" + ); + + // Handle iff the expected data type is "jsonp" or we have a parameter to set + if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) { + + // Get callback name, remembering preexisting value associated with it + callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ? + s.jsonpCallback() : + s.jsonpCallback; + + // Insert callback into url or form data + if ( jsonProp ) { + s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName ); + } else if ( s.jsonp !== false ) { + s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName; + } + + // Use data converter to retrieve json after script execution + s.converters["script json"] = function() { + if ( !responseContainer ) { + jQuery.error( callbackName + " was not called" ); + } + return responseContainer[ 0 ]; + }; + + // force json dataType + s.dataTypes[ 0 ] = "json"; + + // Install callback + overwritten = window[ callbackName ]; + window[ callbackName ] = function() { + responseContainer = arguments; + }; + + // Clean-up function (fires after converters) + jqXHR.always(function() { + // Restore preexisting value + window[ callbackName ] = overwritten; + + // Save back as free + if ( s[ callbackName ] ) { + // make sure that re-using the options doesn't screw things around + s.jsonpCallback = originalSettings.jsonpCallback; + + // save the callback name for future use + oldCallbacks.push( callbackName ); + } + + // Call if it was a function and we have a response + if ( responseContainer && jQuery.isFunction( overwritten ) ) { + overwritten( responseContainer[ 0 ] ); + } + + responseContainer = overwritten = undefined; + }); + + // Delegate to script + return "script"; + } +}); + + + + +// data: string of html +// context (optional): If specified, the fragment will be created in this context, defaults to document +// keepScripts (optional): If true, will include scripts passed in the html string +jQuery.parseHTML = function( data, context, keepScripts ) { + if ( !data || typeof data !== "string" ) { + return null; + } + if ( typeof context === "boolean" ) { + keepScripts = context; + context = false; + } + context = context || document; + + var parsed = rsingleTag.exec( data ), + scripts = !keepScripts && []; + + // Single tag + if ( parsed ) { + return [ context.createElement( parsed[1] ) ]; + } + + parsed = jQuery.buildFragment( [ data ], context, scripts ); + + if ( scripts && scripts.length ) { + jQuery( scripts ).remove(); + } + + return jQuery.merge( [], parsed.childNodes ); +}; + + +// Keep a copy of the old load method +var _load = jQuery.fn.load; + +/** + * Load a url into a page + */ +jQuery.fn.load = function( url, params, callback ) { + if ( typeof url !== "string" && _load ) { + return _load.apply( this, arguments ); + } + + var selector, response, type, + self = this, + off = url.indexOf(" "); + + if ( off >= 0 ) { + selector = jQuery.trim( url.slice( off, url.length ) ); + url = url.slice( 0, off ); + } + + // If it's a function + if ( jQuery.isFunction( params ) ) { + + // We assume that it's the callback + callback = params; + params = undefined; + + // Otherwise, build a param string + } else if ( params && typeof params === "object" ) { + type = "POST"; + } + + // If we have elements to modify, make the request + if ( self.length > 0 ) { + jQuery.ajax({ + url: url, + + // if "type" variable is undefined, then "GET" method will be used + type: type, + dataType: "html", + data: params + }).done(function( responseText ) { + + // Save response for use in complete callback + response = arguments; + + self.html( selector ? + + // If a selector was specified, locate the right elements in a dummy div + // Exclude scripts to avoid IE 'Permission Denied' errors + jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) : + + // Otherwise use the full result + responseText ); + + }).complete( callback && function( jqXHR, status ) { + self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] ); + }); + } + + return this; +}; + + + + +jQuery.expr.filters.animated = function( elem ) { + return jQuery.grep(jQuery.timers, function( fn ) { + return elem === fn.elem; + }).length; +}; + + + + + +var docElem = window.document.documentElement; + +/** + * Gets a window from an element + */ +function getWindow( elem ) { + return jQuery.isWindow( elem ) ? + elem : + elem.nodeType === 9 ? + elem.defaultView || elem.parentWindow : + false; +} + +jQuery.offset = { + setOffset: function( elem, options, i ) { + var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition, + position = jQuery.css( elem, "position" ), + curElem = jQuery( elem ), + props = {}; + + // set position first, in-case top/left are set even on static elem + if ( position === "static" ) { + elem.style.position = "relative"; + } + + curOffset = curElem.offset(); + curCSSTop = jQuery.css( elem, "top" ); + curCSSLeft = jQuery.css( elem, "left" ); + calculatePosition = ( position === "absolute" || position === "fixed" ) && + jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1; + + // need to be able to calculate position if either top or left is auto and position is either absolute or fixed + if ( calculatePosition ) { + curPosition = curElem.position(); + curTop = curPosition.top; + curLeft = curPosition.left; + } else { + curTop = parseFloat( curCSSTop ) || 0; + curLeft = parseFloat( curCSSLeft ) || 0; + } + + if ( jQuery.isFunction( options ) ) { + options = options.call( elem, i, curOffset ); + } + + if ( options.top != null ) { + props.top = ( options.top - curOffset.top ) + curTop; + } + if ( options.left != null ) { + props.left = ( options.left - curOffset.left ) + curLeft; + } + + if ( "using" in options ) { + options.using.call( elem, props ); + } else { + curElem.css( props ); + } + } +}; + +jQuery.fn.extend({ + offset: function( options ) { + if ( arguments.length ) { + return options === undefined ? + this : + this.each(function( i ) { + jQuery.offset.setOffset( this, options, i ); + }); + } + + var docElem, win, + box = { top: 0, left: 0 }, + elem = this[ 0 ], + doc = elem && elem.ownerDocument; + + if ( !doc ) { + return; + } + + docElem = doc.documentElement; + + // Make sure it's not a disconnected DOM node + if ( !jQuery.contains( docElem, elem ) ) { + return box; + } + + // If we don't have gBCR, just use 0,0 rather than error + // BlackBerry 5, iOS 3 (original iPhone) + if ( typeof elem.getBoundingClientRect !== strundefined ) { + box = elem.getBoundingClientRect(); + } + win = getWindow( doc ); + return { + top: box.top + ( win.pageYOffset || docElem.scrollTop ) - ( docElem.clientTop || 0 ), + left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 ) + }; + }, + + position: function() { + if ( !this[ 0 ] ) { + return; + } + + var offsetParent, offset, + parentOffset = { top: 0, left: 0 }, + elem = this[ 0 ]; + + // fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent + if ( jQuery.css( elem, "position" ) === "fixed" ) { + // we assume that getBoundingClientRect is available when computed position is fixed + offset = elem.getBoundingClientRect(); + } else { + // Get *real* offsetParent + offsetParent = this.offsetParent(); + + // Get correct offsets + offset = this.offset(); + if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) { + parentOffset = offsetParent.offset(); + } + + // Add offsetParent borders + parentOffset.top += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true ); + parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true ); + } + + // Subtract parent offsets and element margins + // note: when an element has margin: auto the offsetLeft and marginLeft + // are the same in Safari causing offset.left to incorrectly be 0 + return { + top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ), + left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true) + }; + }, + + offsetParent: function() { + return this.map(function() { + var offsetParent = this.offsetParent || docElem; + + while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) { + offsetParent = offsetParent.offsetParent; + } + return offsetParent || docElem; + }); + } +}); + +// Create scrollLeft and scrollTop methods +jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) { + var top = /Y/.test( prop ); + + jQuery.fn[ method ] = function( val ) { + return access( this, function( elem, method, val ) { + var win = getWindow( elem ); + + if ( val === undefined ) { + return win ? (prop in win) ? win[ prop ] : + win.document.documentElement[ method ] : + elem[ method ]; + } + + if ( win ) { + win.scrollTo( + !top ? val : jQuery( win ).scrollLeft(), + top ? val : jQuery( win ).scrollTop() + ); + + } else { + elem[ method ] = val; + } + }, method, val, arguments.length, null ); + }; +}); + +// Add the top/left cssHooks using jQuery.fn.position +// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084 +// getComputedStyle returns percent when specified for top/left/bottom/right +// rather than make the css module depend on the offset module, we just check for it here +jQuery.each( [ "top", "left" ], function( i, prop ) { + jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition, + function( elem, computed ) { + if ( computed ) { + computed = curCSS( elem, prop ); + // if curCSS returns percentage, fallback to offset + return rnumnonpx.test( computed ) ? + jQuery( elem ).position()[ prop ] + "px" : + computed; + } + } + ); +}); + + +// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods +jQuery.each( { Height: "height", Width: "width" }, function( name, type ) { + jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) { + // margin is only for outerHeight, outerWidth + jQuery.fn[ funcName ] = function( margin, value ) { + var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ), + extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" ); + + return access( this, function( elem, type, value ) { + var doc; + + if ( jQuery.isWindow( elem ) ) { + // As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there + // isn't a whole lot we can do. See pull request at this URL for discussion: + // https://github.com/jquery/jquery/pull/764 + return elem.document.documentElement[ "client" + name ]; + } + + // Get document width or height + if ( elem.nodeType === 9 ) { + doc = elem.documentElement; + + // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest + // unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it. + return Math.max( + elem.body[ "scroll" + name ], doc[ "scroll" + name ], + elem.body[ "offset" + name ], doc[ "offset" + name ], + doc[ "client" + name ] + ); + } + + return value === undefined ? + // Get width or height on the element, requesting but not forcing parseFloat + jQuery.css( elem, type, extra ) : + + // Set width or height on the element + jQuery.style( elem, type, value, extra ); + }, type, chainable ? margin : undefined, chainable, null ); + }; + }); +}); + + +// The number of elements contained in the matched element set +jQuery.fn.size = function() { + return this.length; +}; + +jQuery.fn.andSelf = jQuery.fn.addBack; + + + + +// Register as a named AMD module, since jQuery can be concatenated with other +// files that may use define, but not via a proper concatenation script that +// understands anonymous AMD modules. 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*/ .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ .highlight .w { color: #bbbbbb } /* Text.Whitespace */ +.highlight .mb { color: #208050 } /* Literal.Number.Bin */ .highlight .mf { color: #208050 } /* Literal.Number.Float */ .highlight .mh { color: #208050 } /* Literal.Number.Hex */ .highlight .mi { color: #208050 } /* Literal.Number.Integer */ diff --git a/docs/user/html/pymoose/_static/searchtools.js b/docs/user/snippets/_build/html/_static/searchtools.js similarity index 67% rename from docs/user/html/pymoose/_static/searchtools.js rename to docs/user/snippets/_build/html/_static/searchtools.js index 11b85cb80f1746648236af21c9ddb6f270e0520a..0e794fd3e906970a10812199e11f9f159ab906b5 100644 --- a/docs/user/html/pymoose/_static/searchtools.js +++ b/docs/user/snippets/_build/html/_static/searchtools.js @@ -4,38 +4,11 @@ * * Sphinx JavaScript utilties for the full-text search. * - * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ -/** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words, hlwords is the list of normal, unstemmed - * words. the first one is used to find the occurance, the - * latter for highlighting it. - */ - -jQuery.makeSearchSummary = function(text, keywords, hlwords) { - var textLower = text.toLowerCase(); - var start = 0; - $.each(keywords, function() { - var i = textLower.indexOf(this.toLowerCase()); - if (i > -1) - start = i; - }); - start = Math.max(start - 120, 0); - var excerpt = ((start > 0) ? '...' : '') + - $.trim(text.substr(start, 240)) + - ((start + 240 - text.length) ? '...' : ''); - var rv = $('<div class="context"></div>').text(excerpt); - $.each(hlwords, function() { - rv = rv.highlightText(this, 'highlighted'); - }); - return rv; -} - /** * Porter Stemmer @@ -220,6 +193,38 @@ var Stemmer = function() { } + +/** + * Simple result scoring code. + */ +var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 +}; + + /** * Search Module */ @@ -273,19 +278,20 @@ var Search = { if (this._pulse_status >= 0) return; function pulse() { + var i; Search._pulse_status = (Search._pulse_status + 1) % 4; var dotString = ''; - for (var i = 0; i < Search._pulse_status; i++) + for (i = 0; i < Search._pulse_status; i++) dotString += '.'; Search.dots.text(dotString); if (Search._pulse_status > -1) window.setTimeout(pulse, 500); - }; + } pulse(); }, /** - * perform a search for something + * perform a search for something (or wait until index is loaded) */ performSearch : function(query) { // create the required interface elements @@ -305,41 +311,46 @@ var Search = { this.deferQuery(query); }, + /** + * execute search (requires search index to be loaded) + */ query : function(query) { + var i; var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; - // Stem the searchterms and add them to the correct list + // stem the searchterms and add them to the correct list var stemmer = new Stemmer(); var searchterms = []; var excluded = []; var hlterms = []; var tmp = query.split(/\s+/); var objectterms = []; - for (var i = 0; i < tmp.length; i++) { - if (tmp[i] != "") { + for (i = 0; i < tmp.length; i++) { + if (tmp[i] !== "") { objectterms.push(tmp[i].toLowerCase()); } - if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) || - tmp[i] == "") { + if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] === "") { // skip this "word" continue; } // stem the word - var word = stemmer.stemWord(tmp[i]).toLowerCase(); + var word = stemmer.stemWord(tmp[i].toLowerCase()); + var toAppend; // select the correct list if (word[0] == '-') { - var toAppend = excluded; + toAppend = excluded; word = word.substr(1); } else { - var toAppend = searchterms; + toAppend = searchterms; hlterms.push(tmp[i].toLowerCase()); } // only add if not already in the list - if (!$.contains(toAppend, word)) + if (!$u.contains(toAppend, word)) toAppend.push(word); - }; + } var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); // console.debug('SEARCH: searching for:'); @@ -347,89 +358,51 @@ var Search = { // console.info('excluded: ', excluded); // prepare search - var filenames = this._index.filenames; - var titles = this._index.titles; var terms = this._index.terms; - var fileMap = {}; - var files = null; - // different result priorities - var importantResults = []; - var objectResults = []; - var regularResults = []; - var unimportantResults = []; + var titleterms = this._index.titleterms; + + // array of [filename, title, anchor, descr, score] + var results = []; $('#search-progress').empty(); // lookup as object - for (var i = 0; i < objectterms.length; i++) { - var others = [].concat(objectterms.slice(0,i), - objectterms.slice(i+1, objectterms.length)) - var results = this.performObjectSearch(objectterms[i], others); - // Assume first word is most likely to be the object, - // other words more likely to be in description. - // Therefore put matches for earlier words first. - // (Results are eventually used in reverse order). - objectResults = results[0].concat(objectResults); - importantResults = results[1].concat(importantResults); - unimportantResults = results[2].concat(unimportantResults); - } - - // perform the search on the required terms - for (var i = 0; i < searchterms.length; i++) { - var word = searchterms[i]; - // no match but word was a required one - if ((files = terms[word]) == null) - break; - if (files.length == undefined) { - files = [files]; - } - // create the mapping - for (var j = 0; j < files.length; j++) { - var file = files[j]; - if (file in fileMap) - fileMap[file].push(word); - else - fileMap[file] = [word]; - } + for (i = 0; i < objectterms.length; i++) { + var others = [].concat(objectterms.slice(0, i), + objectterms.slice(i+1, objectterms.length)); + results = results.concat(this.performObjectSearch(objectterms[i], others)); } - // now check if the files don't contain excluded terms - for (var file in fileMap) { - var valid = true; - - // check if all requirements are matched - if (fileMap[file].length != searchterms.length) - continue; - - // ensure that none of the excluded terms is in the - // search result. - for (var i = 0; i < excluded.length; i++) { - if (terms[excluded[i]] == file || - $.contains(terms[excluded[i]] || [], file)) { - valid = false; - break; - } - } + // lookup as search terms in fulltext + results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term)) + .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title)); - // if we have still a valid result we can add it - // to the result list - if (valid) - regularResults.push([filenames[file], titles[file], '', null]); + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + for (i = 0; i < results.length; i++) + results[i][4] = Scorer.score(results[i]); } - // delete unused variables in order to not waste - // memory until list is retrieved completely - delete filenames, titles, terms; - - // now sort the regular results descending by title - regularResults.sort(function(a, b) { - var left = a[1].toLowerCase(); - var right = b[1].toLowerCase(); - return (left > right) ? -1 : ((left < right) ? 1 : 0); + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort(function(a, b) { + var left = a[4]; + var right = b[4]; + if (left > right) { + return 1; + } else if (left < right) { + return -1; + } else { + // same score: sort alphabetically + left = a[1].toLowerCase(); + right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); + } }); - // combine all results - var results = unimportantResults.concat(regularResults) - .concat(objectResults).concat(importantResults); + // for debugging + //Search.lastresults = results.slice(); // a copy + //console.info('search results:', Search.lastresults); // print the results var resultCount = results.length; @@ -438,7 +411,7 @@ var Search = { if (results.length) { var item = results.pop(); var listItem = $('<li style="display:none"></li>'); - if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') { + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') { // dirhtml builder var dirname = item[0] + '/'; if (dirname.match(/\/index\/$/)) { @@ -466,8 +439,8 @@ var Search = { dataType: "text", complete: function(jqxhr, textstatus) { var data = jqxhr.responseText; - if (data !== '') { - listItem.append($.makeSearchSummary(data, searchterms, hlterms)); + if (data !== '' && data !== undefined) { + listItem.append(Search.makeSearchSummary(data, searchterms, hlterms)); } Search.output.append(listItem); listItem.slideDown(5, function() { @@ -496,20 +469,32 @@ var Search = { displayNextItem(); }, + /** + * search for object names + */ performObjectSearch : function(object, otherterms) { var filenames = this._index.filenames; var objects = this._index.objects; var objnames = this._index.objnames; var titles = this._index.titles; - var importantResults = []; - var objectResults = []; - var unimportantResults = []; + var i; + var results = []; for (var prefix in objects) { for (var name in objects[prefix]) { var fullname = (prefix ? prefix + '.' : '') + name; if (fullname.toLowerCase().indexOf(object) > -1) { + var score = 0; + var parts = fullname.split('.'); + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullname == object || parts[parts.length - 1] == object) { + score += Scorer.objNameMatch; + // matches in last name + } else if (parts[parts.length - 1].indexOf(object) > -1) { + score += Scorer.objPartialMatch; + } var match = objects[prefix][name]; var objname = objnames[match[1]][2]; var title = titles[match[0]]; @@ -519,7 +504,7 @@ var Search = { var haystack = (prefix + ' ' + name + ' ' + objname + ' ' + title).toLowerCase(); var allfound = true; - for (var i = 0; i < otherterms.length; i++) { + for (i = 0; i < otherterms.length; i++) { if (haystack.indexOf(otherterms[i]) == -1) { allfound = false; break; @@ -530,37 +515,107 @@ var Search = { } } var descr = objname + _(', in ') + title; - anchor = match[3]; - if (anchor == '') + + var anchor = match[3]; + if (anchor === '') anchor = fullname; else if (anchor == '-') anchor = objnames[match[1]][1] + '-' + fullname; - result = [filenames[match[0]], fullname, '#'+anchor, descr]; - switch (match[2]) { - case 1: objectResults.push(result); break; - case 0: importantResults.push(result); break; - case 2: unimportantResults.push(result); break; + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) { + score += Scorer.objPrio[match[2]]; + } else { + score += Scorer.objPrioDefault; } + results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]); } } } - // sort results descending - objectResults.sort(function(a, b) { - return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); - }); + return results; + }, - importantResults.sort(function(a, b) { - return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); - }); + /** + * search for full-text terms in the index + */ + performTermsSearch : function(searchterms, excluded, terms, score) { + var filenames = this._index.filenames; + var titles = this._index.titles; - unimportantResults.sort(function(a, b) { - return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); - }); + var i, j, file, files; + var fileMap = {}; + var results = []; - return [importantResults, objectResults, unimportantResults] + // perform the search on the required terms + for (i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) === undefined) + break; + if (files.length === undefined) { + files = [files]; + } + // create the mapping + for (j = 0; j < files.length; j++) { + file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } + } + + // now check if the files don't contain excluded terms + for (file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the search result + for (i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $u.