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Dilawar Singh
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Merge branch 'master' of github.com:BhallaLab/moose-core
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‎documentation/cpp/header.html‎

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<!-- HTML header for doxygen 1.8.9.1-->
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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‎documentation/developer/API.txt‎

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API for Python interface.
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1. Key data structures, not accessed directly, but important for concepts:
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- Element: Managers for objects. This includes data, messaging,
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field info and class info. All Elements can be arrays.
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- Finfo: Field information specifiers, used to build up the MOOSE
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interface to the underlying C++ class. Similar to the old MOOSE.
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Major Subclasses:
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- DestFinfo: used for functions of the Object. Can be called
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either using SetGet::set or by messages.
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- SrcFinfo: Used to call messages.
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- ValueFinfo: Used to define fields. The ReadOnly kind has
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just the 'get' function, whereas the normal kind
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also has a 'set' function. Both 'get' and 'set' are
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implemented as DestFinfos.
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- Cinfo: Class information specifier, used to specify class name,
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inheritance, and manage the array of Finfos.
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- Msg: Messages. Many subclasses. Handle communication between Elements.
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All Msgs are between precisely two Elements. So the Elements are nodes
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and the Msgs are edges. Msg have a lot of variety in how they control
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data transfer between individual array entries within the source and
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destination Element. Data transfer can be bidirectional.
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All Msgs provide a handle to an Element called a MsgManager, which
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allows you to inspect the Msg fields and in some cases modify them.
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But you cannot modify the source and destination Elements.
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2. Key data structures that you will access.
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Id: Handle to Elements.
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DataId: Handle to objects on Elements. Has a data part and a field part.
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The data part is the parent object, and is used for any array Element.
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The field part is for array fields within individual data entries,
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in cases where the array fields themselves are accessed like Elements.
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For example, in an IntFire neuron, you could have an
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array of a million IntFire neurons on Element A, and each IntFire
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neuron might have a random individual number, say, 10000, 15000, 8000,
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etc Synapses. To index Synapse 234 on IntFire 999999 you would use a
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DataId( 999999, 234).
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ObjId: Composite of Id and DataId. Allows you to uniquely identify any entity
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in the simulation.
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3. Field assignments and function calls:
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File: SetGet.h
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This has a series of templates for different argument cases.
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1. If you want to call a function foo( int A, double B ) on
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ObjId oid, you would do:
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SetGet2< int, double >::set( oid, "foo", A, B );
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2. To call a function bar( int A, double B, string C ) on oid:
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SetGet3< int, double, string >::set( oid, "bar", A, B, C );
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3. To assign a field value "short abc" on object oid:
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Field< short >::set( oid, "abc", 123 );
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4. To get a field value "double pqr" on object obj:
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double x = Field< short >::get( oid, "pqr" );
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5. To assign the double 'xcoord' field on all the objects on
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element Id id, which has an array of the objects:
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vector< double > newXcoord;
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// Fill up the vector here.
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Field< double >::setVec( id, "xcoord", newXcoord );
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Note that the dimensions of newXcoord should match those of
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the target element.
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You can also use a similar call if it is just a function on id:
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SetGet1< double >::setVec( id, "xcoord_func", newXcoord );
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6. To extract the double vector 'ycoord' field from all the
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objects on id:
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vector< double > oldYcoord; // Do not need to allocate.
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Field< double >::getVec( id, "ycoord", oldYcoord );
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7. To set/get LookupFields, that is fields which have an index
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to lookup:
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double x = LookupField< unsigned int, double >::get( objId, field, index );
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LookupField< unsigned int, double >::set( objId, field, index, value );
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There are lots of other variants here.
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4. Shell commands to use: the ones that start with 'do'.
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Id doCreate( string type, Id parent, string name,
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vector< unsigned int > dimensions );
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bool doDelete( Id id )
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MsgId doAddMsg( const string& msgType,
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ObjId src, const string& srcField,
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ObjId dest, const string& destField);
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void doQuit();
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void doStart( double runtime );
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void doNonBlockingStart( double runtime );
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void doReinit();
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void doStop();
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void doTerminate();
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void doMove( Id orig, Id newParent );
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Id doCopyId orig, Id newParent, string newName,
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unsigned int n, bool copyExtMsgs);
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Id doFind( const string& path ) const
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void doSetClock( unsigned int tickNum, double dt )
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void doUseClock( string path, string field, unsigned int tick );
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Id doLoadModel( const string& fname, const string& modelpath );
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void doSyncDataHandler( Id elm, const string& sizeField, Id tgt );
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5. Important fields of important objects.
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5.1. Shell object. This is the root object, '/' or '/root'.
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This has the following fields of note:
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- bool isRunning: ReadOnlyValue
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- Id cwe: Regular value.
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5.2 Neutral. These fields are shared by all objects.
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string name
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ObjId parent // Parent ObjId. Note this is fully
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// specified, including index.
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vector< Id > children // All child elements.
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string path // Full path
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string className
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unsigned int linearSize // Product of all dimensions
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// Currently not working.
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vector< unsigned int> Dimensions
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unsigned int fieldDimension // Size of field dimension.
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vector< ObjId > msgOut // MsgManagers of all outgoing msgs
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vector< ObjId > msgIn // MsgManagers of all incoming msgs
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vector< Id > msgSrc( string field ) // Ids of source msgs into field
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vector< Id > msgDest( string field ) // Ids of dest msgs into field
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5.3 Class Info objects. These are located in /classes/<classname>
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string docs // currently not implemented
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string baseClass // Name of base class
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5.4 Field Info objects. These are children of the respective ClassInfo and
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are located in /classes/<classname>/<Field category>
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There are 5 field categories:
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srcFinfo
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destFinfo
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valueFinfo
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lookupFinfo
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sharedFinfo
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Each of these is an array, indexed as DataId( 0, <index> )
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since they are FieldElements.
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You can query the # of entries in each category using
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Id classId( "/classes/<classname>" );
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numValueFinfos =
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Field< unsigned int >::get( classId, "num_valueFinfo" );
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Finally each of the field categories has the following fields:
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string name
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string docs // This is implemented
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string type // String with argument types separated by
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// commas. Can handle basic types, Ids,
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// ObjIds, DataIds, strings, and vectors of
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// any of the above.
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vector< string > src // vector of subsidiary srcFinfos, which
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// happens in SharedFinfos.
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vector< string > dest // vector of subsidiary destFinfos, which
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// happens in SharedFinfos and ValueFinfos.
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6. Message traversal, C++ level:
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General approach:
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- If you just want src/dest Id, use the Neutral or Element functions
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to find list of source or target Ids as per spec.
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- Netural::msgSrc( string field );
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- Netural::msgDest( string field );
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- Element::getOutputs( vector< Id >& ret, const SrcFinfo* finfo)
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- Element::getInputs( vector< Id >& ret, const DestFinfo* finfo)
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- If you want to iterate through specific array and/or field
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entries in src/dest Id, then you will have to look up the
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MsgIds themselves.
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- vector< ObjId > Neutral::msgOut():
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Not very specific, just the ObjIds of the MsgManagers
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of all outgoing Msgs.
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- vector< ObjId > Neutral::msgIn():
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All ObjIds of MsgManagers of incoming Msgs.
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- MsgId Element::findCaller( FuncId fid ) const:
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Looks up the first Msg that calls the specified Fid
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- Element::getInputMsgs( vector< MsgId >& caller, FuncId fid)
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Fills up vector of MsgIds that call the specified fid
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- To convert between MsgIds, Msgs, and the manager ObjId:
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- MsgId Msg::mid(): returns the MsgId of the Msg.
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- Msg::manager(): returns the manager Eref of a Msg.
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- Msg::manager().objId(): returns the manager ObjId of a Msg.
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- static const Msg* Msg::getMsg( MsgId mid )
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Returns the Msg ptr given a MsgId.
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- To iterate through Msg targets:
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unsigned int Msg::srcToDestPairs(
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vector< DataId >& src, vector< DataId >& dest) const
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This function gives matching vectors of src and dest
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pairs for the Msg. This should be node-independent,
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but the SparseMsg currently doesn't handle it right,
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and works only on 1 node.
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‎documentation/developer/BuildingNewMOOSEClasses.txt‎

