/**
 * This is a little tricky because we might be mapping between
 * data entries and field entries here.
 * May wish also to apply to exec operations.
 * At this point, the effect of trying to go between regular
 * data entries and field entries is undefined.
 */
Eref OneToOneDataIndexMsg::firstTgt( const Eref& src ) const
{
	if ( src.element() == e1_ ) {
		return Eref( e2_, src.dataIndex(), 0 );
	} else if ( src.element() == e2_ ) {
		return Eref( e1_, src.dataIndex() );
	}
	return Eref( 0, 0 );
}
/**
 * This is a little tricky because we might be mapping between
 * data entries and field entries here.
 * May wish also to apply to exec operations.
 * At this point, the effect of trying to go between regular
 * data entries and field entries is undefined.
 */
Eref OneToOneMsg::firstTgt( const Eref& src ) const 
{
	if ( src.element() == e1_ ) {
		if ( e2_->hasFields() )
			return Eref( e2_, i2_, src.dataIndex() );
		else 
			return Eref( e2_, src.dataIndex(), 0 );
	} else if ( src.element() == e2_ ) {
		return Eref( e1_, src.dataIndex() );
	}
	return Eref( 0, 0 );
}
SingleMsg::SingleMsg( const Eref& e1, const Eref& e2, unsigned int msgIndex)
	: Msg( ObjId( managerId_, (msgIndex != 0 ) ? msgIndex: msg_.size() ), 
					e1.element(), e2.element() ),
	i1_( e1.dataIndex() ), 
	i2_( e2.dataIndex() ),
	f2_( e2.fieldIndex() )
{
	if ( msgIndex == 0 ) {
		msg_.push_back( this );
		return;
	} else if ( msg_.size() <= msgIndex ) {
		msg_.resize( msgIndex + 1 );
	}
	msg_[ msgIndex ] = this;
}
OneToOneMsg::OneToOneMsg( const Eref& e1, const Eref& e2, 
				unsigned int msgIndex )
	: Msg( ObjId( managerId_, (msgIndex != 0) ? msgIndex: msg_.size() ),
					e1.element(), e2.element() ),
	i1_( e1.dataIndex() ),
	i2_( e2.dataIndex() )
{
	if ( msgIndex == 0 ) {
		msg_.push_back( this );
	} else {
		if ( msg_.size() <= msgIndex )
			msg_.resize( msgIndex + 1 );
		msg_[ msgIndex ] = this;
	}
}
Example #5
0
// static function
Id Neutral::child( const Eref& e, const string& name ) 
{
	static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
	static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
	static const FuncId pafid = pf2->getFid();
	static const Finfo* cf = neutralCinfo->findFinfo( "childOut" );
	static const SrcFinfo* cf2 = dynamic_cast< const SrcFinfo* >( cf );
	static const BindIndex bi = cf2->getBindIndex();
	
	const vector< MsgFuncBinding >* bvec = e.element()->getMsgAndFunc( bi );

	vector< Id > ret;

	for ( vector< MsgFuncBinding >::const_iterator i = bvec->begin();
		i != bvec->end(); ++i ) {
		if ( i->fid == pafid ) {
			const Msg* m = Msg::getMsg( i->mid );
			assert( m );
			Element* e2 = m->e2();
			if ( e2->getName() == name ) {
				if ( e.dataIndex() == ALLDATA ) {// Child of any index is OK
					return e2->id();
				} else {
					ObjId parent = m->findOtherEnd( m->getE2() );
					// If child is a fieldElement, then all parent indices
					// are permitted. Otherwise insist parent dataIndex OK.
					if ( e2->hasFields() || parent == e.objId() )
						return e2->id();
				}
			}
		}
	}
	return Id();
}
unsigned int Ksolve::getVoxelIndex( const Eref& e ) const
{
    unsigned int ret = e.dataIndex();
    if ( ret < startVoxel_  || ret >= startVoxel_ + pools_.size() )
        return OFFNODE;
    return ret - startVoxel_;
}
Example #7
0
/**
 * Assigns the Stoich Id to the parent.
 */
void MeshEntry::reinit( const Eref& e, ProcPtr info )
{
	if ( e.dataIndex() == 0 ) {
		ObjId pa = Neutral::parent( e );
		// parent_->lookupStoich( pa );
	}
}
Example #8
0
/// Utility function to find the size of a pool. We assume one-to-one
/// match between pool indices and mesh indices: that is what they are for.
double lookupVolumeFromMesh( const Eref& e )
{
	ObjId compt = getCompt( e.id() );
	if ( compt == ObjId() )
		return 1.0;
	return LookupField< unsigned int, double >::
			get( compt, "oneVoxelVolume", e.dataIndex() );
}
Example #9
0
// Static function
void Neutral::children( const Eref& e, vector< Id >& ret )
{
		/*
	vector< Id > temp;
	getNeighbors( ret, neutralCinfo->findFinfo( "childOut" ) );
	for ( vector< Id >::iterator i = temp.begin(); i != temp.end(); ++i ) {
		if ( ret
	}
	*/



	static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
	static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
	static const FuncId pafid = pf2->getFid();
	static const Finfo* cf = neutralCinfo->findFinfo( "childOut" );
	static const SrcFinfo* cf2 = dynamic_cast< const SrcFinfo* >( cf );
	static const BindIndex bi = cf2->getBindIndex();
	