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } + } + + // if we have still a valid result we can add it to the result list + if (valid) { + results.push([filenames[file], titles[file], '', null, score]); + } + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words, hlwords is the list of normal, unstemmed + * words. the first one is used to find the occurance, the + * latter for highlighting it. + */ + makeSearchSummary : function(text, keywords, hlwords) { + var textLower = text.toLowerCase(); + var start = 0; + $.each(keywords, function() { + var i = textLower.indexOf(this.toLowerCase()); + if (i > -1) + start = i; + }); + start = Math.max(start - 120, 0); + var excerpt = ((start > 0) ? '...' : '') + + $.trim(text.substr(start, 240)) + + ((start + 240 - text.length) ? '...' : ''); + var rv = $('<div class="context"></div>').text(excerpt); + $.each(hlwords, function() { + rv = rv.highlightText(this, 'highlighted'); + }); + return rv; } -} +}; $(document).ready(function() { Search.init(); diff --git a/docs/user/html/pymoose/_static/underscore.js b/docs/user/snippets/_build/html/_static/underscore-1.3.1.js similarity index 57% rename from docs/user/html/pymoose/_static/underscore.js rename to docs/user/snippets/_build/html/_static/underscore-1.3.1.js index a12f0d96cfb48a02d518427b26c333bac622810a..208d4cd890c3183d946092ebe982738ade565061 100644 --- a/docs/user/html/pymoose/_static/underscore.js +++ b/docs/user/snippets/_build/html/_static/underscore-1.3.1.js @@ -1,7 +1,10 @@ -// Underscore.js 1.4.4 -// http://underscorejs.org -// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. -// Underscore may be freely distributed under the MIT license. +// Underscore.js 1.3.1 +// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. +// Underscore is freely distributable under the MIT license. +// Portions of Underscore are inspired or borrowed from Prototype, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore (function() { @@ -21,9 +24,8 @@ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; // Create quick reference variables for speed access to core prototypes. - var push = ArrayProto.push, - slice = ArrayProto.slice, - concat = ArrayProto.concat, + var slice = ArrayProto.slice, + unshift = ArrayProto.unshift, toString = ObjProto.toString, hasOwnProperty = ObjProto.hasOwnProperty; @@ -44,11 +46,7 @@ nativeBind = FuncProto.bind; // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; + var _ = function(obj) { return new wrapper(obj); }; // Export the Underscore object for **Node.js**, with // backwards-compatibility for the old `require()` API. If we're in @@ -60,11 +58,11 @@ } exports._ = _; } else { - root._ = _; + root['_'] = _; } // Current version. - _.VERSION = '1.4.4'; + _.VERSION = '1.3.1'; // Collection Functions // -------------------- @@ -78,7 +76,7 @@ obj.forEach(iterator, context); } else if (obj.length === +obj.length) { for (var i = 0, l = obj.length; i < l; i++) { - if (iterator.call(context, obj[i], i, obj) === breaker) return; + if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return; } } else { for (var key in obj) { @@ -98,11 +96,10 @@ each(obj, function(value, index, list) { results[results.length] = iterator.call(context, value, index, list); }); + if (obj.length === +obj.length) results.length = obj.length; return results; }; - var reduceError = 'Reduce of empty array with no initial value'; - // **Reduce** builds up a single result from a list of values, aka `inject`, // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available. _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) { @@ -120,7 +117,7 @@ memo = iterator.call(context, memo, value, index, list); } }); - if (!initial) throw new TypeError(reduceError); + if (!initial) throw new TypeError('Reduce of empty array with no initial value'); return memo; }; @@ -133,22 +130,9 @@ if (context) iterator = _.bind(iterator, context); return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); } - var length = obj.length; - if (length !== +length) { - var keys = _.keys(obj); - length = keys.length; - } - each(obj, function(value, index, list) { - index = keys ? keys[--length] : --length; - if (!initial) { - memo = obj[index]; - initial = true; - } else { - memo = iterator.call(context, memo, obj[index], index, list); - } - }); - if (!initial) throw new TypeError(reduceError); - return memo; + var reversed = _.toArray(obj).reverse(); + if (context && !initial) iterator = _.bind(iterator, context); + return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator); }; // Return the first value which passes a truth test. Aliased as `detect`. @@ -178,23 +162,25 @@ // Return all the elements for which a truth test fails. _.reject = function(obj, iterator, context) { - return _.filter(obj, function(value, index, list) { - return !iterator.call(context, value, index, list); - }, context); + var results = []; + if (obj == null) return results; + each(obj, function(value, index, list) { + if (!iterator.call(context, value, index, list)) results[results.length] = value; + }); + return results; }; // Determine whether all of the elements match a truth test. // Delegates to **ECMAScript 5**'s native `every` if available. // Aliased as `all`. _.every = _.all = function(obj, iterator, context) { - iterator || (iterator = _.identity); var result = true; if (obj == null) return result; if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context); each(obj, function(value, index, list) { if (!(result = result && iterator.call(context, value, index, list))) return breaker; }); - return !!result; + return result; }; // Determine if at least one element in the object matches a truth test. @@ -211,22 +197,23 @@ return !!result; }; - // Determine if the array or object contains a given value (using `===`). - // Aliased as `include`. - _.contains = _.include = function(obj, target) { - if (obj == null) return false; + // Determine if a given value is included in the array or object using `===`. + // Aliased as `contains`. + _.include = _.contains = function(obj, target) { + var found = false; + if (obj == null) return found; if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1; - return any(obj, function(value) { + found = any(obj, function(value) { return value === target; }); + return found; }; // Invoke a method (with arguments) on every item in a collection. _.invoke = function(obj, method) { var args = slice.call(arguments, 2); - var isFunc = _.isFunction(method); return _.map(obj, function(value) { - return (isFunc ? method : value[method]).apply(value, args); + return (_.isFunction(method) ? method || value : value[method]).apply(value, args); }); }; @@ -235,33 +222,11 @@ return _.map(obj, function(value){ return value[key]; }); }; - // Convenience version of a common use case of `filter`: selecting only objects - // containing specific `key:value` pairs. - _.where = function(obj, attrs, first) { - if (_.isEmpty(attrs)) return first ? null : []; - return _[first ? 'find' : 'filter'](obj, function(value) { - for (var key in attrs) { - if (attrs[key] !== value[key]) return false; - } - return true; - }); - }; - - // Convenience version of a common use case of `find`: getting the first object - // containing specific `key:value` pairs. - _.findWhere = function(obj, attrs) { - return _.where(obj, attrs, true); - }; - // Return the maximum element or (element-based computation). - // Can't optimize arrays of integers longer than 65,535 elements. - // See: https://bugs.webkit.org/show_bug.cgi?id=80797 _.max = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.max.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return -Infinity; - var result = {computed : -Infinity, value: -Infinity}; + var result = {computed : -Infinity}; each(obj, function(value, index, list) { var computed = iterator ? iterator.call(context, value, index, list) : value; computed >= result.computed && (result = {value : value, computed : computed}); @@ -271,11 +236,9 @@ // Return the minimum element (or element-based computation). _.min = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.min.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return Infinity; - var result = {computed : Infinity, value: Infinity}; + var result = {computed : Infinity}; each(obj, function(value, index, list) { var computed = iterator ? iterator.call(context, value, index, list) : value; computed < result.computed && (result = {value : value, computed : computed}); @@ -285,110 +248,81 @@ // Shuffle an array. _.shuffle = function(obj) { - var rand; - var index = 0; - var shuffled = []; - each(obj, function(value) { - rand = _.random(index++); - shuffled[index - 1] = shuffled[rand]; - shuffled[rand] = value; + var shuffled = [], rand; + each(obj, function(value, index, list) { + if (index == 0) { + shuffled[0] = value; + } else { + rand = Math.floor(Math.random() * (index + 1)); + shuffled[index] = shuffled[rand]; + shuffled[rand] = value; + } }); return shuffled; }; - // An internal function to generate lookup iterators. - var lookupIterator = function(value) { - return _.isFunction(value) ? value : function(obj){ return obj[value]; }; - }; - // Sort the object's values by a criterion produced by an iterator. - _.sortBy = function(obj, value, context) { - var iterator = lookupIterator(value); + _.sortBy = function(obj, iterator, context) { return _.pluck(_.map(obj, function(value, index, list) { return { value : value, - index : index, criteria : iterator.call(context, value, index, list) }; }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index < right.index ? -1 : 1; + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; }), 'value'); }; - // An internal function used for aggregate "group by" operations. - var group = function(obj, value, context, behavior) { + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = function(obj, val) { var result = {}; - var iterator = lookupIterator(value || _.identity); + var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; }; each(obj, function(value, index) { - var key = iterator.call(context, value, index, obj); - behavior(result, key, value); + var key = iterator(value, index); + (result[key] || (result[key] = [])).push(value); }); return result; }; - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = function(obj, value, context) { - return group(obj, value, context, function(result, key, value) { - (_.has(result, key) ? result[key] : (result[key] = [])).push(value); - }); - }; - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = function(obj, value, context) { - return group(obj, value, context, function(result, key) { - if (!_.has(result, key)) result[key] = 0; - result[key]++; - }); - }; - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iterator, context) { - iterator = iterator == null ? _.identity : lookupIterator(iterator); - var value = iterator.call(context, obj); + // Use a comparator function to figure out at what index an object should + // be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iterator) { + iterator || (iterator = _.identity); var low = 0, high = array.length; while (low < high) { - var mid = (low + high) >>> 1; - iterator.call(context, array[mid]) < value ? low = mid + 1 : high = mid; + var mid = (low + high) >> 1; + iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid; } return low; }; // Safely convert anything iterable into a real, live array. - _.toArray = function(obj) { - if (!obj) return []; - if (_.isArray(obj)) return slice.call(obj); - if (obj.length === +obj.length) return _.map(obj, _.identity); - return _.values(obj); + _.toArray = function(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + if (_.isArray(iterable)) return slice.call(iterable); + if (_.isArguments(iterable)) return slice.call(iterable); + return _.values(iterable); }; // Return the number of elements in an object. _.size = function(obj) { - if (obj == null) return 0; - return (obj.length === +obj.length) ? obj.length : _.keys(obj).length; + return _.toArray(obj).length; }; // Array Functions // --------------- // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { - if (array == null) return void 0; + // values in the array. Aliased as `head`. The **guard** check allows it to work + // with `_.map`. + _.first = _.head = function(array, n, guard) { return (n != null) && !guard ? slice.call(array, 0, n) : array[0]; }; - // Returns everything but the last entry of the array. Especially useful on + // Returns everything but the last entry of the array. Especcialy useful on // the arguments object. Passing **n** will return all the values in // the array, excluding the last N. The **guard** check allows it to work with // `_.map`. @@ -399,7 +333,6 @@ // Get the last element of an array. Passing **n** will return the last N // values in the array. The **guard** check allows it to work with `_.map`. _.last = function(array, n, guard) { - if (array == null) return void 0; if ((n != null) && !guard) { return slice.call(array, Math.max(array.length - n, 0)); } else { @@ -407,34 +340,26 @@ } }; - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. The **guard** + // Returns everything but the first entry of the array. Aliased as `tail`. + // Especially useful on the arguments object. Passing an **index** will return + // the rest of the values in the array from that index onward. The **guard** // check allows it to work with `_.map`. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, (n == null) || guard ? 1 : n); + _.rest = _.tail = function(array, index, guard) { + return slice.call(array, (index == null) || guard ? 1 : index); }; // Trim out all falsy values from an array. _.compact = function(array) { - return _.filter(array, _.identity); - }; - - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, output) { - each(input, function(value) { - if (_.isArray(value)) { - shallow ? push.apply(output, value) : flatten(value, shallow, output); - } else { - output.push(value); - } - }); - return output; + return _.filter(array, function(value){ return !!value; }); }; // Return a completely flattened version of an array. _.flatten = function(array, shallow) { - return flatten(array, shallow, []); + return _.reduce(array, function(memo, value) { + if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value)); + memo[memo.length] = value; + return memo; + }, []); }; // Return a version of the array that does not contain the specified value(s). @@ -445,33 +370,28 @@ // Produce a duplicate-free version of the array. If the array has already // been sorted, you have the option of using a faster algorithm. // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iterator, context) { - if (_.isFunction(isSorted)) { - context = iterator; - iterator = isSorted; - isSorted = false; - } - var initial = iterator ? _.map(array, iterator, context) : array; - var results = []; - var seen = []; - each(initial, function(value, index) { - if (isSorted ? (!index || seen[seen.length - 1] !== value) : !_.contains(seen, value)) { - seen.push(value); - results.push(array[index]); + _.uniq = _.unique = function(array, isSorted, iterator) { + var initial = iterator ? _.map(array, iterator) : array; + var result = []; + _.reduce(initial, function(memo, el, i) { + if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) { + memo[memo.length] = el; + result[result.length] = array[i]; } - }); - return results; + return memo; + }, []); + return result; }; // Produce an array that contains the union: each distinct element from all of // the passed-in arrays. _.union = function() { - return _.uniq(concat.apply(ArrayProto, arguments)); + return _.uniq(_.flatten(arguments, true)); }; // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { + // passed-in arrays. (Aliased as "intersect" for back-compat.) + _.intersection = _.intersect = function(array) { var rest = slice.call(arguments, 1); return _.filter(_.uniq(array), function(item) { return _.every(rest, function(other) { @@ -483,8 +403,8 @@ // Take the difference between one array and a number of other arrays. // Only the elements present in just the first array will remain. _.difference = function(array) { - var rest = concat.apply(ArrayProto, slice.call(arguments, 1)); - return _.filter(array, function(value){ return !_.contains(rest, value); }); + var rest = _.flatten(slice.call(arguments, 1)); + return _.filter(array, function(value){ return !_.include(rest, value); }); }; // Zip together multiple lists into a single array -- elements that share @@ -493,28 +413,10 @@ var args = slice.call(arguments); var length = _.max(_.pluck(args, 'length')); var results = new Array(length); - for (var i = 0; i < length; i++) { - results[i] = _.pluck(args, "" + i); - } + for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i); return results; }; - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - if (list == null) return {}; - var result = {}; - for (var i = 0, l = list.length; i < l; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**), // we need this function. Return the position of the first occurrence of an // item in an array, or -1 if the item is not included in the array. @@ -523,29 +425,22 @@ // for **isSorted** to use binary search. _.indexOf = function(array, item, isSorted) { if (array == null) return -1; - var i = 0, l = array.length; + var i, l; if (isSorted) { - if (typeof isSorted == 'number') { - i = (isSorted < 0 ? Math.max(0, l + isSorted) : isSorted); - } else { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; - } + i = _.sortedIndex(array, item); + return array[i] === item ? i : -1; } - if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item, isSorted); - for (; i < l; i++) if (array[i] === item) return i; + if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item); + for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i; return -1; }; // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available. - _.lastIndexOf = function(array, item, from) { + _.lastIndexOf = function(array, item) { if (array == null) return -1; - var hasIndex = from != null; - if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) { - return hasIndex ? array.lastIndexOf(item, from) : array.lastIndexOf(item); - } - var i = (hasIndex ? from : array.length); - while (i--) if (array[i] === item) return i; + if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item); + var i = array.length; + while (i--) if (i in array && array[i] === item) return i; return -1; }; @@ -574,23 +469,25 @@ // Function (ahem) Functions // ------------------ + // Reusable constructor function for prototype setting. + var ctor = function(){}; + // Create a function bound to a given object (assigning `this`, and arguments, - // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if - // available. - _.bind = function(func, context) { + // optionally). Binding with arguments is also known as `curry`. + // Delegates to **ECMAScript 5**'s native `Function.bind` if available. + // We check for `func.bind` first, to fail fast when `func` is undefined. + _.bind = function bind(func, context) { + var bound, args; if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); - var args = slice.call(arguments, 2); - return function() { - return func.apply(context, args.concat(slice.call(arguments))); - }; - }; - - // Partially apply a function by creating a version that has had some of its - // arguments pre-filled, without changing its dynamic `this` context. - _.partial = function(func) { - var args = slice.call(arguments, 1); - return function() { - return func.apply(this, args.concat(slice.call(arguments))); + if (!_.isFunction(func)) throw new TypeError; + args = slice.call(arguments, 2); + return bound = function() { + if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments))); + ctor.prototype = func.prototype; + var self = new ctor; + var result = func.apply(self, args.concat(slice.call(arguments))); + if (Object(result) === result) return result; + return self; }; }; @@ -598,7 +495,7 @@ // all callbacks defined on an object belong to it. _.bindAll = function(obj) { var funcs = slice.call(arguments, 1); - if (funcs.length === 0) funcs = _.functions(obj); + if (funcs.length == 0) funcs = _.functions(obj); each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); }); return obj; }; @@ -617,7 +514,7 @@ // it with the arguments supplied. _.delay = function(func, wait) { var args = slice.call(arguments, 2); - return setTimeout(function(){ return func.apply(null, args); }, wait); + return setTimeout(function(){ return func.apply(func, args); }, wait); }; // Defers a function, scheduling it to run after the current call stack has @@ -629,47 +526,39 @@ // Returns a function, that, when invoked, will only be triggered at most once // during a given window of time. _.throttle = function(func, wait) { - var context, args, timeout, result; - var previous = 0; - var later = function() { - previous = new Date; - timeout = null; - result = func.apply(context, args); - }; + var context, args, timeout, throttling, more; + var whenDone = _.debounce(function(){ more = throttling = false; }, wait); return function() { - var now = new Date; - var remaining = wait - (now - previous); - context = this; - args = arguments; - if (remaining <= 0) { - clearTimeout(timeout); + context = this; args = arguments; + var later = function() { timeout = null; - previous = now; - result = func.apply(context, args); - } else if (!timeout) { - timeout = setTimeout(later, remaining); + if (more) func.apply(context, args); + whenDone(); + }; + if (!timeout) timeout = setTimeout(later, wait); + if (throttling) { + more = true; + } else { + func.apply(context, args); } - return result; + whenDone(); + throttling = true; }; }; // Returns a function, that, as long as it continues to be invoked, will not // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, result; + // N milliseconds. + _.debounce = function(func, wait) { + var timeout; return function() { var context = this, args = arguments; var later = function() { timeout = null; - if (!immediate) result = func.apply(context, args); + func.apply(context, args); }; - var callNow = immediate && !timeout; clearTimeout(timeout); timeout = setTimeout(later, wait); - if (callNow) result = func.apply(context, args); - return result; }; }; @@ -680,9 +569,7 @@ return function() { if (ran) return memo; ran = true; - memo = func.apply(this, arguments); - func = null; - return memo; + return memo = func.apply(this, arguments); }; }; @@ -691,8 +578,7 @@ // conditionally execute the original function. _.wrap = function(func, wrapper) { return function() { - var args = [func]; - push.apply(args, arguments); + var args = [func].concat(slice.call(arguments, 0)); return wrapper.apply(this, args); }; }; @@ -714,9 +600,7 @@ _.after = function(times, func) { if (times <= 0) return func(); return function() { - if (--times < 1) { - return func.apply(this, arguments); - } + if (--times < 1) { return func.apply(this, arguments); } }; }; @@ -734,23 +618,7 @@ // Retrieve the values of an object's properties. _.values = function(obj) { - var values = []; - for (var key in obj) if (_.has(obj, key)) values.push(obj[key]); - return values; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var pairs = []; - for (var key in obj) if (_.has(obj, key)) pairs.push([key, obj[key]]); - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - for (var key in obj) if (_.has(obj, key)) result[obj[key]] = key; - return result; + return _.map(obj, _.identity); }; // Return a sorted list of the function names available on the object. @@ -766,42 +634,18 @@ // Extend a given object with all the properties in passed-in object(s). _.extend = function(obj) { each(slice.call(arguments, 1), function(source) { - if (source) { - for (var prop in source) { - obj[prop] = source[prop]; - } + for (var prop in source) { + obj[prop] = source[prop]; } }); return obj; }; - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - each(keys, function(key) { - if (key in obj) copy[key] = obj[key]; - }); - return copy; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - for (var key in obj) { - if (!