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Building new MOOSE classes.
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- Take your existing class.
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- Set it up to use access functions of this form:
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For things that should look like Read/Write variables to the user:
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void setField( FieldType value );
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FieldType getField() const;
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For things that should look like ReadOnly variables to the user:
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FieldType getField() const;
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For things that should look like functions to the user:
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( MOOSE can handle up to 6 arguments )
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void func( Type1 arg1, Type2 arg2 );
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- Put in the following function in the header:
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static const Cinfo* initCinfo();
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- Figure out your MOOSE interface. There are three main kinds of fields,
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which are going to be set up using Finfo objects (short for Field
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Information).
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The three are:
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- DestFinfos: These handle function requests.
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- SrcFinfos: These call functions on other objects. In other
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words, they send messages.
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- ValueFinfos: These support field assignment and readout.
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- Define initCinfo() in your .cpp, as follows:
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‎documentation/developer/CodingConventions.txt‎

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Naming conventions:
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General: Use CamelCase
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Don't use underscores as word separators.
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Classes start with caps
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Fields and functions start with lower case, except for scientific
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conventions (e.g., Vm_) in which case the scientific convention is used.
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Private fields end with an underscore (e.g., Vm_ );
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Use spaces liberally, and always after a comma.
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Field assignment functions (set/get) start with set/get<fieldName>
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Naming of MOOSE fields and functions:
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Fields (ValueFinfos): Just use the name of the field, e.g., Vm, x, y, z.
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Message sources (SrcFinfos): Use the name of the field, e.g., output,
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unless there is a name-clash with a Fields. Then use name<Suffix>
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e.g., nOut, xOut, VmOut.
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If the message source is to request a return value, generally use the
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form request<fieldName>
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Message destination (DestFinfos): Use the name of the function, typically a
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verb. e.g., increment, process.
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Special case comes up with the internal set/get functions of fields,
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which are implemented as DestFinfos. Here the DestFinfos are
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automatically named set_<fieldname> and get_<fieldname>
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If the message dest handles a request or other operation as part of
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a shared message, generally use the form
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handle<name>
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If there is an overlap with a SharedMessage or field after applying
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all these rules, then use the form handle<name>.
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Shared messages (SharedFinfos): Use the name of the message.
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If there is an overlap with any other message, the SharedMessage takes
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precedence. This is because Shared Messages are the interface users
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will normally use. Try to avoid overlaps with field names.
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