_.contains(keys, key)) copy[key] = obj[key]; - } - return copy; - }; - // Fill in a given object with default properties. _.defaults = function(obj) { each(slice.call(arguments, 1), function(source) { - if (source) { - for (var prop in source) { - if (obj[prop] == null) obj[prop] = source[prop]; - } + for (var prop in source) { + if (obj[prop] == null) obj[prop] = source[prop]; } }); return obj; @@ -821,16 +665,19 @@ return obj; }; - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { + // Internal recursive comparison function. + function eq(a, b, stack) { // Identical objects are equal. `0 === -0`, but they aren't identical. // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal. if (a === b) return a !== 0 || 1 / a == 1 / b; // A strict comparison is necessary because `null == undefined`. if (a == null || b == null) return a === b; // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; + if (a._chain) a = a._wrapped; + if (b._chain) b = b._wrapped; + // Invoke a custom `isEqual` method if one is provided. + if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b); + if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a); // Compare `[[Class]]` names. var className = toString.call(a); if (className != toString.call(b)) return false; @@ -860,15 +707,14 @@ if (typeof a != 'object' || typeof b != 'object') return false; // Assume equality for cyclic structures. The algorithm for detecting cyclic // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = aStack.length; + var length = stack.length; while (length--) { // Linear search. Performance is inversely proportional to the number of // unique nested structures. - if (aStack[length] == a) return bStack[length] == b; + if (stack[length] == a) return true; } // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); + stack.push(a); var size = 0, result = true; // Recursively compare objects and arrays. if (className == '[object Array]') { @@ -878,24 +724,20 @@ if (result) { // Deep compare the contents, ignoring non-numeric properties. while (size--) { - if (!(result = eq(a[size], b[size], aStack, bStack))) break; + // Ensure commutative equality for sparse arrays. + if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break; } } } else { - // Objects with different constructors are not equivalent, but `Object`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if (aCtor !== bCtor && !(_.isFunction(aCtor) && (aCtor instanceof aCtor) && - _.isFunction(bCtor) && (bCtor instanceof bCtor))) { - return false; - } + // Objects with different constructors are not equivalent. + if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false; // Deep compare objects. for (var key in a) { if (_.has(a, key)) { // Count the expected number of properties. size++; // Deep compare each member. - if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; + if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break; } } // Ensure that both objects contain the same number of properties. @@ -907,20 +749,18 @@ } } // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); + stack.pop(); return result; - }; + } // Perform a deep comparison to check if two objects are equal. _.isEqual = function(a, b) { - return eq(a, b, [], []); + return eq(a, b, []); }; // Is a given array, string, or object empty? // An "empty" object has no enumerable own-properties. _.isEmpty = function(obj) { - if (obj == null) return true; if (_.isArray(obj) || _.isString(obj)) return obj.length === 0; for (var key in obj) if (_.has(obj, key)) return false; return true; @@ -928,7 +768,7 @@ // Is a given value a DOM element? _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); + return !!(obj && obj.nodeType == 1); }; // Is a given value an array? @@ -942,36 +782,35 @@ return obj === Object(obj); }; - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. - each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) == '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE), where - // there isn't any inspectable "Arguments" type. + // Is a given variable an arguments object? + _.isArguments = function(obj) { + return toString.call(obj) == '[object Arguments]'; + }; if (!_.isArguments(arguments)) { _.isArguments = function(obj) { return !!(obj && _.has(obj, 'callee')); }; } - // Optimize `isFunction` if appropriate. - if (typeof (/./) !== 'function') { - _.isFunction = function(obj) { - return typeof obj === 'function'; - }; - } + // Is a given value a function? + _.isFunction = function(obj) { + return toString.call(obj) == '[object Function]'; + }; - // Is a given object a finite number? - _.isFinite = function(obj) { - return isFinite(obj) && !isNaN(parseFloat(obj)); + // Is a given value a string? + _.isString = function(obj) { + return toString.call(obj) == '[object String]'; }; - // Is the given value `NaN`? (NaN is the only number which does not equal itself). + // Is a given value a number? + _.isNumber = function(obj) { + return toString.call(obj) == '[object Number]'; + }; + + // Is the given value `NaN`? _.isNaN = function(obj) { - return _.isNumber(obj) && obj != +obj; + // `NaN` is the only value for which `===` is not reflexive. + return obj !== obj; }; // Is a given value a boolean? @@ -979,6 +818,16 @@ return obj === true || obj === false || toString.call(obj) == '[object Boolean]'; }; + // Is a given value a date? + _.isDate = function(obj) { + return toString.call(obj) == '[object Date]'; + }; + + // Is the given value a regular expression? + _.isRegExp = function(obj) { + return toString.call(obj) == '[object RegExp]'; + }; + // Is a given value equal to null? _.isNull = function(obj) { return obj === null; @@ -989,8 +838,7 @@ return obj === void 0; }; - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). + // Has own property? _.has = function(obj, key) { return hasOwnProperty.call(obj, key); }; @@ -1011,67 +859,20 @@ }; // Run a function **n** times. - _.times = function(n, iterator, context) { - var accum = Array(n); - for (var i = 0; i < n; i++) accum[i] = iterator.call(context, i); - return accum; - }; - - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + Math.floor(Math.random() * (max - min + 1)); - }; - - // List of HTML entities for escaping. - var entityMap = { - escape: { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '/': '/' - } + _.times = function (n, iterator, context) { + for (var i = 0; i < n; i++) iterator.call(context, i); }; - entityMap.unescape = _.invert(entityMap.escape); - - // Regexes containing the keys and values listed immediately above. - var entityRegexes = { - escape: new RegExp('[' + _.keys(entityMap.escape).join('') + ']', 'g'), - unescape: new RegExp('(' + _.keys(entityMap.unescape).join('|') + ')', 'g') - }; - - // Functions for escaping and unescaping strings to/from HTML interpolation. - _.each(['escape', 'unescape'], function(method) { - _[method] = function(string) { - if (string == null) return ''; - return ('' + string).replace(entityRegexes[method], function(match) { - return entityMap[method][match]; - }); - }; - }); - // If the value of the named property is a function then invoke it; - // otherwise, return it. - _.result = function(object, property) { - if (object == null) return null; - var value = object[property]; - return _.isFunction(value) ? value.call(object) : value; + // Escape a string for HTML interpolation. + _.escape = function(string) { + return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/'); }; - // Add your own custom functions to the Underscore object. + // Add your own custom functions to the Underscore object, ensuring that + // they're correctly added to the OOP wrapper as well. _.mixin = function(obj) { each(_.functions(obj), function(name){ - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result.call(this, func.apply(_, args)); - }; + addToWrapper(name, _[name] = obj[name]); }); }; @@ -1079,7 +880,7 @@ // Useful for temporary DOM ids. var idCounter = 0; _.uniqueId = function(prefix) { - var id = ++idCounter + ''; + var id = idCounter++; return prefix ? prefix + id : id; }; @@ -1094,80 +895,41 @@ // When customizing `templateSettings`, if you don't want to define an // interpolation, evaluation or escaping regex, we need one that is // guaranteed not to match. - var noMatch = /(.)^/; + var noMatch = /.^/; - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\t': 't', - '\u2028': 'u2028', - '\u2029': 'u2029' + // Within an interpolation, evaluation, or escaping, remove HTML escaping + // that had been previously added. + var unescape = function(code) { + return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'"); }; - var escaper = /\\|'|\r|\n|\t|\u2028|\u2029/g; - // JavaScript micro-templating, similar to John Resig's implementation. // Underscore templating handles arbitrary delimiters, preserves whitespace, // and correctly escapes quotes within interpolated code. - _.template = function(text, data, settings) { - var render; - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = new RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset) - .replace(escaper, function(match) { return '\\' + escapes[match]; }); - - if (escape) { - source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; - } - if (interpolate) { - source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; - } - if (evaluate) { - source += "';\n" + evaluate + "\n__p+='"; - } - index = offset + match.length; - return match; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + "return __p;\n"; - - try { - render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - if (data) return render(data, _); - var template = function(data) { - return render.call(this, data, _); + _.template = function(str, data) { + var c = _.templateSettings; + var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' + + 'with(obj||{}){__p.push(\'' + + str.replace(/\\/g, '\\\\') + .replace(/'/g, "\\'") + .replace(c.escape || noMatch, function(match, code) { + return "',_.escape(" + unescape(code) + "),'"; + }) + .replace(c.interpolate || noMatch, function(match, code) { + return "'," + unescape(code) + ",'"; + }) + .replace(c.evaluate || noMatch, function(match, code) { + return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('"; + }) + .replace(/\r/g, '\\r') + .replace(/\n/g, '\\n') + .replace(/\t/g, '\\t') + + "');}return __p.join('');"; + var func = new Function('obj', '_', tmpl); + if (data) return func(data, _); + return function(data) { + return func.call(this, data, _); }; - - // Provide the compiled function source as a convenience for precompilation. - template.source = 'function(' + (settings.variable || 'obj') + '){\n' + source + '}'; - - return template; }; // Add a "chain" function, which will delegate to the wrapper. @@ -1175,15 +937,29 @@ return _(obj).chain(); }; - // OOP + // The OOP Wrapper // --------------- + // If Underscore is called as a function, it returns a wrapped object that // can be used OO-style. This wrapper holds altered versions of all the // underscore functions. Wrapped objects may be chained. + var wrapper = function(obj) { this._wrapped = obj; }; + + // Expose `wrapper.prototype` as `_.prototype` + _.prototype = wrapper.prototype; // Helper function to continue chaining intermediate results. - var result = function(obj) { - return this._chain ? _(obj).chain() : obj; + var result = function(obj, chain) { + return chain ? _(obj).chain() : obj; + }; + + // A method to easily add functions to the OOP wrapper. + var addToWrapper = function(name, func) { + wrapper.prototype[name] = function() { + var args = slice.call(arguments); + unshift.call(args, this._wrapped); + return result(func.apply(_, args), this._chain); + }; }; // Add all of the Underscore functions to the wrapper object. @@ -1192,35 +968,32 @@ // Add all mutator Array functions to the wrapper. each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name == 'shift' || name == 'splice') && obj.length === 0) delete obj[0]; - return result.call(this, obj); + wrapper.prototype[name] = function() { + var wrapped = this._wrapped; + method.apply(wrapped, arguments); + var length = wrapped.length; + if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0]; + return result(wrapped, this._chain); }; }); // Add all accessor Array functions to the wrapper. each(['concat', 'join', 'slice'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - return result.call(this, method.apply(this._wrapped, arguments)); + wrapper.prototype[name] = function() { + return result(method.apply(this._wrapped, arguments), this._chain); }; }); - _.extend(_.prototype, { - - // Start chaining a wrapped Underscore object. - chain: function() { - this._chain = true; - return this; - }, - - // Extracts the result from a wrapped and chained object. - value: function() { - return this._wrapped; - } + // Start chaining a wrapped Underscore object. + wrapper.prototype.chain = function() { + this._chain = true; + return this; + }; - }); + // Extracts the result from a wrapped and chained object. + wrapper.prototype.value = function() { + return this._wrapped; + }; }).call(this); diff --git a/docs/user/snippets/_build/html/_static/underscore.js b/docs/user/snippets/_build/html/_static/underscore.js new file mode 100644 index 0000000000000000000000000000000000000000..5b55f32beaca186f84cca115514f02cddbd1bbd5 --- /dev/null +++ b/docs/user/snippets/_build/html/_static/underscore.js @@ -0,0 +1,31 @@ +// Underscore.js 1.3.1 +// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. +// Underscore is freely distributable under the MIT license. +// Portions of Underscore are inspired or borrowed from Prototype, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore +(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source== +c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c, +h)&&!f--)break;g=!f}}d.pop();return g}var r=this,G=r._,n={},k=Array.prototype,o=Object.prototype,i=k.slice,H=k.unshift,l=o.toString,I=o.hasOwnProperty,w=k.forEach,x=k.map,y=k.reduce,z=k.reduceRight,A=k.filter,B=k.every,C=k.some,p=k.indexOf,D=k.lastIndexOf,o=Array.isArray,J=Object.keys,s=Function.prototype.bind,b=function(a){return new m(a)};if(typeof exports!=="undefined"){if(typeof module!=="undefined"&&module.exports)exports=module.exports=b;exports._=b}else r._=b;b.VERSION="1.3.1";var j=b.each= +b.forEach=function(a,c,d){if(a!=null)if(w&&a.forEach===w)a.forEach(c,d);else if(a.length===+a.length)for(var e=0,f=a.length;e<f;e++){if(e in a&&c.call(d,a[e],e,a)===n)break}else for(e in a)if(b.has(a,e)&&c.call(d,a[e],e,a)===n)break};b.map=b.collect=function(a,c,b){var e=[];if(a==null)return e;if(x&&a.map===x)return a.map(c,b);j(a,function(a,g,h){e[e.length]=c.call(b,a,g,h)});if(a.length===+a.length)e.length=a.length;return e};b.reduce=b.foldl=b.inject=function(a,c,d,e){var f=arguments.length>2;a== +null&&(a=[]);if(y&&a.reduce===y)return e&&(c=b.bind(c,e)),f?a.reduce(c,d):a.reduce(c);j(a,function(a,b,i){f?d=c.call(e,d,a,b,i):(d=a,f=true)});if(!f)throw new TypeError("Reduce of empty array with no initial value");return d};b.reduceRight=b.foldr=function(a,c,d,e){var f=arguments.length>2;a==null&&(a=[]);if(z&&a.reduceRight===z)return e&&(c=b.bind(c,e)),f?a.reduceRight(c,d):a.reduceRight(c);var g=b.toArray(a).reverse();e&&!f&&(c=b.bind(c,e));return f?b.reduce(g,c,d,e):b.reduce(g,c)};b.find=b.detect= +function(a,c,b){var e;E(a,function(a,g,h){if(c.call(b,a,g,h))return e=a,true});return e};b.filter=b.select=function(a,c,b){var e=[];if(a==null)return e;if(A&&a.filter===A)return a.filter(c,b);j(a,function(a,g,h){c.call(b,a,g,h)&&(e[e.length]=a)});return e};b.reject=function(a,c,b){var e=[];if(a==null)return e;j(a,function(a,g,h){c.call(b,a,g,h)||(e[e.length]=a)});return e};b.every=b.all=function(a,c,b){var e=true;if(a==null)return e;if(B&&a.every===B)return a.every(c,b);j(a,function(a,g,h){if(!(e= +e&&c.call(b,a,g,h)))return n});return e};var E=b.some=b.any=function(a,c,d){c||(c=b.identity);var e=false;if(a==null)return e;if(C&&a.some===C)return a.some(c,d);j(a,function(a,b,h){if(e||(e=c.call(d,a,b,h)))return n});return!!e};b.include=b.contains=function(a,c){var b=false;if(a==null)return b;return p&&a.indexOf===p?a.indexOf(c)!=-1:b=E(a,function(a){return a===c})};b.invoke=function(a,c){var d=i.call(arguments,2);return b.map(a,function(a){return(b.isFunction(c)?c||a:a[c]).apply(a,d)})};b.pluck= +function(a,c){return b.map(a,function(a){return a[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);if(!c&&b.isEmpty(a))return-Infinity;var e={computed:-Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b>=e.computed&&(e={value:a,computed:b})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);if(!c&&b.isEmpty(a))return Infinity;var e={computed:Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b<e.computed&&(e={value:a,computed:b})}); 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hide($(this).attr('id').substring(2)); }); - $('a.vote').live("click", function(event) { + $(document).on("click", 'a.vote', function(event) { event.preventDefault(); handleVote($(this)); }); - $('a.reply').live("click", function(event) { + $(document).on("click", 'a.reply', function(event) { event.preventDefault(); openReply($(this).attr('id').substring(2)); }); - $('a.close-reply').live("click", function(event) { + $(document).on("click", 'a.close-reply', function(event) { event.preventDefault(); closeReply($(this).attr('id').substring(2)); }); - $('a.sort-option').live("click", function(event) { + $(document).on("click", 'a.sort-option', function(event) { event.preventDefault(); handleReSort($(this)); }); - $('a.show-proposal').live("click", function(event) { + $(document).on("click", 'a.show-proposal', function(event) { event.preventDefault(); showProposal($(this).attr('id').substring(2)); }); - $('a.hide-proposal').live("click", function(event) { + $(document).on("click", 'a.hide-proposal', function(event) { event.preventDefault(); hideProposal($(this).attr('id').substring(2)); }); - $('a.show-propose-change').live("click", function(event) { + $(document).on("click", 'a.show-propose-change', function(event) { event.preventDefault(); showProposeChange($(this).attr('id').substring(2)); }); - $('a.hide-propose-change').live("click", function(event) { + $(document).on("click", 'a.hide-propose-change', function(event) { event.preventDefault(); hideProposeChange($(this).attr('id').substring(2)); }); - $('a.accept-comment').live("click", function(event) { + $(document).on("click", 'a.accept-comment', function(event) { event.preventDefault(); acceptComment($(this).attr('id').substring(2)); }); - $('a.delete-comment').live("click", function(event) { + $(document).on("click", 'a.delete-comment', function(event) { event.preventDefault(); deleteComment($(this).attr('id').substring(2)); }); - $('a.comment-markup').live("click", function(event) { + $(document).on("click", 'a.comment-markup', function(event) { event.preventDefault(); toggleCommentMarkupBox($(this).attr('id').substring(2)); }); @@ -700,8 +700,8 @@ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\ <div class="comment-markup-box" id="mb<%id%>">\ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \ - <tt>``code``</tt>, \ - code blocks: <tt>::</tt> and an indented block after blank line</div>\ + <code>``code``</code>, \ + code blocks: <code>::</code> and an indented block after blank line</div>\ <form method="post" id="cf<%id%>" class="comment-form" action="">\ <textarea name="comment" cols="80"></textarea>\ <p class="propose-button">\ diff --git a/docs/user/snippets/_build/html/genindex.html b/docs/user/snippets/_build/html/genindex.html new file mode 100644 index 0000000000000000000000000000000000000000..387390cc866e38a5a55b0b025507c495e8da66f1 --- /dev/null +++ b/docs/user/snippets/_build/html/genindex.html @@ -0,0 +1,270 @@ + + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>Index — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="index.html"/> + + + <script src="_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="index.html">Docs</a> »</li> + + <li></li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + +<h1 id="index">Index</h1> + +<div class="genindex-jumpbox"> + <a href="#C"><strong>C</strong></a> + | <a href="#L"><strong>L</strong></a> + | <a href="#M"><strong>M</strong></a> + | <a href="#S"><strong>S</strong></a> + +</div> +<h2 id="C">C</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#module-convert_Genesis2Sbml">convert_Genesis2Sbml (module)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="L">L</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#module-loadCspaceModel">loadCspaceModel (module)</a> + </dt> + + + <dt><a href="snippet.html#module-loadKineticModel">loadKineticModel (module)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#module-loadSbmlmodel">loadSbmlmodel (module)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="M">M</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#convert_Genesis2Sbml.main">main() (in module convert_Genesis2Sbml)</a> + </dt> + + <dd><dl> + + <dt><a href="snippet.html#loadCspaceModel.main">(in module loadCspaceModel)</a> + </dt> + + + <dt><a href="snippet.html#loadKineticModel.main">(in module loadKineticModel)</a> + </dt> + + + <dt><a href="snippet.html#loadSbmlmodel.main">(in module loadSbmlmodel)</a> + </dt> + + </dl></dd> + </dl></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#module-scriptKineticModel">scriptKineticModel (module)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="snippet.html#module-scriptKineticSolver">scriptKineticSolver (module)</a> + </dt> + + </dl></td> +</tr></table> + + + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'./', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_build/html/index.html b/docs/user/snippets/_build/html/index.html new file mode 100644 index 0000000000000000000000000000000000000000..0353ed4e16001fe3a5f76236cc7ccf35dcf1ff80 --- /dev/null +++ b/docs/user/snippets/_build/html/index.html @@ -0,0 +1,218 @@ + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>Snippets of MOOSE — MOOSE 3.2 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> + + + + + + <link rel="top" title="MOOSE 3.2 documentation" href="#"/> + <link rel="next" title="1. MOOSE Snippet" href="snippet.html"/> + + + <script src="_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav" role="document"> + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> MOOSE + + + + + <img src="_static/moose_logo.png" class="logo" /> + + </a> + + + + <div class="version"> + 3.2 + </div> + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="snippet.html">1. MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="#">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="#">Docs</a> »</li> + + <li>Snippets of MOOSE</li> + <li class="wy-breadcrumbs-aside"> + + + <a href="_sources/index.txt" rel="nofollow"> View page source</a> + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <div class="section" id="snippets-of-moose"> +<h1>Snippets of MOOSE<a class="headerlink" href="#snippets-of-moose" title="Permalink to this headline">¶</a></h1> +<p>A diverse collection of snippets: (mostly) short code examples illustrating different features of MOOSE</p> +<div class="toctree-wrapper compound"> +<ul> +<li class="toctree-l1"><a class="reference internal" href="snippet.html">1. MOOSE Snippet</a><ul> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#scripting-parser">1.1. Scripting Parser</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#class-features">1.2. Class features</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#network-models">1.3. Network Models</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#single-neuron-models">1.4. Single Neuron Models</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#signaling-pathways">1.5. Signaling Pathways</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#multi-scale-models">1.6. Multi scale models</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#d-graphics">1.7. 3-D graphics</a></li> +<li class="toctree-l2"><a class="reference internal" href="snippet.html#load-run-saving-pre-existing-model-files">1.8. Load-Run-Saving pre-existing model files</a></li> +</ul> +</li> +</ul> +</div> +</div> + + + </div> + </div> + <footer> + + <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> + + <a href="snippet.html" class="btn btn-neutral float-right" title="1. 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MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="index.html">Docs</a> »</li> + + <li></li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + + <h1>Python Module Index</h1> + + <div class="modindex-jumpbox"> + <a href="#cap-c"><strong>c</strong></a> | + <a href="#cap-l"><strong>l</strong></a> | + <a href="#cap-s"><strong>s</strong></a> + </div> + + <table class="indextable modindextable" cellspacing="0" cellpadding="2"> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-c"><td></td><td> + <strong>c</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-convert_Genesis2Sbml"><code class="xref">convert_Genesis2Sbml</code></a></td><td> + <em></em></td></tr> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-l"><td></td><td> + <strong>l</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadCspaceModel"><code class="xref">loadCspaceModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadKineticModel"><code class="xref">loadKineticModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadSbmlmodel"><code class="xref">loadSbmlmodel</code></a></td><td> + <em></em></td></tr> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-s"><td></td><td> + <strong>s</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-scriptKineticModel"><code class="xref">scriptKineticModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-scriptKineticSolver"><code class="xref">scriptKineticSolver</code></a></td><td> + <em></em></td></tr> + </table> + + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'./', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; 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MOOSE Snippet</a></li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="index.html">Docs</a> »</li> + + <li></li> + <li class="wy-breadcrumbs-aside"> + + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + + <h1>Python Module Index</h1> + + <div class="modindex-jumpbox"> + <a href="#cap-c"><strong>c</strong></a> | + <a href="#cap-l"><strong>l</strong></a> | + <a href="#cap-s"><strong>s</strong></a> + </div> + + <table class="indextable modindextable" cellspacing="0" cellpadding="2"> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-c"><td></td><td> + <strong>c</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-convert_Genesis2Sbml"><code class="xref">convert_Genesis2Sbml</code></a></td><td> + <em></em></td></tr> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-l"><td></td><td> + <strong>l</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadCspaceModel"><code class="xref">loadCspaceModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadKineticModel"><code class="xref">loadKineticModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-loadSbmlmodel"><code class="xref">loadSbmlmodel</code></a></td><td> + <em></em></td></tr> + <tr class="pcap"><td></td><td> </td><td></td></tr> + <tr class="cap" id="cap-s"><td></td><td> + <strong>s</strong></td><td></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-scriptKineticModel"><code class="xref">scriptKineticModel</code></a></td><td> + <em></em></td></tr> + <tr> + <td></td> + <td> + <a href="snippet.html#module-scriptKineticSolver"><code class="xref">scriptKineticSolver</code></a></td><td> + <em></em></td></tr> + </table> + + + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'./', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; 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MOOSE Snippet</a><ul> +<li class="toctree-l2"><a class="reference internal" href="#scripting-parser">1.1. Scripting Parser</a></li> +<li class="toctree-l2"><a class="reference internal" href="#class-features">1.2. Class features</a></li> +<li class="toctree-l2"><a class="reference internal" href="#network-models">1.3. Network Models</a></li> +<li class="toctree-l2"><a class="reference internal" href="#single-neuron-models">1.4. Single Neuron Models</a></li> +<li class="toctree-l2"><a class="reference internal" href="#signaling-pathways">1.5. Signaling Pathways</a><ul> +<li class="toctree-l3"><a class="reference internal" href="#module-scriptKineticModel">1.5.1. Define a kinetic model using the scripting in moose</a></li> +<li class="toctree-l3"><a class="reference internal" href="#module-scriptKineticSolver">1.5.2. Set up of kinetic solver</a></li> +</ul> +</li> +<li class="toctree-l2"><a class="reference internal" href="#multi-scale-models">1.6. Multi scale models</a></li> +<li class="toctree-l2"><a class="reference internal" href="#d-graphics">1.7. 3-D graphics</a></li> +<li class="toctree-l2"><a class="reference internal" href="#load-run-saving-pre-existing-model-files">1.8. Load-Run-Saving pre-existing model files</a><ul> +<li class="toctree-l3"><a class="reference internal" href="#module-loadKineticModel">1.8.1. Load Kinetics Models</a></li> +<li class="toctree-l3"><a class="reference internal" href="#module-loadSbmlmodel">1.8.2. Load SBML Models</a></li> +<li class="toctree-l3"><a class="reference internal" href="#module-loadCspaceModel">1.8.3. Load Cspace Models</a></li> +<li class="toctree-l3"><a class="reference internal" href="#module-convert_Genesis2Sbml">1.8.4. Save Models to Sbml format</a></li> +</ul> +</li> +</ul> +</li> +</ul> + + + + </div> + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="index.html">MOOSE</a> + </nav> + + + + <div class="wy-nav-content"> + <div class="rst-content"> + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + <ul class="wy-breadcrumbs"> + <li><a href="http://moose.ncbs.res.in">MOOSE</a> »</li> + <li><a href="index.html">Docs</a> »</li> + + <li>1. MOOSE Snippet</li> + <li class="wy-breadcrumbs-aside"> + + + <a href="_sources/snippet.txt" rel="nofollow"> View page source</a> + + + </li> + </ul> + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + <div class="section" id="moose-snippet"> +<h1>1. MOOSE Snippet<a class="headerlink" href="#moose-snippet" title="Permalink to this headline">¶</a></h1> +<p>The MOOSE Snippet contains examples showing you how to do specific +tasks in MOOSE.</p> +<div class="section" id="scripting-parser"> +<h2>1.1. Scripting Parser<a class="headerlink" href="#scripting-parser" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="class-features"> +<h2>1.2. Class features<a class="headerlink" href="#class-features" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="network-models"> +<h2>1.3. Network Models<a class="headerlink" href="#network-models" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="single-neuron-models"> +<h2>1.4. Single Neuron Models<a class="headerlink" href="#single-neuron-models" title="Permalink to this headline">¶</a></h2> +<p>Some salient properties of neuronal building blocks in MOOSE are described below.</p> +</div> +<div class="section" id="signaling-pathways"> +<h2>1.5. Signaling Pathways<a class="headerlink" href="#signaling-pathways" title="Permalink to this headline">¶</a></h2> +<p>This section show some of the chemical signaling pathways related settings</p> +<div class="section" id="module-scriptKineticModel"> +<span id="define-a-kinetic-model-using-the-scripting-in-moose"></span><h3>1.5.1. Define a kinetic model using the scripting in moose<a class="headerlink" href="#module-scriptKineticModel" title="Permalink to this headline">¶</a></h3> +<p>This example illustrates how to define a kinetic model using the +scripting interface. Normally one uses standard model formats like +SBML or kkit to concisely define kinetic models, but in some cases one +would like to modify the model through the script. +This example creates a bistable model having two enzymes and a reaction. +One of the enzymes is autocatalytic. +The model is set up to run using default Exponential Euler integration. +The snippet scriptKineticSolver.py uses the much better GSL +Runge-Kutta-Fehlberg integration scheme on this same model.</p> +</div> +<div class="section" id="module-scriptKineticSolver"> +<span id="set-up-of-kinetic-solver"></span><h3>1.5.2. Set up of kinetic solver<a class="headerlink" href="#module-scriptKineticSolver" title="Permalink to this headline">¶</a></h3> +</div> +</div> +<div class="section" id="multi-scale-models"> +<h2>1.6. Multi scale models<a class="headerlink" href="#multi-scale-models" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="d-graphics"> +<h2>1.7. 3-D graphics<a class="headerlink" href="#d-graphics" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="load-run-saving-pre-existing-model-files"> +<h2>1.8. Load-Run-Saving pre-existing model files<a class="headerlink" href="#load-run-saving-pre-existing-model-files" title="Permalink to this headline">¶</a></h2> +<p>This section of the documentation explains how to load-run-save predefined models in MOOSE.</p> +<div class="section" id="module-loadKineticModel"> +<span id="load-kinetics-models"></span><h3>1.8.1. Load Kinetics Models<a class="headerlink" href="#module-loadKineticModel" title="Permalink to this headline">¶</a></h3> +<dl class="function"> +<dt id="loadKineticModel.main"> +<code class="descclassname">loadKineticModel.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/loadKineticModel.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loadKineticModel.main" title="Permalink to this definition">¶</a></dt> +<dd><p>This example illustrates loading, running, and saving a kinetic model +defined in kkit format. It uses a default kkit model but you can specify another using the command line <code class="docutils literal"><span class="pre">python</span> <span class="pre">filename</span> <span class="pre">runtime</span> <span class="pre">solver</span></code>. We use the gsl solver here. The model already defines a couple of plots and sets the runtime to 20 seconds.</p> +</dd></dl> + +</div> +<div class="section" id="module-loadSbmlmodel"> +<span id="load-sbml-models"></span><h3>1.8.2. Load SBML Models<a class="headerlink" href="#module-loadSbmlmodel" title="Permalink to this headline">¶</a></h3> +<dl class="function"> +<dt id="loadSbmlmodel.main"> +<code class="descclassname">loadSbmlmodel.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/loadSbmlmodel.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loadSbmlmodel.main" title="Permalink to this definition">¶</a></dt> +<dd><p>This example illustrates loading, running of an SBML model defined in XML format.</p> +<p>The model 00001-sbml-l3v1.xml is taken from l3v1 SBML testcase.</p> +<p>Plots are setup.</p> +<p>Model is run for 20sec.</p> +<p>As a general rule we created model under ‘/path/model’ and plots under ‘/path/graphs’.</p> +</dd></dl> + +</div> +<div class="section" id="module-loadCspaceModel"> +<span id="load-cspace-models"></span><h3>1.8.3. Load Cspace Models<a class="headerlink" href="#module-loadCspaceModel" title="Permalink to this headline">¶</a></h3> +<dl class="function"> +<dt id="loadCspaceModel.main"> +<code class="descclassname">loadCspaceModel.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/loadCspaceModel.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loadCspaceModel.main" title="Permalink to this definition">¶</a></dt> +<dd><p>This example illustrates loading and running, a kinetic model +defined in cspace format. We use the gsl solver here. The model already +defines a couple of plots and sets the runtime to 3000 seconds.</p> +</dd></dl> + +</div> +<div class="section" id="module-convert_Genesis2Sbml"> +<span id="save-models-to-sbml-format"></span><h3>1.8.4. Save Models to Sbml format<a class="headerlink" href="#module-convert_Genesis2Sbml" title="Permalink to this headline">¶</a></h3> +<dl class="function"> +<dt id="convert_Genesis2Sbml.main"> +<code class="descclassname">convert_Genesis2Sbml.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/convert_Genesis2Sbml.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#convert_Genesis2Sbml.main" title="Permalink to this definition">¶</a></dt> +<dd><p>This example illustrates loading a kinetic model defined in Genesis format +into Moose using loadModel function and using writeSBML function +one can save the model into SBML format.</p> +<p>Moose needs to be compiled with libsbml</p> +</dd></dl> + +</div> +</div> +</div> + + + </div> + </div> + <footer> + + <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> + + + <a href="index.html" class="btn btn-neutral" title="Snippets of MOOSE" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a> + + </div> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2016. + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT:'./', + VERSION:'3.2', + COLLAPSE_INDEX:false, + FILE_SUFFIX:'.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + + + + + + <script type="text/javascript" src="_static/js/theme.js"></script> + + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.StickyNav.enable(); + }); + </script> + + +</body> +</html> \ No newline at end of file diff --git a/docs/user/snippets/_templates/layout.html b/docs/user/snippets/_templates/layout.html new file mode 100644 index 0000000000000000000000000000000000000000..75df84926246f910c90895c58dcb9a5bce462bb4 --- /dev/null +++ b/docs/user/snippets/_templates/layout.html @@ -0,0 +1,33 @@ +{% extends "!layout.html" %} +{% block rootrellink %} + <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> + {{ super() }} +{% endblock %} +{% block sidebartitle %} + + {% if logo and theme_logo_only %} + <a href="http://moose.ncbs.res.in"> + + {% else %} + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> {{ project }} + {% endif %} + + {% if logo %} + {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #} + <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" /> + {% endif %} + </a> + {% if theme_display_version %} + {%- set nav_version = version %} + {% if READTHEDOCS and current_version %} + {%- set nav_version = current_version %} + {% endif %} + {% if nav_version %} + <div class="version"> + {{ nav_version }} + </div> + {% endif %} + {% endif %} + + {% include "searchbox.html" %} +{% endblock %} diff --git a/docs/user/snippets/conf.py b/docs/user/snippets/conf.py new file mode 100644 index 0000000000000000000000000000000000000000..05b119541e4e6263629d60b6cdd164aec9d870fd --- /dev/null +++ b/docs/user/snippets/conf.py @@ -0,0 +1,250 @@ +# -*- coding: utf-8 -*- +# +# MOOSE documentation build configuration file, created by +# sphinx-quickstart on Tue Jul 1 19:05:47 2014. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('../../moose/moose-core/python')) +sys.path.append(os.path.abspath('../../../moose-examples/snippets')) +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', + 'sphinx.ext.mathjax', + 'sphinx.ext.autosummary', + 'sphinx.ext.viewcode', + 'numpydoc'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'MOOSE' +copyright = u'2016' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '3.2' +# The full version, including alpha/beta/rc tags. +release = '3.2' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = True + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'sphinx_rtd_theme' +#html_theme = 'better' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# html_theme_options = {'stickysidebar': 'true', +# 'sidebarwidth': '300'} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [better_theme_path] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +html_logo = '../../images/moose_logo.png' + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'MOOSEdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'MOOSE.tex', u'MOOSE Documentation', + u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +latex_logo = '../images/moose_logo.png' + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +latex_show_pagerefs = True + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'moose', u'MOOSE Documentation', + [u'Upinder Bhalla, Aviral Goel and Harsha Rani'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'MOOSE', u'MOOSE Documentation', + u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.', + 'Science'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +#numpydoc option +numpydoc_show_class_members = True diff --git a/docs/user/snippets/index.rst b/docs/user/snippets/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..e91f8041fb5e5bde93c3a92d48ef2533fcf25f41 --- /dev/null +++ b/docs/user/snippets/index.rst @@ -0,0 +1,15 @@ +.. MOOSE documentation master file, created by + sphinx-quickstart on Tue Feb 2 14:05:47 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Snippets of MOOSE +================================== +A diverse collection of snippets: (mostly) short code examples illustrating different features of MOOSE + +.. toctree:: + :maxdepth: 2 + :numbered: + + + snippet diff --git a/docs/user/snippets/snippet.rst b/docs/user/snippets/snippet.rst new file mode 100644 index 0000000000000000000000000000000000000000..fff4d674d06b85384ed81dada2a03a1b7a804fb9 --- /dev/null +++ b/docs/user/snippets/snippet.rst @@ -0,0 +1,66 @@ +.. A snippets for MOOSE +.. Lists all the snippets in moose-examples/snippets directory + +MOOSE Snippet +============== + +The MOOSE Snippet contains examples showing you how to do specific +tasks in MOOSE. + +Scripting Parser +---------------- + +Class features +-------------- + +Network Models +-------------- + +Single Neuron Models +--------------------- +Some salient properties of neuronal building blocks in MOOSE are described below. + +Signaling Pathways +------------------ +This section show some of the chemical signaling pathways related settings + +Define a kinetic model using the scripting in moose +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: scriptKineticModel + :members: + +Set up of kinetic solver +^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: scriptKineticSolver + :members: + +Multi scale models +------------------- + +3-D graphics +------------- + +Load-Run-Saving pre-existing model files +---------------------------------------- +This section of the documentation explains how to load-run-save predefined models in MOOSE. + +Load Kinetics Models +^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: loadKineticModel + :members: + +Load SBML Models +^^^^^^^^^^^^^^^^^ +.. automodule:: loadSbmlmodel + :members: + +Load Cspace Models +^^^^^^^^^^^^^^^^^^^ +.. automodule:: loadCspaceModel + :members: + +Save Models to Sbml format +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. automodule:: convert_Genesis2Sbml + :members: + diff --git a/docs/user/tutorials/Makefile b/docs/user/tutorials/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..182070907cae692fced766d21141b1ccbc52a887 --- /dev/null +++ b/docs/user/tutorials/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. 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The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/user/tutorials/_static/3-D_DisplayofReactionDiffusion.html b/docs/user/tutorials/_static/3-D_DisplayofReactionDiffusion.html new file mode 100644 index 0000000000000000000000000000000000000000..cc9f3bcb7b5350770e5007c303a9be40a4b4bd85 --- /dev/null +++ b/docs/user/tutorials/_static/3-D_DisplayofReactionDiffusion.html @@ -0,0 +1,4997 @@ +<!DOCTYPE html> +<html> +<head> +<meta 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+.dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} +.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default} +.open{*z-index:1000}.open>.dropdown-menu{display:block} +.dropdown-backdrop{position:fixed;left:0;right:0;bottom:0;top:0;z-index:990} +.pull-right>.dropdown-menu{right:0;left:auto} +.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000;content:""} +.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px} +.dropdown-submenu{position:relative} +.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;border-radius:0 6px 6px 6px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px} +.dropdown-submenu:hover>.dropdown-menu{display:block} +.dropup .dropdown-submenu>.dropdown-menu{top:auto;bottom:0;margin-top:0;margin-bottom:-2px;border-radius:5px 5px 5px 0;-webkit-border-radius:5px 5px 5px 0;-moz-border-radius:5px 5px 5px 0;border-radius:5px 5px 5px 0} +.dropdown-submenu>a:after{display:block;content:" ";float:right;width:0;height:0;border-color:transparent;border-style:solid;border-width:5px 0 5px 5px;border-left-color:#ccc;margin-top:5px;margin-right:-10px} +.dropdown-submenu:hover>a:after{border-left-color:#fff} +.dropdown-submenu.pull-left{float:none}.dropdown-submenu.pull-left>.dropdown-menu{left:-100%;margin-left:10px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px} +.dropdown .dropdown-menu .nav-header{padding-left:20px;padding-right:20px} +.typeahead{z-index:1051;margin-top:2px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px} 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="3-D-graphics-for-the-reaction-diffusion-product-using-Rdesigner">3-D graphics for the reaction-diffusion product using Rdesigner<a class="anchor-link" href="#3-D-graphics-for-the-reaction-diffusion-product-using-Rdesigner">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [*]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="o">%</span><span class="k">matplotlib</span> <span class="n">inline</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">turnOffElec</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> + <span class="n">chemProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'makeChemOscillator()'</span><span class="p">,</span> <span class="s">'osc'</span><span class="p">]],</span> + <span class="n">chemDistrib</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'osc'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'install'</span><span class="p">,</span> <span class="s">'1'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'Concentration of a'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/b'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'Concentration of b'</span><span class="p">]],</span> + <span class="n">moogList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'a Conc'</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">360</span> <span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">bv</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">vec</span><span class="p">(</span> <span class="s">'/model/chem/dend/b'</span> <span class="p">)</span> +<span class="n">bv</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">concInit</span> <span class="o">*=</span> <span class="mi">2</span> +<span class="n">bv</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">concInit</span> <span class="o">*=</span> <span class="mi">2</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">displayMoogli</span><span class="p">(</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">400</span><span class="p">,</span> <span class="mf">0.001</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 1 compartments. +Chem part of model has 250 dendrite voxels X 3 pools, + + +</pre> +</div> +</div> +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> +<img src="rdes5_reacdiff.png"> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYsAAAEZCAYAAABmTgnDAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzs3Xd8W9XB//GPtmTJkm3Zli3veCQecezgbMgkzDBaSlJm +OugAukh/UEKhUKAlTyl00TzQQtmEHUICCYQkJnsP4zjee0qybGtLlu75/eHn5zZlpL8nJC3tfb9e +fr1yj+45OvdKOV/dq3OvFEIIgUwmk8lkn0H5z+6ATCaTyf71yWEhk8lkslOSw0Imk8lkpySHhUwm 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directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<!-- Loading mathjax macro --> +<!-- Load mathjax --> + <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script> + <!-- MathJax configuration --> + <script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ], + processEscapes: true, + processEnvironments: true + }, + // Center justify equations in code and markdown cells. Elsewhere + // we use CSS to left justify single line equations in code cells. + displayAlign: 'center', + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}}, + linebreaks: { automatic: true } + } + }); + </script> + <!-- End of mathjax configuration --> + +</head> +<body> + <div tabindex="-1" id="notebook" class="border-box-sizing"> + <div class="container" id="notebook-container"> + +<div class="cell border-box-sizing text_cell rendered"> +<div class="prompt input_prompt"> +</div> +<div class="inner_cell"> +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="This-example-illustrates-how-to-define-a-kinetic-model-using-the-scripting-interface.Normally-one-uses-standard-model-formats-like-SBML-or-kkit-to-concisely-define-kinetic-models,-but-in-some-cases-one-would-like-to-modify-the-model-through-the-script.">This example illustrates how to define a kinetic model using the scripting interface.Normally one uses standard model formats like SBML or kkit to concisely define kinetic models, but in some cases one would like to modify the model through the script.<a class="anchor-link" href="#This-example-illustrates-how-to-define-a-kinetic-model-using-the-scripting-interface.Normally-one-uses-standard-model-formats-like-SBML-or-kkit-to-concisely-define-kinetic-models,-but-in-some-cases-one-would-like-to-modify-the-model-through-the-script.">¶</a></h1><h2 id="This-example-creates-a-reaction-model">This example creates a reaction model<a class="anchor-link" href="#This-example-creates-a-reaction-model">¶</a></h2> +</div> +</div> +</div> +<div class="cell border-box-sizing code_cell rendered"> +<div class="input"> +<div class="prompt input_prompt">In [1]:</div> +<div class="inner_cell"> + <div class="input_area"> +<div class=" highlight hl-ipython2"><pre><span class="c"># first step is to import moose</span> +<span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="o">%</span><span class="k">matplotlib</span> inline +<span class="c"># create container for model</span> +<span class="n">model</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'model'</span> <span class="p">)</span> + +<span class="c">#create chemical compartment either `CubeMesh` or `CylMesh` and set the volume</span> +<span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">CubeMesh</span><span class="p">(</span> <span class="s">'/model/compartment'</span> <span class="p">)</span> +<span class="n">compartment</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="mf">1e-20</span> + +<span class="c"># create molecules and reactions</span> +<span class="n">sub</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Pool</span><span class="p">(</span> <span class="s">'/model/compartment/Sub'</span> <span class="p">)</span> +<span class="n">sub</span><span class="o">.</span><span class="n">concInit</span> <span class="o">=</span> <span class="mf">0.001</span> +<span class="n">prd</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Pool</span><span class="p">(</span> <span class="s">'/model/compartment/Prd'</span> <span class="p">)</span> +<span class="n">reac</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Reac</span><span class="p">(</span> <span class="s">'/model/compartment/reac'</span> <span class="p">)</span> +<span class="n">reac</span><span class="o">.</span><span class="n">Kf</span> <span class="o">=</span> <span class="mf">0.1</span> +<span class="n">reac</span><span class="o">.</span><span class="n">Kb</span> <span class="o">=</span> <span class="mf">0.001</span> + +<span class="c"># connect them up for reactions</span> +<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">reac</span><span class="p">,</span> <span class="s">'sub'</span><span class="p">,</span> <span class="n">sub</span><span class="p">,</span> <span class="s">'reac'</span> <span class="p">)</span> +<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">reac</span><span class="p">,</span> <span class="s">'prd'</span><span class="p">,</span> <span class="n">prd</span><span class="p">,</span> <span class="s">'reac'</span> <span class="p">)</span> + + +<span class="c">#setting up the KSolve</span> +<span class="n">gsolve</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Ksolve</span><span class="p">(</span> <span class="s">'/model/compartment/ksolve'</span> <span class="p">)</span> +<span class="n">stoich</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Stoich</span><span class="p">(</span> <span class="s">'/model/compartment/stoich'</span> <span class="p">)</span> +<span class="n">stoich</span><span class="o">.</span><span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment'</span> <span class="p">)</span> +<span class="n">stoich</span><span class="o">.</span><span class="n">ksolve</span> <span class="o">=</span> <span class="n">gsolve</span> +<span class="n">stoich</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="s">"/model/compartment/##"</span> +<span class="n">moose</span><span class="o">.</span><span class="n">setClock</span><span class="p">(</span> <span class="mi">15</span><span class="p">,</span> <span class="mf">1.0</span> <span class="p">)</span> <span class="c"># clock for the solver</span> +<span class="n">moose</span><span class="o">.</span><span class="n">useClock</span><span class="p">(</span> <span class="mi">15</span><span class="p">,</span> <span class="s">'/model/compartment/gsolve'</span><span class="p">,</span> <span class="s">'process'</span> <span class="p">)</span> + +<span class="c"># Create the output tables</span> +<span class="n">graphs</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'/model/graphs'</span> <span class="p">)</span> +<span class="n">outputA</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/model/graphs/concA'</span> <span class="p">)</span> +<span class="n">outputB</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/model/graphs/concB'</span> <span class="p">)</span> + +<span class="c"># connect up the tables for plot substrate and product concentration</span> +<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputA</span><span class="p">,</span> <span class="s">'requestOut'</span><span class="p">,</span> <span class="n">sub</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span> +<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputB</span><span class="p">,</span> <span class="s">'requestOut'</span><span class="p">,</span> <span class="n">prd</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span> + +<span class="c"># reinit and run for 100s</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span> + +<span class="c">#setting up displaying plots in matplotlib</span> +<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/graphs/#[TYPE=Table2]'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> +<span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> +<span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> +</pre></div> + +</div> +</div> +</div> + +<div class="output_wrapper"> +<div class="output"> + + +<div class="output_area"><div class="prompt"></div> + + +<div class="output_png output_subarea "> 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5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #fff} +.dropdown-menu>li>a{display:block;padding:3px 20px;clear:both;font-weight:normal;line-height:20px;color:#333;white-space:nowrap} +.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus,.dropdown-submenu:hover>a,.dropdown-submenu:focus>a{text-decoration:none;color:#fff;background-color:#0081c2;background-image:-moz-linear-gradient(top, #08c, #0077b3);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#08c), to(#0077b3));background-image:-webkit-linear-gradient(top, #08c, #0077b3);background-image:-o-linear-gradient(top, #08c, #0077b3);background-image:linear-gradient(to bottom, #08c, #0077b3);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0)} 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";float:right;width:0;height:0;border-color:transparent;border-style:solid;border-width:5px 0 5px 5px;border-left-color:#ccc;margin-top:5px;margin-right:-10px} +.dropdown-submenu:hover>a:after{border-left-color:#fff} +.dropdown-submenu.pull-left{float:none}.dropdown-submenu.pull-left>.dropdown-menu{left:-100%;margin-left:10px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px} +.dropdown .dropdown-menu .nav-header{padding-left:20px;padding-right:20px} +.typeahead{z-index:1051;margin-top:2px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px} +.well{min-height:20px;padding:19px;margin-bottom:20px;background-color:#f5f5f5;border:1px solid #e3e3e3;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.05);-moz-box-shadow:inset 0 1px 1px rgba(0,0,0,0.05);box-shadow:inset 0 1px 1px rgba(0,0,0,0.05)}.well blockquote{border-color:#ddd;border-color:rgba(0,0,0,0.15)} +.well-large{padding:24px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px} +.well-small{padding:9px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} +.fade{opacity:0;-webkit-transition:opacity .15s linear;-moz-transition:opacity .15s linear;-o-transition:opacity .15s linear;transition:opacity .15s linear}.fade.in{opacity:1} +.collapse{position:relative;height:0;overflow:hidden;-webkit-transition:height .35s ease;-moz-transition:height .35s ease;-o-transition:height .35s ease;transition:height .35s ease}.collapse.in{height:auto} +.close{float:right;font-size:20px;font-weight:bold;line-height:20px;color:#000;text-shadow:0 1px 0 #fff;opacity:.2;filter:alpha(opacity=20)}.close:hover,.close:focus{color:#000;text-decoration:none;cursor:pointer;opacity:.4;filter:alpha(opacity=40)} 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="The-chemical-oscillator-model-is-predefined-in-the-rdesigneur-prototypes">The chemical oscillator model is predefined in the rdesigneur prototypes<a class="anchor-link" href="#The-chemical-oscillator-model-is-predefined-in-the-rdesigneur-prototypes">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [2]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="o">%</span><span class="k">matplotlib</span> <span class="n">inline</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">turnOffElec</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> + <span class="n">diffusionLength</span> <span class="o">=</span> <span class="mf">1e-3</span><span class="p">,</span> <span class="c"># Default diffusion length is 2 microns</span> + <span class="n">chemProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'makeChemOscillator()'</span><span class="p">,</span> <span class="s">'osc'</span><span class="p">]],</span> + <span class="n">chemDistrib</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'osc'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'install'</span><span class="p">,</span> <span class="s">'1'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'a Conc'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/b'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'b Conc'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">b</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/chem/dend/b'</span> <span class="p">)</span> +<span class="n">b</span><span class="o">.</span><span class="n">concInit</span> <span class="o">*=</span> <span class="mi">5</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mi">200</span> <span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">display</span><span class="p">()</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 1 compartments. +Chem part of model has 1 dendrite voxels X 3 pools, + + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYoAAAEZCAYAAACJjGL9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz 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directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<!-- Loading mathjax macro --> +<!-- Load mathjax --> + <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script> + <!-- MathJax configuration --> + <script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ], + processEscapes: true, + processEnvironments: true + }, + // Center justify equations in code and markdown cells. Elsewhere + // we use CSS to left justify single line equations in code cells. + displayAlign: 'center', + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}}, + linebreaks: { automatic: true } + } + }); + </script> + <!-- End of mathjax configuration --> + +</head> +<body> + <div tabindex="-1" id="notebook" class="border-box-sizing"> + <div class="container" id="notebook-container"> + +<div class="cell border-box-sizing text_cell rendered"> +<div class="prompt input_prompt"> +</div> +<div class="inner_cell"> +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="This-example-illustrates-setting-up-of-Deterministic-solver,-loading,-running,-and-saving-a-kinetic-model-defined-in-kkit-format">This example illustrates setting up of Deterministic solver, loading, running, and saving a kinetic model defined in kkit format<a class="anchor-link" href="#This-example-illustrates-setting-up-of-Deterministic-solver,-loading,-running,-and-saving-a-kinetic-model-defined-in-kkit-format">¶</a></h1> +</div> +</div> +</div> +<div class="cell border-box-sizing code_cell rendered"> +<div class="input"> +<div class="prompt input_prompt">In [1]:</div> +<div class="inner_cell"> + <div class="input_area"> +<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">sys</span> +<span class="o">%</span><span class="k">matplotlib</span> inline + +<span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates setting up of Deterministic solver, loading, running, and saving a kinetic model </span> +<span class="sd"> defined in kkit format. """</span> + <span class="n">solver</span> <span class="o">=</span> <span class="s">"gsl"</span> <span class="c"># Setting up Deterministic solver</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="s">'../genesis/Kholodenko.g'</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="mf">6000.0</span> + <span class="n">modelId</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="n">mfile</span><span class="p">,</span> <span class="s">'model'</span><span class="p">,</span> <span class="n">solver</span> <span class="p">)</span> + + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="n">runtime</span> <span class="p">)</span> + + <span class="c"># Display all plots.</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/#graphs/conc#/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="o">.</span><span class="n">dt</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + +</div> +</div> +</div> + +<div class="output_wrapper"> +<div class="output"> + + +<div class="output_area"><div class="prompt"></div> + + +<div class="output_png output_subarea "> +<img 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5px;border-left-color:#000} +.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000} +.popover{position:absolute;top:0;left:0;z-index:1010;display:none;max-width:276px;padding:1px;text-align:left;background-color:#fff;-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;border:1px solid #ccc;border:1px solid rgba(0,0,0,0.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0,0,0,0.2);-moz-box-shadow:0 5px 10px rgba(0,0,0,0.2);box-shadow:0 5px 10px rgba(0,0,0,0.2);white-space:normal}.popover.top{margin-top:-10px} +.popover.right{margin-left:10px} +.popover.bottom{margin-top:10px} +.popover.left{margin-left:-10px} +.popover-title{margin:0;padding:8px 14px;font-size:14px;font-weight:normal;line-height:18px;background-color:#f7f7f7;border-bottom:1px solid #ebebeb;border-radius:5px 5px 0 0;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom 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+a.thumbnail:hover,a.thumbnail:focus{border-color:#08c;-webkit-box-shadow:0 1px 4px rgba(0,105,214,0.25);-moz-box-shadow:0 1px 4px rgba(0,105,214,0.25);box-shadow:0 1px 4px rgba(0,105,214,0.25)} +.thumbnail>img{display:block;max-width:100%;margin-left:auto;margin-right:auto} +.thumbnail .caption{padding:9px;color:#555} +.media,.media-body{overflow:hidden;*overflow:visible;zoom:1} +.media,.media .media{margin-top:15px} +.media:first-child{margin-top:0} +.media-object{display:block} +.media-heading{margin:0 0 5px} +.media>.pull-left{margin-right:10px} +.media>.pull-right{margin-left:10px} +.media-list{margin-left:0;list-style:none} +.label,.badge{display:inline-block;padding:2px 4px;font-size:10.998px;font-weight:bold;line-height:14px;color:#fff;vertical-align:baseline;white-space:nowrap;text-shadow:0 -1px 0 rgba(0,0,0,0.25);background-color:#999} +.label{border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} +.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="In-this-toy-model-we-have-an-HH-squid-type-single-compartment-electrical-model,-cohabiting-with-a-chemical-oscillator.">In this toy model we have an HH-squid type single compartment electrical model, cohabiting with a chemical oscillator.<a class="anchor-link" href="#In-this-toy-model-we-have-an-HH-squid-type-single-compartment-electrical-model,-cohabiting-with-a-chemical-oscillator.">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [2]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="c"># We want just one compartment so we set diffusion length to be</span> + <span class="c"># bigger than the 0.5 mm HH axon compartment default. </span> + <span class="n">diffusionLength</span> <span class="o">=</span> <span class="mf">1e-3</span><span class="p">,</span> + <span class="n">chanProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'make_HH_Na()'</span><span class="p">,</span> <span class="s">'Na'</span><span class="p">],</span> <span class="p">[</span><span class="s">'make_HH_K()'</span><span class="p">,</span> <span class="s">'K'</span><span class="p">]],</span> + <span class="n">chanDistrib</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">'Na'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'Gbar'</span><span class="p">,</span> <span class="s">'1200'</span> <span class="p">],</span> + <span class="p">[</span><span class="s">'K'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'Gbar'</span><span class="p">,</span> <span class="s">'360'</span> <span class="p">]],</span> + <span class="n">chemProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'makeChemOscillator()'</span><span class="p">,</span> <span class="s">'osc'</span><span class="p">]],</span> + <span class="n">chemDistrib</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'osc'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'install'</span><span class="p">,</span> <span class="s">'1'</span> <span class="p">]],</span> + <span class="c"># These adaptor parameters give interesting-looking but not</span> + <span class="c"># particularly physiological behaviour.</span> + <span class="n">adaptorList</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'Na'</span><span class="p">,</span> <span class="s">'modulation'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">5.0</span> <span class="p">],</span> + <span class="p">[</span> <span class="s">'dend/b'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'K'</span><span class="p">,</span> <span class="s">'modulation'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">],</span> + <span class="p">[</span> <span class="s">'dend/b'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0e-7</span><span class="p">,</span> <span class="mf">4e-7</span> <span class="p">],</span> + <span class="p">[</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'dend/s'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="mf">2.5</span><span class="p">,</span> <span class="mf">20.0</span> <span class="p">]</span> + <span class="p">],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'a Conc'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/b'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'b Conc'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/s'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'s Conc'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Na'</span><span class="p">,</span> <span class="s">'Gk'</span><span class="p">,</span> <span class="s">'Na Gk'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">]</span> + <span class="p">]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mi">250</span> <span class="p">)</span> <span class="c"># Takes a few seconds to run this.</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">display</span><span class="p">()</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 1 compartments. +Chem part of model has 1 dendrite voxels X 3 pools, + + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYoAAAEZCAYAAACJjGL9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJztnXdcFHf6xz9LUVERUREQjBgBFUTAmqIRg2hMlJjTYLl4 +XGJy+SWX4qnJGa9EL1Hx7tI0Mf0sSS62nC1GY8WeqCg2VCygdAuiYgPc+f3xuOsCW2anLuzzfr32 +pezOznx3WOYzTzcIgiCAYRiGYWzgofcCGIZhGNeGhYJhGIaxCwsFwzAMYxcWCoZhGMYuLBQMwzCM +XVgoGIZhGLuwUDAMwzB2YaFgGCfIzs7G008/jYCAADRv3hyxsbH44IMPYDQa9V4aw6gGCwXDiOT0 +6dPo3bs32rVrhyNHjqCsrAxLly5FRkYGrl27pvfyGEY1WCgYtyYtLQ3h4eFo1qwZoqOjsWLFCpvb +vv322+jTpw/+/e9/IzAwEAAQGRmJb7/9Fn5+fgCAVatWITo6Gv7+/ujfvz+OHz9ufn9YWBjee+89 +xMbGonnz5hg1ahRu375tfn3lypWIi4uDn58fwsPD8fPPP6v0qRnGSQSGcWOWLl0qFBUVCYIgCIsX +LxaaNGli/rkmQUFBwvz5823u68SJE0KTJk2EjRs3ClVVVcI///lPITw8XKisrBQEQRDCwsKE3r17 +C0VFRUJpaanQuXNn4bPPPhMEQRB+/fVXwc/PT9i4caMgCIJQUFAgHD9+XMmPyjCSYYuCcWtGjBiB 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Build-an-active-neuron-model-by-putting-channels-into-a-morphology-file">Build an active neuron model by putting channels into a morphology file<a class="anchor-link" href="#Build-an-active-neuron-model-by-putting-channels-into-a-morphology-file">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [*]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">chanProto</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">'./chans/hd.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kap.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kad.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kdr.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/na3.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/nax.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/CaConc.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/Ca.xml'</span><span class="p">]</span> + <span class="p">],</span> + <span class="n">cellProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'./cells/h10.CNG.swc'</span><span class="p">,</span> <span class="s">'elec'</span><span class="p">]],</span> + <span class="n">chanDistrib</span> <span class="o">=</span> <span class="p">[</span> \ + <span class="p">[</span><span class="s">"hd"</span><span class="p">,</span> <span class="s">"#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50e-2*(1+(p*3e4))"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kdr"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"p < 50e-6 ? 500 : 100"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"na3"</span><span class="p">,</span> <span class="s">"#soma#,#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"850"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"nax"</span><span class="p">,</span> <span class="s">"#soma#,#axon#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"1250"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kap"</span><span class="p">,</span> <span class="s">"#axon#,#soma#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"300"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kap"</span><span class="p">,</span> <span class="s">"#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> + <span class="s">"300*(H(100-p*1e6)) * (1+(p*1e4))"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"Ca_conc"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"tau"</span><span class="p">,</span> <span class="s">"0.0133"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kad"</span><span class="p">,</span> <span class="s">"#soma#,#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"Ca"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50"</span> <span class="p">]</span> + <span class="p">],</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'(t>0.02) * 1e-9'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Ca conc (uM)'</span><span class="p">]],</span> + <span class="n">moogList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Calcium conc (uM)'</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">120</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Soma potential'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> + +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">displayMoogli</span><span class="p">(</span> <span class="mf">0.0002</span><span class="p">,</span> <span class="mf">0.052</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +[INFO] Loading Ca pool Ca_conc into /library . </span> +Rdesigneur: Elec model has 204 compartments and 0 spines on 0 compartments. + +</pre> +</div> +</div> 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5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom 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+.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), 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endColorstr='#ff339bb9', GradientType=0)} +.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Hodgkin-Huxley-squid-model-channels-into-a-passive-compartment">Hodgkin-Huxley squid model channels into a passive compartment<a class="anchor-link" href="#Hodgkin-Huxley-squid-model-channels-into-a-passive-compartment">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [2]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="o">%</span><span class="k">matplotlib</span> <span class="n">inline</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">chanProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'make_HH_Na()'</span><span class="p">,</span> <span class="s">'Na'</span><span class="p">],</span> <span class="p">[</span><span class="s">'make_HH_K()'</span><span class="p">,</span> <span class="s">'K'</span><span class="p">]],</span> + <span class="n">chanDistrib</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">'Na'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'Gbar'</span><span class="p">,</span> <span class="s">'1200'</span> <span class="p">],</span> + <span class="p">[</span><span class="s">'K'</span><span class="p">,</span> <span class="s">'soma'</span><span class="p">,</span> <span class="s">'Gbar'</span><span class="p">,</span> <span class="s">'360'</span> <span class="p">]],</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'(t>0.1 && t<0.2) * 1e-8'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">0.3</span> <span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">display</span><span class="p">()</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 0 compartments. + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAY0AAAEZCAYAAABrUHmEAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzt3XlcVOX+B/DPoKOigamoCKMioCEqiFtaFngTDbsqZZnw +y4tpVrcszeuW1RUyRS0tyTQtNS01tEUwldSQzC2VW7mguSKbqLmiyDIzz++PpxmGZZgzzDkz58x8 +368XL5jtO88wM8/3POtRMcYYCCGEEAHcHF0AQgghykFJgxBCiGCUNAghhAhGSYMQQohglDQIIYQI +RkmDEEKIYJQ0iFOKj4/H6NGjHV0MxcnJyYGHhweEzMTPyMhA27Zt7VAqIieUNIjk/Pz80LBhQ1y7 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5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom 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+.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), 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endColorstr='#ff339bb9', GradientType=0)} +.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, 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label{display:inline-block;height:15px;line-height:15px;vertical-align:top} +.celltoolbar label span{font-size:85%} +.celltoolbar input[type=checkbox]{margin:0;margin-left:4px;margin-right:4px} +.celltoolbar .ui-button{border:none;vertical-align:top;height:20px} +div.input{page-break-inside:avoid;display:-webkit-box;-webkit-box-orient:horizontal;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:horizontal;-moz-box-align:stretch;display:box;box-orient:horizontal;box-align:stretch} +div.input_area{border:1px solid #cfcfcf;border-radius:4px;background:#f7f7f7} +div.input_prompt{color:#000080;border-top:1px solid transparent} +div.output_wrapper{margin-top:5px;position:relative;display:-webkit-box;-webkit-box-orient:vertical;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:vertical;-moz-box-align:stretch;display:box;box-orient:vertical;box-align:stretch;width:100%} +div.output_scroll{height:24em;width:100%;overflow:auto;border-radius:4px;-webkit-box-shadow:inset 0 2px 8px rgba(0,0,0,0.8);-moz-box-shadow:inset 0 2px 8px rgba(0,0,0,0.8);box-shadow:inset 0 2px 8px rgba(0,0,0,0.8)} +div.output_collapsed{margin:0;padding:0;display:-webkit-box;-webkit-box-orient:vertical;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:vertical;-moz-box-align:stretch;display:box;box-orient:vertical;box-align:stretch;width:100%} +div.out_prompt_overlay{height:100%;padding:0 .4em;position:absolute;border-radius:4px} +div.out_prompt_overlay:hover{-webkit-box-shadow:inset 0 0 1px #000;-moz-box-shadow:inset 0 0 1px #000;box-shadow:inset 0 0 1px #000;background:rgba(240,240,240,0.5)} +div.output_prompt{color:#8b0000} +.CodeMirror{line-height:1.231em;height:auto;background:none;} +.CodeMirror-scroll{overflow-y:hidden;overflow-x:auto} +@-moz-document url-prefix(){.CodeMirror-scroll{overflow-x:hidden}}.CodeMirror-lines{padding:.4em} +.CodeMirror-linenumber{padding:0 8px 0 4px} +.CodeMirror-gutters{border-bottom-left-radius:4px;border-top-left-radius:4px} +.CodeMirror pre{padding:0;border:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0} +.completions{position:absolute;z-index:10;overflow:hidden;border:1px solid #ababab;border-radius:4px;-webkit-box-shadow:0 6px 10px -1px #adadad;-moz-box-shadow:0 6px 10px -1px #adadad;box-shadow:0 6px 10px -1px #adadad} +.completions select{background:#fff;outline:none;border:none;padding:0;margin:0;overflow:auto;font-family:monospace;font-size:110%;color:#000} +.completions select option.context{color:#0064cd} +pre code{display:block;padding:.5em} +.highlight-base,pre code,pre .subst,pre .tag .title,pre .lisp .title,pre .clojure .built_in,pre .nginx .title{color:#000} +.highlight-string,pre .string,pre .constant,pre .parent,pre .tag .value,pre .rules .value,pre .rules .value .number,pre .preprocessor,pre .ruby .symbol,pre .ruby .symbol .string,pre .aggregate,pre .template_tag,pre .django .variable,pre .smalltalk .class,pre .addition,pre .flow,pre .stream,pre .bash .variable,pre 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+div.raw_input{padding-top:0;padding-bottom:0;height:1em;line-height:1em;font-family:monospace} +span.input_prompt{font-family:inherit} +input.raw_input{font-family:inherit;font-size:inherit;color:inherit;width:auto;margin:-2px 0 0 1px;padding-left:1px;padding-top:2px;height:1em} +p.p-space{margin-bottom:10px} +div#pager_splitter{height:8px} +#pager-container{position:relative;padding:15px 0} +div#pager{overflow:auto;display:none}div#pager pre{font-size:13px;line-height:1.231em;color:#000;background-color:#f7f7f7;padding:.4em} +.shortcut_key{display:inline-block;width:15ex;text-align:right;font-family:monospace} +.shortcut_descr{display:inline-block} +div.quickhelp{float:left;width:50%} +.rendered_html{color:#000;}.rendered_html em{font-style:italic} +.rendered_html strong{font-weight:bold} +.rendered_html u{text-decoration:underline} +.rendered_html :link{text-decoration:underline} +.rendered_html :visited{text-decoration:underline} +.rendered_html h1{font-size:197%;margin:.65em 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Build-a-passive-model-using-a-morphology-file-in-the-.swc-file-format">Build a passive model using a morphology file in the .swc file format<a class="anchor-link" href="#Build-a-passive-model-using-a-morphology-file-in-the-.swc-file-format">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [*]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">cellProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'./cells/h10.CNG.swc'</span><span class="p">,</span> <span class="s">'elec'</span><span class="p">]],</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'t * 25e-9'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Ca conc (uM)'</span><span class="p">]],</span> + <span class="n">moogList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Soma potential'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> + +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">displayMoogli</span><span class="p">(</span> <span class="mf">0.0002</span><span class="p">,</span> <span class="mf">0.1</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 204 compartments and 0 spines on 0 compartments. + +</pre> +</div> +</div> +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="h10_CNG_swc.png"> +</div> +</div> +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAY0AAAEZCAYAAABrUHmEAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzs3Xd0E1f+//+nJMuy3HvHGAPGGGNqCB3TOzj0EnovoQRC +CxDTe6gJhF5C79Whm94NGJtiwA3j3qssS5rvH/tb/z7Z3STsEmKS3Mc5OQdp5LnvuZMzL83cOyOZ +JEkSgiAIgvAO5KVdgCAIgvDnIUJDEARBeGciNARBEIR3JkJDEARBeGciNARBEIR3JkJDEARBeGci +NIS/pKCgIPr161faZfzpxMXFYWFhwbvMxA8JCaFMmTJ/QFXCx0SEhvDBeXp6olKpSE9P/9n7NWrU +QC6XExcX97u3KZPJfvd1fgwGDhzIrFmzfrf1eXp6cunSpZLXHh4e5Obm/mX7T3h/IjSED04mk+Hl 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+.dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} +.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default} +.open{*z-index:1000}.open>.dropdown-menu{display:block} +.dropdown-backdrop{position:fixed;left:0;right:0;bottom:0;top:0;z-index:990} +.pull-right>.dropdown-menu{right:0;left:auto} +.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000;content:""} +.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px} +.dropdown-submenu{position:relative} +.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;border-radius:0 6px 6px 6px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px} 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20px;list-style:none;background-color:#f5f5f5;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px}.breadcrumb>li{display:inline-block;*display:inline;*zoom:1;text-shadow:0 1px 0 #fff}.breadcrumb>li>.divider{padding:0 5px;color:#ccc} +.breadcrumb>.active{color:#999} +.pagination{margin:20px 0} +.pagination ul{display:inline-block;*display:inline;*zoom:1;margin-left:0;margin-bottom:0;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 2px rgba(0,0,0,0.05);-moz-box-shadow:0 1px 2px rgba(0,0,0,0.05);box-shadow:0 1px 2px rgba(0,0,0,0.05)} +.pagination ul>li{display:inline} +.pagination ul>li>a,.pagination ul>li>span{float:left;padding:4px 12px;line-height:20px;text-decoration:none;background-color:#fff;border:1px solid #ddd;border-left-width:0} +.pagination ul>li>a:hover,.pagination ul>li>a:focus,.pagination ul>.active>a,.pagination ul>.active>span{background-color:#f5f5f5} +.pagination ul>.active>a,.pagination ul>.active>span{color:#999;cursor:default} +.pagination ul>.disabled>span,.pagination ul>.disabled>a,.pagination ul>.disabled>a:hover,.pagination ul>.disabled>a:focus{color:#999;background-color:transparent;cursor:default} +.pagination ul>li:first-child>a,.pagination ul>li:first-child>span{border-left-width:1px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px} +.pagination ul>li:last-child>a,.pagination ul>li:last-child>span{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px} +.pagination-centered{text-align:center} +.pagination-right{text-align:right} +.pagination-large ul>li>a,.pagination-large ul>li>span{padding:11px 19px;font-size:16.25px} +.pagination-large 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5px;border-left-color:#000} +.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000} +.popover{position:absolute;top:0;left:0;z-index:1010;display:none;max-width:276px;padding:1px;text-align:left;background-color:#fff;-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;border:1px solid #ccc;border:1px solid rgba(0,0,0,0.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0,0,0,0.2);-moz-box-shadow:0 5px 10px rgba(0,0,0,0.2);box-shadow:0 5px 10px rgba(0,0,0,0.2);white-space:normal}.popover.top{margin-top:-10px} +.popover.right{margin-left:10px} +.popover.bottom{margin-top:10px} +.popover.left{margin-left:-10px} +.popover-title{margin:0;padding:8px 14px;font-size:14px;font-weight:normal;line-height:18px;background-color:#f7f7f7;border-bottom:1px solid #ebebeb;border-radius:5px 5px 0 0;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom 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+a.thumbnail:hover,a.thumbnail:focus{border-color:#08c;-webkit-box-shadow:0 1px 4px rgba(0,105,214,0.25);-moz-box-shadow:0 1px 4px rgba(0,105,214,0.25);box-shadow:0 1px 4px rgba(0,105,214,0.25)} +.thumbnail>img{display:block;max-width:100%;margin-left:auto;margin-right:auto} +.thumbnail .caption{padding:9px;color:#555} +.media,.media-body{overflow:hidden;*overflow:visible;zoom:1} +.media,.media .media{margin-top:15px} +.media:first-child{margin-top:0} +.media-object{display:block} +.media-heading{margin:0 0 5px} +.media>.pull-left{margin-right:10px} +.media>.pull-right{margin-left:10px} +.media-list{margin-left:0;list-style:none} +.label,.badge{display:inline-block;padding:2px 4px;font-size:10.998px;font-weight:bold;line-height:14px;color:#fff;vertical-align:baseline;white-space:nowrap;text-shadow:0 -1px 0 rgba(0,0,0,0.25);background-color:#999} +.label{border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} +.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="A-passive-model-using-a-morphology-file-in-the-.swc-file-forma">A passive model using a morphology file in the .swc file forma<a class="anchor-link" href="#A-passive-model-using-a-morphology-file-in-the-.swc-file-forma">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [*]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">cellProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'./cells/h10.CNG.swc'</span><span class="p">,</span> <span class="s">'elec'</span><span class="p">]],</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'t * 25e-9'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Ca conc (uM)'</span><span class="p">]],</span> + <span class="n">moogList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Soma potential'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> + +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">displayMoogli</span><span class="p">(</span> <span class="mf">0.0002</span><span class="p">,</span> <span class="mf">0.1</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 204 compartments and 0 spines on 0 compartments. + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAY0AAAEZCAYAAABrUHmEAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzs3Xd0E1f+//+nJMuy3HvHGAPGGGNqCB3TOzj0EnovoQRC +CxDTe6gJhF5C79Whm94NGJtiwA3j3qssS5rvH/tb/z7Z3STsEmKS3Mc5OQdp5LnvuZMzL83cOyOZ +JEkSgiAIgvAO5KVdgCAIgvDnIUJDEARBeGciNARBEIR3JkJDEARBeGciNARBEIR3JkJDEARBeGci +NIS/pKCgIPr161faZfzpxMXFYWFhwbvMxA8JCaFMmTJ/QFXCx0SEhvDBeXp6olKpSE9P/9n7NWrU +QC6XExcX97u3KZPJfvd1fgwGDhzIrFmzfrf1eXp6cunSpZLXHh4e5Obm/mX7T3h/IjSED04mk+Hl +5cXevXtL3nvy5AmFhYUf7OD039yzqtPpPkgNfwYymey/6itBEKEh/CE+//xzdu7cWfJ6x44d9O/f +/2cHrKKiIiZPnkzZsmVxdnZm1KhRaDQa4B+XQtzd3Vm2bBmOjo64urpy7Ngxzpw5g7e3N3Z2dixe 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+.dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} +.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default} +.open{*z-index:1000}.open>.dropdown-menu{display:block} +.dropdown-backdrop{position:fixed;left:0;right:0;bottom:0;top:0;z-index:990} +.pull-right>.dropdown-menu{right:0;left:auto} +.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000;content:""} +.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px} +.dropdown-submenu{position:relative} +.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;border-radius:0 6px 6px 6px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px} +.dropdown-submenu:hover>.dropdown-menu{display:block} +.dropup .dropdown-submenu>.dropdown-menu{top:auto;bottom:0;margin-top:0;margin-bottom:-2px;border-radius:5px 5px 5px 0;-webkit-border-radius:5px 5px 5px 0;-moz-border-radius:5px 5px 5px 0;border-radius:5px 5px 5px 0} +.dropdown-submenu>a:after{display:block;content:" ";float:right;width:0;height:0;border-color:transparent;border-style:solid;border-width:5px 0 5px 5px;border-left-color:#ccc;margin-top:5px;margin-right:-10px} +.dropdown-submenu:hover>a:after{border-left-color:#fff} +.dropdown-submenu.pull-left{float:none}.dropdown-submenu.pull-left>.dropdown-menu{left:-100%;margin-left:10px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px} +.dropdown .dropdown-menu .nav-header{padding-left:20px;padding-right:20px} +.typeahead{z-index:1051;margin-top:2px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px} 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Create-a-single-passive-compartment-model,-current-is-injected-as-the-simulation-runs.-This-script-displays-the-membrane-potential-of-the-soma-as-it-charges-and-discharges.">Create a single passive compartment model, current is injected as the simulation runs. This script displays the membrane potential of the soma as it charges and discharges.<a class="anchor-link" href="#Create-a-single-passive-compartment-model,-current-is-injected-as-the-simulation-runs.-This-script-displays-the-membrane-potential-of-the-soma-as-it-charges-and-discharges.">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [1]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="o">%</span><span class="k">matplotlib</span> <span class="n">inline</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'(t>0.1 && t<0.2) * 2e-8'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Soma membrane potential'</span><span class="p">]]</span> +<span class="p">)</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">0.3</span> <span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">display</span><span class="p">()</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 0 compartments. + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAY0AAAEZCAYAAABrUHmEAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzt3XlUVOf5B/DvDIuCAiKgAhMYWRRQwDGowWgcU0nURA+a +xoiNtXHJVlONJvHXpComorVVk6Me1Ca2kVSjSdpEG5doEqlxBVziHlwYQRYDiGwuCLy/PyZMQRhn 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5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom 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+.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), 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endColorstr='#ff339bb9', GradientType=0)} +.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, 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label{display:inline-block;height:15px;line-height:15px;vertical-align:top} +.celltoolbar label span{font-size:85%} +.celltoolbar input[type=checkbox]{margin:0;margin-left:4px;margin-right:4px} +.celltoolbar .ui-button{border:none;vertical-align:top;height:20px} +div.input{page-break-inside:avoid;display:-webkit-box;-webkit-box-orient:horizontal;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:horizontal;-moz-box-align:stretch;display:box;box-orient:horizontal;box-align:stretch} +div.input_area{border:1px solid #cfcfcf;border-radius:4px;background:#f7f7f7} +div.input_prompt{color:#000080;border-top:1px solid transparent} +div.output_wrapper{margin-top:5px;position:relative;display:-webkit-box;-webkit-box-orient:vertical;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:vertical;-moz-box-align:stretch;display:box;box-orient:vertical;box-align:stretch;width:100%} +div.output_scroll{height:24em;width:100%;overflow:auto;border-radius:4px;-webkit-box-shadow:inset 0 2px 8px rgba(0,0,0,0.8);-moz-box-shadow:inset 0 2px 8px rgba(0,0,0,0.8);box-shadow:inset 0 2px 8px rgba(0,0,0,0.8)} +div.output_collapsed{margin:0;padding:0;display:-webkit-box;-webkit-box-orient:vertical;-webkit-box-align:stretch;display:-moz-box;-moz-box-orient:vertical;-moz-box-align:stretch;display:box;box-orient:vertical;box-align:stretch;width:100%} +div.out_prompt_overlay{height:100%;padding:0 .4em;position:absolute;border-radius:4px} +div.out_prompt_overlay:hover{-webkit-box-shadow:inset 0 0 1px #000;-moz-box-shadow:inset 0 0 1px #000;box-shadow:inset 0 0 1px #000;background:rgba(240,240,240,0.5)} +div.output_prompt{color:#8b0000} +.CodeMirror{line-height:1.231em;height:auto;background:none;} +.CodeMirror-scroll{overflow-y:hidden;overflow-x:auto} +@-moz-document url-prefix(){.CodeMirror-scroll{overflow-x:hidden}}.CodeMirror-lines{padding:.4em} +.CodeMirror-linenumber{padding:0 8px 0 4px} +.CodeMirror-gutters{border-bottom-left-radius:4px;border-top-left-radius:4px} +.CodeMirror pre{padding:0;border:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0} +.completions{position:absolute;z-index:10;overflow:hidden;border:1px solid #ababab;border-radius:4px;-webkit-box-shadow:0 6px 10px -1px #adadad;-moz-box-shadow:0 6px 10px -1px #adadad;box-shadow:0 6px 10px -1px #adadad} +.completions select{background:#fff;outline:none;border:none;padding:0;margin:0;overflow:auto;font-family:monospace;font-size:110%;color:#000} +.completions select option.context{color:#0064cd} +pre code{display:block;padding:.5em} +.highlight-base,pre code,pre .subst,pre .tag .title,pre .lisp .title,pre .clojure .built_in,pre .nginx .title{color:#000} +.highlight-string,pre .string,pre .constant,pre .parent,pre .tag .value,pre .rules .value,pre .rules .value .number,pre .preprocessor,pre .ruby .symbol,pre .ruby .symbol .string,pre .aggregate,pre .template_tag,pre .django .variable,pre .smalltalk .class,pre .addition,pre .flow,pre .stream,pre .bash .variable,pre 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+div.raw_input{padding-top:0;padding-bottom:0;height:1em;line-height:1em;font-family:monospace} +span.input_prompt{font-family:inherit} +input.raw_input{font-family:inherit;font-size:inherit;color:inherit;width:auto;margin:-2px 0 0 1px;padding-left:1px;padding-top:2px;height:1em} +p.p-space{margin-bottom:10px} +div#pager_splitter{height:8px} +#pager-container{position:relative;padding:15px 0} +div#pager{overflow:auto;display:none}div#pager pre{font-size:13px;line-height:1.231em;color:#000;background-color:#f7f7f7;padding:.4em} +.shortcut_key{display:inline-block;width:15ex;text-align:right;font-family:monospace} +.shortcut_descr{display:inline-block} +div.quickhelp{float:left;width:50%} +.rendered_html{color:#000;}.rendered_html em{font-style:italic} +.rendered_html strong{font-weight:bold} +.rendered_html u{text-decoration:underline} +.rendered_html :link{text-decoration:underline} +.rendered_html :visited{text-decoration:underline} +.rendered_html h1{font-size:197%;margin:.65em 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h2 id="Creates-Single-Passive-Compartment-Model">Creates Single Passive Compartment Model<a class="anchor-link" href="#Creates-Single-Passive-Compartment-Model">¶</a></h2> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [2]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">()</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">showfields</span><span class="p">(</span> <span class="n">rdes</span><span class="o">.</span><span class="n">soma</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 1 compartments and 0 spines on 0 compartments. + +[ /model[0]/elec[0]/soma[0] ] +diameter = 0.0005 +fieldIndex = 0 +Ra = 7639437.26841 +y0 = 0.0 +Rm = 424413.177334 +index = 0 +numData = 1 +inject = 0.0 +initVm = -0.065 +Em = -0.0544 +y = 0.0 +numField = 1 +path = /model[0]/elec[0]/soma[0] +dt = 0.0 +tick = -2 +z0 = 0.0 +name = soma +Cm = 7.85398163398e-09 +x0 = 0.0 +Vm = -0.06 +className = ZombieCompartment +idValue = 465 +length = 0.0005 +Im = 1.3194689277e-08 +x = 0.0005 +z = 0.0 + +</pre> +</div> +</div> + +</div> +</div> + +</div> +</body> +</html> diff --git a/docs/user/tutorials/_static/Spiny_neuron_reaction-diffusion_system.html 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+.dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} +.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default} +.open{*z-index:1000}.open>.dropdown-menu{display:block} +.dropdown-backdrop{position:fixed;left:0;right:0;bottom:0;top:0;z-index:990} +.pull-right>.dropdown-menu{right:0;left:auto} +.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000;content:""} +.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px} +.dropdown-submenu{position:relative} +.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;border-radius:0 6px 6px 6px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px} +.dropdown-submenu:hover>.dropdown-menu{display:block} +.dropup .dropdown-submenu>.dropdown-menu{top:auto;bottom:0;margin-top:0;margin-bottom:-2px;border-radius:5px 5px 5px 0;-webkit-border-radius:5px 5px 5px 0;-moz-border-radius:5px 5px 5px 0;border-radius:5px 5px 5px 0} +.dropdown-submenu>a:after{display:block;content:" ";float:right;width:0;height:0;border-color:transparent;border-style:solid;border-width:5px 0 5px 5px;border-left-color:#ccc;margin-top:5px;margin-right:-10px} +.dropdown-submenu:hover>a:after{border-left-color:#fff} +.dropdown-submenu.pull-left{float:none}.dropdown-submenu.pull-left>.dropdown-menu{left:-100%;margin-left:10px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px} +.dropdown .dropdown-menu .nav-header{padding-left:20px;padding-right:20px} +.typeahead{z-index:1051;margin-top:2px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px} +.well{min-height:20px;padding:19px;margin-bottom:20px;background-color:#f5f5f5;border:1px solid #e3e3e3;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.05);-moz-box-shadow:inset 0 1px 1px rgba(0,0,0,0.05);box-shadow:inset 0 1px 1px rgba(0,0,0,0.05)}.well blockquote{border-color:#ddd;border-color:rgba(0,0,0,0.15)} +.well-large{padding:24px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px} +.well-small{padding:9px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} +.fade{opacity:0;-webkit-transition:opacity .15s linear;-moz-transition:opacity .15s linear;-o-transition:opacity .15s linear;transition:opacity .15s linear}.fade.in{opacity:1} +.collapse{position:relative;height:0;overflow:hidden;-webkit-transition:height .35s ease;-moz-transition:height .35s ease;-o-transition:height .35s ease;transition:height .35s ease}.collapse.in{height:auto} +.close{float:right;font-size:20px;font-weight:bold;line-height:20px;color:#000;text-shadow:0 1px 0 #fff;opacity:.2;filter:alpha(opacity=20)}.close:hover,.close:focus{color:#000;text-decoration:none;cursor:pointer;opacity:.4;filter:alpha(opacity=40)} +button.close{padding:0;cursor:pointer;background:transparent;border:0;-webkit-appearance:none} +.btn{display:inline-block;*display:inline;*zoom:1;padding:4px 12px;margin-bottom:0;font-size:13px;line-height:20px;text-align:center;vertical-align:middle;cursor:pointer;color:#333;text-shadow:0 1px 1px rgba(255,255,255,0.75);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #fff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #fff, #e6e6e6);background-image:-o-linear-gradient(top, #fff, #e6e6e6);background-image:linear-gradient(to bottom, #fff, 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5px 0 0;border-radius:5px 5px 0 0}.popover-title:empty{display:none} +.popover-content{padding:9px 14px} +.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid} +.popover .arrow{border-width:11px} +.popover .arrow:after{border-width:10px;content:""} +.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0,0,0,0.25);bottom:-11px}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#fff} +.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0,0,0,0.25)}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#fff} +.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0,0,0,0.25);top:-11px}.popover.bottom .arrow:after{top:1px;margin-left:-10px;border-top-width:0;border-bottom-color:#fff} +.popover.left .arrow{top:50%;right:-11px;margin-top:-11px;border-right-width:0;border-left-color:#999;border-left-color:rgba(0,0,0,0.25)}.popover.left .arrow:after{right:1px;border-right-width:0;border-left-color:#fff;bottom:-10px} +.thumbnails{margin-left:-20px;list-style:none;*zoom:1}.thumbnails:before,.thumbnails:after{display:table;content:"";line-height:0} +.thumbnails:after{clear:both} +.row-fluid .thumbnails{margin-left:0} +.thumbnails>li{float:left;margin-bottom:20px;margin-left:20px} +.thumbnail{display:block;padding:4px;line-height:20px;border:1px solid #ddd;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0,0,0,0.055);-moz-box-shadow:0 1px 3px rgba(0,0,0,0.055);box-shadow:0 1px 3px rgba(0,0,0,0.055);-webkit-transition:all .2s ease-in-out;-moz-transition:all .2s ease-in-out;-o-transition:all .2s ease-in-out;transition:all .2s ease-in-out} +a.thumbnail:hover,a.thumbnail:focus{border-color:#08c;-webkit-box-shadow:0 1px 4px rgba(0,105,214,0.25);-moz-box-shadow:0 1px 4px rgba(0,105,214,0.25);box-shadow:0 1px 4px rgba(0,105,214,0.25)} +.thumbnail>img{display:block;max-width:100%;margin-left:auto;margin-right:auto} +.thumbnail .caption{padding:9px;color:#555} +.media,.media-body{overflow:hidden;*overflow:visible;zoom:1} +.media,.media .media{margin-top:15px} +.media:first-child{margin-top:0} +.media-object{display:block} +.media-heading{margin:0 0 5px} +.media>.pull-left{margin-right:10px} +.media>.pull-right{margin-left:10px} +.media-list{margin-left:0;list-style:none} +.label,.badge{display:inline-block;padding:2px 4px;font-size:10.998px;font-weight:bold;line-height:14px;color:#fff;vertical-align:baseline;white-space:nowrap;text-shadow:0 -1px 0 rgba(0,0,0,0.25);background-color:#999} +.label{border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} +.badge{padding-left:9px;padding-right:9px;border-radius:9px;-webkit-border-radius:9px;-moz-border-radius:9px;border-radius:9px} +.label:empty,.badge:empty{display:none} +a.label:hover,a.label:focus,a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} +.label-important,.badge-important{background-color:#b94a48} +.label-important[href],.badge-important[href]{background-color:#953b39} +.label-warning,.badge-warning{background-color:#f89406} +.label-warning[href],.badge-warning[href]{background-color:#c67605} +.label-success,.badge-success{background-color:#468847} +.label-success[href],.badge-success[href]{background-color:#356635} +.label-info,.badge-info{background-color:#3a87ad} +.label-info[href],.badge-info[href]{background-color:#2d6987} +.label-inverse,.badge-inverse{background-color:#333} +.label-inverse[href],.badge-inverse[href]{background-color:#1a1a1a} +.btn .label,.btn .badge{position:relative;top:-1px} +.btn-mini .label,.btn-mini .badge{top:0} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', 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rgba(0,0,0,0.15);box-shadow:inset 0 -1px 0 rgba(0,0,0,0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width .6s ease;-moz-transition:width .6s ease;-o-transition:width .6s ease;transition:width .6s ease} +.progress .bar+.bar{-webkit-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-moz-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15)} +.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px} +.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite} +.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0)} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent)} +.progress-success .bar,.progress .bar-success{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(to bottom, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff62c462', endColorstr='#ff57a957', GradientType=0)} +.progress-success.progress-striped .bar,.progress-striped .bar-success{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent)} +.progress-info .bar,.progress .bar-info{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(to bottom, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0)} +.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent)} +.progress-warning .bar,.progress .bar-warning{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(to bottom, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0)} +.progress-warning.progress-striped .bar,.progress-striped .bar-warning{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, 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#e5e5e5;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px} +.accordion-heading{border-bottom:0} +.accordion-heading .accordion-toggle{display:block;padding:8px 15px} +.accordion-toggle{cursor:pointer} +.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5} +.carousel{position:relative;margin-bottom:20px;line-height:1} +.carousel-inner{overflow:hidden;width:100%;position:relative} +.carousel-inner>.item{display:none;position:relative;-webkit-transition:.6s ease-in-out left;-moz-transition:.6s ease-in-out left;-o-transition:.6s ease-in-out left;transition:.6s ease-in-out left}.carousel-inner>.item>img,.carousel-inner>.item>a>img{display:block;line-height:1} +.carousel-inner>.active,.carousel-inner>.next,.carousel-inner>.prev{display:block} +.carousel-inner>.active{left:0} +.carousel-inner>.next,.carousel-inner>.prev{position:absolute;top:0;width:100%} +.carousel-inner>.next{left:100%} +.carousel-inner>.prev{left:-100%} +.carousel-inner>.next.left,.carousel-inner>.prev.right{left:0} +.carousel-inner>.active.left{left:-100%} +.carousel-inner>.active.right{left:100%} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#fff;text-align:center;background:#222;border:3px solid #fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{left:auto;right:15px} +.carousel-control:hover,.carousel-control:focus{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)} +.carousel-indicators{position:absolute;top:15px;right:15px;z-index:5;margin:0;list-style:none}.carousel-indicators li{display:block;float:left;width:10px;height:10px;margin-left:5px;text-indent:-999px;background-color:#ccc;background-color:rgba(255,255,255,0.25);border-radius:5px} +.carousel-indicators .active{background-color:#fff} +.carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:15px;background:#333;background:rgba(0,0,0,0.75)} +.carousel-caption h4,.carousel-caption p{color:#fff;line-height:20px} +.carousel-caption h4{margin:0 0 5px} +.carousel-caption p{margin-bottom:0} +.hero-unit{padding:60px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:30px;color:inherit;background-color:#eee;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px} +.hero-unit li{line-height:30px} +.pull-right{float:right} +.pull-left{float:left} +.hide{display:none} +.show{display:block} +.invisible{visibility:hidden} +.affix{position:fixed} +.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:"";line-height:0} +.clearfix:after{clear:both} +.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0} 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Spiny-neuron-from-a-morphology-file-together-with-reaction-diffusion-system-in-it">Spiny neuron from a morphology file together with reaction-diffusion system in it<a class="anchor-link" href="#Spiny-neuron-from-a-morphology-file-together-with-reaction-diffusion-system-in-it">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [2]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> + +<span class="n">library</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'/library'</span> <span class="p">)</span> +<span class="n">compt</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">makeChemOscillator</span><span class="p">(</span> <span class="s">'osc'</span> <span class="p">)</span> +<span class="n">compt</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="mf">1e-18</span> +<span class="n">moose</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span> <span class="n">compt</span><span class="p">,</span> <span class="s">'/library/osc'</span><span class="p">,</span> <span class="s">'spine'</span> <span class="p">)</span> +<span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/library/osc/spine'</span> <span class="p">)</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="mf">1e-19</span> +<span class="n">moose</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span> <span class="n">compt</span><span class="p">,</span> <span class="s">'/library/osc'</span><span class="p">,</span> <span class="s">'psd'</span> <span class="p">)</span> +<span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/library/osc/psd'</span> <span class="p">)</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="mf">1e-20</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">turnOffElec</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> + <span class="n">useGssa</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> + <span class="n">cellProto</span> <span class="o">=</span> <span class="p">[[</span> <span class="s">'./cells/h10.CNG.swc'</span><span class="p">,</span> <span class="s">'elec'</span><span class="p">]],</span> + <span class="n">spineProto</span> <span class="o">=</span> <span class="p">[[</span> <span class="s">'makePassiveSpine()'</span><span class="p">,</span> <span class="s">'spine'</span> <span class="p">]</span> <span class="p">],</span> + <span class="n">spineDistrib</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="s">"spine"</span><span class="p">,</span> <span class="s">'#apical#,#dend#'</span><span class="p">,</span> <span class="s">'10e-6'</span><span class="p">,</span> <span class="s">'1e-6'</span> <span class="p">]],</span> + <span class="n">chemProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'/library/osc'</span><span class="p">,</span> <span class="s">'osc'</span><span class="p">]],</span> + <span class="n">chemDistrib</span> <span class="o">=</span><span class="p">[[</span> <span class="s">'osc'</span><span class="p">,</span> <span class="s">'#apical#,#dend#'</span><span class="p">,</span> <span class="s">'install'</span><span class="p">,</span> <span class="s">'H(p - 5e-4)'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'psd/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'conc of a in PSD'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'spine/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'conc of a in spine'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'dend/a'</span><span class="p">,</span> <span class="s">'conc'</span><span class="p">,</span> <span class="s">'conc of a in Dend'</span><span class="p">]</span> + <span class="p">]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> + +<span class="n">av</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">vec</span><span class="p">(</span> <span class="s">'/model/chem/psd/a'</span> <span class="p">)</span> +<span class="n">av</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">concInit</span> <span class="o">*=</span> <span class="mi">10</span> + +<span class="sd">'''</span> +<span class="sd">dv = moose.vec( '/model/chem/dend/a' )</span> +<span class="sd">print len( dv )</span> +<span class="sd">dv[0].concInit *= 2</span> +<span class="sd">'''</span> + +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mi">100</span> <span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">display</span><span class="p">()</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +Rdesigneur: Elec model has 204 compartments and 1164 spines on 21 compartments. +Chem part of model has 744 dendrite voxels X 3 pools, + +180 spine voxels X 3 pools, 180 psd voxels X 3 pools. + +</pre> +</div> +</div> + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img 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visible; + padding: 8px; +} +.input_area { + padding: 0.2em; +} + +pre { + padding: 0.2em; + border: none; + margin: 0px; + font-size: 13px; +} +</style> + +<!-- Custom stylesheet, it must be in the same directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<script src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS_HTML" type="text/javascript"></script> +<script type="text/javascript"> +init_mathjax = function() { + if (window.MathJax) { + // MathJax loaded + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ] + }, + displayAlign: 'left', // Change this to 'center' to center equations. + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}} + } + }); + MathJax.Hub.Queue(["Typeset",MathJax.Hub]); + } +} +init_mathjax(); +</script> +</head> +<body> + +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Build-a-spiny-neuron-from-a-morphology-file-and-put-active-channels-in-it">Build a spiny neuron from a morphology file and put active channels in it<a class="anchor-link" href="#Build-a-spiny-neuron-from-a-morphology-file-and-put-active-channels-in-it">¶</a></h1> +</div> + +<div class="cell border-box-sizing code_cell vbox"> +<div class="input hbox"> +<div class="prompt input_prompt"> +In [*]: +</div> +<div class="input_area box-flex1"> +<div class="highlight"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">rdesigneur</span> <span class="kn">as</span> <span class="nn">rd</span> +<span class="o">%</span><span class="k">matplotlib</span> <span class="n">inline</span> + +<span class="n">rdes</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">rdesigneur</span><span class="p">(</span> + <span class="n">chanProto</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">'./chans/hd.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kap.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kad.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/kdr.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/na3.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/nax.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/CaConc.xml'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'./chans/Ca.xml'</span><span class="p">]</span> + <span class="p">],</span> + <span class="n">cellProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'./cells/h10.CNG.swc'</span><span class="p">,</span> <span class="s">'elec'</span><span class="p">]],</span> + <span class="n">spineProto</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'makeActiveSpine()'</span><span class="p">,</span> <span class="s">'spine'</span><span class="p">]],</span> + <span class="n">chanDistrib</span> <span class="o">=</span> <span class="p">[</span> + <span class="p">[</span><span class="s">"hd"</span><span class="p">,</span> <span class="s">"#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50e-2*(1+(p*3e4))"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kdr"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"p < 50e-6 ? 500 : 100"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"na3"</span><span class="p">,</span> <span class="s">"#soma#,#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"850"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"nax"</span><span class="p">,</span> <span class="s">"#soma#,#axon#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"1250"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kap"</span><span class="p">,</span> <span class="s">"#axon#,#soma#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"300"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kap"</span><span class="p">,</span> <span class="s">"#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> + <span class="s">"300*(H(100-p*1e6)) * (1+(p*1e4))"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"Ca_conc"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"tau"</span><span class="p">,</span> <span class="s">"0.0133"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"kad"</span><span class="p">,</span> <span class="s">"#soma#,#dend#,#apical#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50"</span> <span class="p">],</span> + <span class="p">[</span><span class="s">"Ca"</span><span class="p">,</span> <span class="s">"#"</span><span class="p">,</span> <span class="s">"Gbar"</span><span class="p">,</span> <span class="s">"50"</span> <span class="p">]</span> + <span class="p">],</span> + <span class="n">spineDistrib</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'spine'</span><span class="p">,</span> <span class="s">'#dend#,#apical#'</span><span class="p">,</span> <span class="s">'20e-6'</span><span class="p">,</span> <span class="s">'1e-6'</span><span class="p">]],</span> + <span class="n">stimList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'soma'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'inject'</span><span class="p">,</span> <span class="s">'(t>0.02) * 1e-9'</span> <span class="p">]],</span> + <span class="n">plotList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Membrane potential'</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Ca conc (uM)'</span><span class="p">]],</span> + <span class="n">moogList</span> <span class="o">=</span> <span class="p">[[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'Ca_conc'</span><span class="p">,</span> <span class="s">'Ca'</span><span class="p">,</span> <span class="s">'Calcium conc (uM)'</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">120</span><span class="p">],</span> + <span class="p">[</span><span class="s">'#'</span><span class="p">,</span> <span class="s">'1'</span><span class="p">,</span> <span class="s">'.'</span><span class="p">,</span> <span class="s">'Vm'</span><span class="p">,</span> <span class="s">'Soma potential'</span><span class="p">]]</span> +<span class="p">)</span> + +<span class="n">rdes</span><span class="o">.</span><span class="n">buildModel</span><span class="p">()</span> + +<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> +<span class="n">rdes</span><span class="o">.</span><span class="n">displayMoogli</span><span class="p">(</span> <span class="mf">0.0002</span><span class="p">,</span> <span class="mf">0.0255</span> <span class="p">)</span> +</pre></div> + +</div> +</div> + +<div class="vbox output_wrapper"> +<div class="output vbox"> + + +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_stream output_stdout"> +<pre> +[INFO] Loading Ca pool Ca_conc into /library . </span> +Rdesigneur: Elec model has 204 compartments and 556 spines on 0 compartments. + +</pre> +</div> +</div> +<div class="hbox output_area"><div class="prompt"></div> +<div class="box-flex1 output_subarea output_display_data"> + + +<img src="_static/Neuro_Morophy_activeChanA.png"> +<img src="_static/Neuro_Morophy_activeChanB.png"> +</div></div> + +<div class="hbox output_area"><div 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directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<!-- Loading mathjax macro --> +<!-- Load mathjax --> + <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script> + <!-- MathJax configuration --> + <script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ], + processEscapes: true, + processEnvironments: true + }, + // Center justify equations in code and markdown cells. Elsewhere + // we use CSS to left justify single line equations in code cells. + displayAlign: 'center', + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}}, + linebreaks: { automatic: true } + } + }); + </script> + <!-- End of mathjax configuration --> + +</head> +<body> + <div tabindex="-1" id="notebook" class="border-box-sizing"> + <div class="container" id="notebook-container"> + +<div class="cell border-box-sizing text_cell rendered"> +<div class="prompt input_prompt"> +</div> +<div class="inner_cell"> +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="Finding-a-Steady-State-in-MOOSE">Finding a Steady State in MOOSE<a class="anchor-link" href="#Finding-a-Steady-State-in-MOOSE">¶</a></h1> +</div> +</div> +</div> +<div class="cell border-box-sizing code_cell rendered"> +<div class="input"> +<div class="prompt input_prompt">In [1]:</div> +<div class="inner_cell"> + <div class="input_area"> +<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">math</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">moose</span> + +<span class="o">%</span><span class="k">matplotlib</span> inline + +<span class="k">def</span> <span class="nf">displayPlots</span><span class="p">():</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/graphs/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + +<span class="k">def</span> <span class="nf">getState</span><span class="p">(</span> <span class="n">ksolve</span><span class="p">,</span> <span class="n">state</span> <span class="p">):</span> + <span class="n">state</span><span class="o">.</span><span class="n">randomInit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">0.1</span> <span class="p">)</span> <span class="c"># Run the model for 2 seconds.</span> + <span class="n">state</span><span class="o">.</span><span class="n">settle</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">20.0</span> <span class="p">)</span> <span class="c"># Run model for 10 seconds, just for display</span> + + +<span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="c">#One can build own model or load pre-existing model</span> + <span class="c">#Here we have taken pre-existing model which is in cspace format</span> + <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="s">'../../../../moose-examples/genesis/M1719.cspace'</span><span class="p">,</span> <span class="s">'/model'</span><span class="p">,</span> <span class="s">'ee'</span> <span class="p">)</span> + <span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'model/kinetics'</span> <span class="p">)</span> + <span class="n">compartment</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'compartment'</span> + <span class="c">#setting up the solver</span> + <span class="n">ksolve</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Ksolve</span><span class="p">(</span> <span class="s">'/model/compartment/ksolve'</span> <span class="p">)</span> + <span class="n">stoich</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Stoich</span><span class="p">(</span> <span class="s">'/model/compartment/stoich'</span> <span class="p">)</span> + <span class="n">stoich</span><span class="o">.</span><span class="n">compartment</span> <span class="o">=</span> <span class="n">compartment</span> + <span class="n">stoich</span><span class="o">.</span><span class="n">ksolve</span> <span class="o">=</span> <span class="n">ksolve</span> + <span class="n">stoich</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="s">"/model/compartment/##"</span> + <span class="c">#setting up state</span> + <span class="n">state</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">SteadyState</span><span class="p">(</span> <span class="s">'/model/compartment/state'</span> <span class="p">)</span> + + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">state</span><span class="o">.</span><span class="n">stoich</span> <span class="o">=</span> <span class="n">stoich</span> + <span class="n">state</span><span class="o">.</span><span class="n">convergenceCriterion</span> <span class="o">=</span> <span class="mf">1e-7</span> + + <span class="n">a</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/a'</span> <span class="p">)</span> + <span class="n">b</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/b'</span> <span class="p">)</span> + <span class="n">c</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/c'</span> <span class="p">)</span> + + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">100</span> <span class="p">):</span> + <span class="n">getState</span><span class="p">(</span> <span class="n">ksolve</span><span class="p">,</span> <span class="n">state</span> <span class="p">)</span> + + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span> + + <span class="n">b</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/b'</span> <span class="p">)</span> + <span class="n">c</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/c'</span> <span class="p">)</span> + + <span class="c"># move most molecules over to b</span> + <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.95</span> + <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.05</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span> + + <span class="c"># move most molecules back to a</span> + <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">+</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.95</span> + <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.05</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span> + + <span class="c"># Iterate through all plots, dump their contents to data.plot.</span> + <span class="n">displayPlots</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + +</div> +</div> +</div> + +<div class="output_wrapper"> +<div class="output"> + + +<div class="output_area"><div class="prompt"></div> + + +<div class="output_png output_subarea "> +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZYAAAD9CAYAAACfvFG7AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzsnXlcVFX/xz/n3tmRZQBFWRQFFFAj3NAsw0oTK0ztl0s9 +j6aV6aNmmblVZmlmZouZPlqZT4tLm6mFPrahbYALjyvqoKAsgrKvs977+2O4MAPD7APDcN+v17zg +3nuW7zn33PM953zPQliWBQ8PDw8Pj7Og2lsAHh4eHh7PglcsPDw8PDxOhVcsPDw8PDxOhVcsPDw8 +PDxOhVcsPDw8PDxOhVcsPDw8PDxOxSHFcvjw4XHR0dEXo6KiFOvXr19qys3ChQs3RUVFKeLi4k5n +ZmbGW/L78ssvvx4XF3f69ttv/9+99977S15eXhj3bN26dcujoqIU0dHRF48cOTLWEdl5eHh4eFwE 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directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<!-- Loading mathjax macro --> +<!-- Load mathjax --> + <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script> + <!-- MathJax configuration --> + <script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ], + processEscapes: true, + processEnvironments: true + }, + // Center justify equations in code and markdown cells. Elsewhere + // we use CSS to left justify single line equations in code cells. + displayAlign: 'center', + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}}, + linebreaks: { automatic: true } + } + }); + </script> + <!-- End of mathjax configuration --> + +</head> +<body> + <div tabindex="-1" id="notebook" class="border-box-sizing"> + <div class="container" id="notebook-container"> + +<div class="cell border-box-sizing text_cell rendered"> +<div class="prompt input_prompt"> +</div> +<div class="inner_cell"> +<div class="text_cell_render border-box-sizing rendered_html"> +<h1 id="This-example-illustrates-how-to-loading,-running,-setting-up-solver-and-plotting-a-kinetic-model-defined-in-kkit-format.">This example illustrates how to loading, running, setting up solver and plotting a kinetic model defined in kkit format.<a class="anchor-link" href="#This-example-illustrates-how-to-loading,-running,-setting-up-solver-and-plotting-a-kinetic-model-defined-in-kkit-format.">¶</a></h1> +</div> +</div> +</div> +<div class="cell border-box-sizing code_cell rendered"> +<div class="input"> +<div class="prompt input_prompt">In [1]:</div> +<div class="inner_cell"> + <div class="input_area"> +<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">sys</span> +<span class="o">%</span><span class="k">matplotlib</span> inline + +<span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates setting up of Stochastic solver, loading, running, and saving a kinetic model </span> +<span class="sd"> defined in kkit format. """</span> + <span class="n">solver</span> <span class="o">=</span> <span class="s">"gssa"</span> <span class="c"># Setting up Stochastic solver</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="s">'../genesis/kkit_objects_example.g'</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="mf">20.0</span> + <span class="n">modelId</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="n">mfile</span><span class="p">,</span> <span class="s">'model'</span><span class="p">,</span> <span class="n">solver</span> <span class="p">)</span> + + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="n">runtime</span> <span class="p">)</span> + + <span class="c"># Display all plots.</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/#graphs/conc#/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="o">.</span><span class="n">dt</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + +</div> +</div> +</div> + +<div class="output_wrapper"> +<div class="output"> + + +<div class="output_area"><div class="prompt"></div> + + +<div class="output_png output_subarea "> +<img 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directory as the html file --> +<link rel="stylesheet" href="custom.css"> + +<!-- Loading mathjax macro --> +<!-- Load mathjax --> + <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script> + <!-- MathJax configuration --> + <script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + displayMath: [ ['$$','$$'], ["\\[","\\]"] ], + processEscapes: true, + processEnvironments: true + }, + // Center justify equations in code and markdown cells. Elsewhere + // we use CSS to left justify single line equations in code cells. + displayAlign: 'center', + "HTML-CSS": { + styles: {'.MathJax_Display': {"margin": 0}}, + linebreaks: { automatic: true } + } + }); + </script> + <!-- End of mathjax configuration --> + +</head> +<body> + <div tabindex="-1" id="notebook" class="border-box-sizing"> + <div class="container" id="notebook-container"> + +<div class="cell border-box-sizing text_cell rendered"> +<div class="prompt input_prompt"> +</div> +<div class="inner_cell"> +<div class="text_cell_render border-box-sizing rendered_html"> +<h3 id="This-example-illustrates-loading,-running-and-plotting-a-kinetic-model-defined-in-kkit-format">This example illustrates loading, running and plotting a kinetic model defined in kkit format<a class="anchor-link" href="#This-example-illustrates-loading,-running-and-plotting-a-kinetic-model-defined-in-kkit-format">¶</a></h3> +</div> +</div> +</div> +<div class="cell border-box-sizing code_cell rendered"> +<div class="input"> +<div class="prompt input_prompt">In [1]:</div> +<div class="inner_cell"> + <div class="input_area"> +<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">moose</span> +<span class="kn">import</span> <span class="nn">pylab</span> +<span class="kn">import</span> <span class="nn">numpy</span> +<span class="kn">import</span> <span class="nn">sys</span> +<span class="o">%</span><span class="k">matplotlib</span> inline + +<span class="k">def</span> <span class="nf">main</span><span class="p">():</span> + <span class="sd">""" This example illustrates loading, running, and saving a kinetic model </span> +<span class="sd"> defined in kkit format. It uses a default kkit model but you can specify another using the command line ``python filename runtime solver``. We use the gsl solver here. The model already defines a couple of plots and sets the runtime to 20 seconds.</span> +<span class="sd"> """</span> + <span class="n">solver</span> <span class="o">=</span> <span class="s">"gsl"</span> <span class="c"># Pick any of gsl, gssa, ee..</span> + <span class="n">mfile</span> <span class="o">=</span> <span class="s">'../genesis/kkit_objects_example.g'</span> + <span class="n">runtime</span> <span class="o">=</span> <span class="mf">20.0</span> + <span class="n">modelId</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="n">mfile</span><span class="p">,</span> <span class="s">'model'</span><span class="p">,</span> <span class="n">solver</span> <span class="p">)</span> + <span class="c"># Increase volume so that the stochastic solver gssa </span> + <span class="c"># gives an interesting output</span> + <span class="c">#compt = moose.element( '/model/kinetics' )</span> + <span class="c">#compt.volume = 1e-19 </span> + + <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span> + <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="n">runtime</span> <span class="p">)</span> + + <span class="c"># Display all plots.</span> + <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/#graphs/conc#/#'</span> <span class="p">):</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="o">.</span><span class="n">dt</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span> + <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span> + + <span class="n">quit</span><span class="p">()</span> + +<span class="c"># Run the 'main' if this script is executed standalone.</span> +<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span> + <span class="n">main</span><span class="p">()</span> +</pre></div> + +</div> +</div> +</div> + +<div class="output_wrapper"> +<div class="output"> + + +<div class="output_area"><div class="prompt"></div> + + +<div class="output_png output_subarea "> +<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYgAAAD9CAYAAACm2+DgAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz +AAALEgAACxIB0t1+/AAAIABJREFUeJzsnXdcU+f3x08CBMJKQthDokxFRXHgBBytoLhRwUq1amut +itrq19HWVXHXXWe1TlyoBRHUijJlCAKKIENBwoaQwcx8fn/0y/dHKSOEhJvgfb9e54/ce+7zfO5D +uCf3WYeAEAIcHBwcHJzWELEWgIODg4OjnOABAgcHBwenTfAAgYODg4PTJniAwMHBwcFpEzxA4ODg +4OC0CR4gcHBwcHDapNMA8ejRI09HR8d3dnZ2efv379/Ulk9AQMBxOzu7PGdn54y0tLShnV27cePG +g/379892dnbOmDNnzj0ul0tpPrd3794tdnZ2eY6Oju+ePHnyeXdvEAcHBwdHRhBC7ZpIJFKzsbHJ +LygoYAgEAg1nZ+f0rKys/i19Hj58ONXLyyscIQSJiYmurq6uiZ1d++TJk8/EYjERIQSbNm3at2nT +pn0IIXj79u0AZ2fndIFAoFFQUMCwsbHJb/bDDTfccMOtZ63DN4jk5OSRtra2+QwGo1BDQ0Po6+t7 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b/docs/user/tutorials/_static/rdes5_reacdiff.png new file mode 100644 index 0000000000000000000000000000000000000000..28727e5e385d87d980ad899405db172e57a05389 Binary files /dev/null and b/docs/user/tutorials/_static/rdes5_reacdiff.png differ diff --git a/docs/user/tutorials/_templates/layout.html b/docs/user/tutorials/_templates/layout.html new file mode 100644 index 0000000000000000000000000000000000000000..75df84926246f910c90895c58dcb9a5bce462bb4 --- /dev/null +++ b/docs/user/tutorials/_templates/layout.html @@ -0,0 +1,33 @@ +{% extends "!layout.html" %} +{% block rootrellink %} + <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li> + {{ super() }} +{% endblock %} +{% block sidebartitle %} + + {% if logo and theme_logo_only %} + <a href="http://moose.ncbs.res.in"> + + {% else %} + <a href="http://moose.ncbs.res.in/" class="icon icon-home"> {{ project }} + {% endif %} + + {% if logo %} + {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #} + <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" /> + {% endif %} + </a> + {% if theme_display_version %} + {%- set nav_version = version %} + {% if READTHEDOCS and current_version %} + {%- set nav_version = current_version %} + {% endif %} + {% if nav_version %} + <div class="version"> + {{ nav_version }} + </div> + {% endif %} + {% endif %} + + {% include "searchbox.html" %} +{% endblock %} diff --git a/docs/user/tutorials/conf.py b/docs/user/tutorials/conf.py new file mode 100644 index 0000000000000000000000000000000000000000..b2b36b187bef3aa98b9dd0a21e98f19ce5d15ad2 --- /dev/null +++ b/docs/user/tutorials/conf.py @@ -0,0 +1,250 @@ +# -*- coding: utf-8 -*- +# +# MOOSE documentation build configuration file, created by +# sphinx-quickstart on Tue Jul 1 19:05:47 2014. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('../../moose/moose-core/python')) +sys.path.append(os.path.abspath('../../../../moose-examples/snippets')) +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', + 'sphinx.ext.mathjax', + 'sphinx.ext.autosummary', + 'sphinx.ext.viewcode', + 'numpydoc'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'MOOSE' +copyright = u'2016' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '3.2' +# The full version, including alpha/beta/rc tags. +release = '3.2' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = True + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'sphinx_rtd_theme' +#html_theme = 'better' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# html_theme_options = {'stickysidebar': 'true', +# 'sidebarwidth': '300'} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [better_theme_path] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +html_logo = '../../images/moose_logo.png' + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'MOOSEdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'MOOSE.tex', u'MOOSE Documentation', + u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +latex_logo = '../images/moose_logo.png' + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +latex_show_pagerefs = True + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'moose', u'MOOSE Documentation', + [u'Upinder Bhalla, Aviral Goel and Harsha Rani'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'MOOSE', u'MOOSE Documentation', + u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.', + 'Science'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +#numpydoc option +numpydoc_show_class_members = True diff --git a/docs/user/tutorials/index.rst b/docs/user/tutorials/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..1474657e23e8957342f1a3b768d139f361c5f21d --- /dev/null +++ b/docs/user/tutorials/index.rst @@ -0,0 +1,15 @@ +.. MOOSE documentation master file, created by + sphinx-quickstart on Tue Feb 2 14:05:47 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Tutorials for MOOSE +================================== +A set of tutorials for teaching a range of topics, including integrate-and-fire networks, chemical bistables, and oscillators. Has stand-alone graphics and the Python scripts are meant to tinker with. + +.. toctree:: + :maxdepth: 2 + :numbered: + + + tutorial diff --git a/docs/user/tutorials/tutorial.rst b/docs/user/tutorials/tutorial.rst new file mode 100644 index 0000000000000000000000000000000000000000..f3f3ee4ec256400107266d9ddd3418fc188e8c3d --- /dev/null +++ b/docs/user/tutorials/tutorial.rst @@ -0,0 +1,37 @@ +.. A tutorials for MOOSE +.. This tutorials walks through some of the simple and practical approch related to MOOSE + +Audience +This reference has been prepared for the beginners to help them understand the basic to advanced concepts related to MOOSE. +This tutorial walks through a range of topics, including integrate-and-fire networks, chemical bistables, and oscillators. +Has stand-alone graphics and the Python scripts are meant to tinker with. + +MOOSE Tutorial +============== + +This reference has prepared for the users to help them understand from the basic to complex modeling building in MOOSE + +Chemical Signalling Models +^^^^^^^^^^^^^^^^^^^^^^^^^^ +`Load Kinetic Model <_static/loadKineticModel.html>`_ +------------------------------------------------------ + +`Deterministic Simulation <_static/DeterministicSolver.html>`_ +---------------------------------------------------------------- + +`Stochastic Simulation <_static/StochasticSolver.html>`_ +----------------------------------------------------------- + +`Finding Steady State <_static/SteadyState.html>`_ +---------------------------------------------------- + +`Building Simple Reaction Model <_static/Building_Simple_Reaction_Model.html>`_ +-------------------------------------------------------------------------------- + + + +Building of Electical Signalling Models +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Building Chemical-Electrical Signalling Models using Rdesigneur +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ \ No newline at end of file diff --git a/moose-examples/snippets/loadSbmlmodel.py b/moose-examples/snippets/loadSbmlmodel.py index 2781d9fcfaecd7fb864e1119326dd316a8394e1c..9323a467ff664bc068fa695dc75fe57aebd4023f 100644 --- a/moose-examples/snippets/loadSbmlmodel.py +++ b/moose-examples/snippets/loadSbmlmodel.py @@ -70,8 +70,10 @@ def main(): # Loading the sbml file into MOOSE, models are loaded in path/model sbmlId = mooseReadSBML(mfile,'/sbml') - - if sbmlId.path != '/': + if isinstance(sbmlId, (list, tuple)): + print sbmlId + elif sbmlId.path != '/': + s1 = moose.element('/sbml/model/compartment/S1') s2= moose.element('/sbml/model/compartment/S2')