	const vector< MsgFuncBinding >* bvec = e.element()->getMsgAndFunc( bi );

	for ( vector< MsgFuncBinding >::const_iterator i = bvec->begin();
		i != bvec->end(); ++i ) {
		if ( i->fid == pafid ) {
			const Msg* m = Msg::getMsg( i->mid );
			assert( m );
			vector< vector< Eref > > kids;
			m->targets( kids );
			if ( e.dataIndex() == ALLDATA ) {
				for ( vector< vector< Eref > >::iterator
					i = kids.begin(); i != kids.end(); ++i ) {
					for ( vector< Eref >::iterator
						j = i->begin(); j != i->end(); ++j )
						ret.push_back( j->id() );
				}
			} else {
				const vector< Eref >& temp = kids[e.dataIndex()];
				for ( vector< Eref >::const_iterator
							i = temp.begin(); i != temp.end(); ++i )
					ret.push_back( i->id() );
			}
		}
	}
}
void Synapse::addSpike( const Eref& e, double time )
{
	static bool report = false;
	static unsigned int tgtDataIndex = 0;
	// static unsigned int tgtFieldIndex = 0;
	if ( report && e.dataIndex() == tgtDataIndex ) {
		cout << "	" << time << "," << e.fieldIndex();
	}
	handler_->addSpike( e.fieldIndex(), time + delay_, weight_ );
}
Example #11
0
void HDF5DataWriter::reinit(const Eref & e, ProcPtr p)
{
    steps_ = 0;
    for (unsigned int ii = 0; ii < data_.size(); ++ii){
        H5Dclose(datasets_[ii]);
    }
    data_.clear();
    src_.clear();
    func_.clear();
    datasets_.clear();
    unsigned int numTgt = e.element()->getMsgTargetAndFunctions(e.dataIndex(),
                                                                requestOut(),
                                                                src_,
                                                                func_);
    assert(numTgt ==  src_.size());
    // TODO: what to do when reinit is called? Close the existing file
    // and open a new one in append mode? Or keep adding to the
    // current file?
    if (filename_.empty()){
        filename_ = "moose_data.h5";
    }
    if (filehandle_ > 0 ){
        close();
    }
    if (numTgt == 0){
        return;
    }
    openFile();
    for (unsigned int ii = 0; ii < src_.size(); ++ii){
        string varname = func_[ii];
        size_t found = varname.find("get");
        if (found == 0){
            varname = varname.substr(3);
            if (varname.length() == 0){
                varname = func_[ii];
            } else {
                // TODO: there is no way we can get back the original
                // field-name case. tolower will get the right name in
                // most cases as field names start with lower case by
                // convention in MOOSE.
                varname[0] = tolower(varname[0]);
            }
        }
        assert(varname.length() > 0);
        string path = src_[ii].path() + "/" + varname;
        hid_t dataset_id = getDataset(path);
        datasets_.push_back(dataset_id);
    }
    data_.resize(src_.size());
}
Example #12
0
Eref SparseMsg::firstTgt( const Eref& src ) const 
{
	if ( matrix_.nEntries() == 0 )
		return Eref( 0, 0 );

	if ( src.element() == e1_ ) {
		const unsigned int* fieldIndex;
		const unsigned int* colIndex;
		unsigned int n = matrix_.getRow( src.dataIndex(),
			&fieldIndex, &colIndex );
		if ( n != 0 ) {
			return Eref( e2_, colIndex[0], fieldIndex[0] );
		}
	} else if ( src.element() == e2_ ) {
		return Eref( e1_, 0 );
	}
	return Eref( 0, 0 );
}
Example #13
0
vector< string > Neutral::getMsgDestFunctions( const Eref& e, string field ) const
{
	vector< string > ret( 0 );
	const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
	const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( finfo );
	if ( sf ) {
		vector< ObjId > tgt;
		vector< string > func;
		e.element()->getMsgTargetAndFunctions( e.dataIndex(), sf,
			tgt, func );
		return func;
	} else {
		cout << "Warning: Neutral::getMsgDestFunctions: Id.Field '" << 
				e.id().path() << "." << field <<
				"' not found or not a SrcFinfo\n";
	}
	return ret;
}
Example #14
0
void NSDFWriter::sortOutUniformSources(const Eref& eref)
{
    vars_.clear();
    classFieldToSrcIndex_.clear();
    objectField_.clear();
    objectFieldToIndex_.clear();
    const SrcFinfo * requestOut = (SrcFinfo*)eref.element()->cinfo()->findFinfo("requestOut");
    unsigned int numTgt = eref.element()->getMsgTargetAndFunctions(eref.dataIndex(),
                                                                requestOut,
                                                                src_,
                                                                func_);
    assert(numTgt ==  src_.size());
    /////////////////////////////////////////////////////////////
    // Go through all the sources and determine the index of the
    // source message in the dataset
    /////////////////////////////////////////////////////////////
    
    for (unsigned int ii = 0; ii < func_.size(); ++ii){
        string varname = func_[ii];
        size_t found = varname.find("get");
        if (found == 0){
            varname = varname.substr(3);
            if (varname.length() == 0){
                varname = func_[ii];
            } else {
                varname[0] = tolower(varname[0]);
            }
        }
        assert(varname.length() > 0);
        string className = Field<string>::get(src_[ii], "className");
        string datasetPath = className + "/"+ varname;
        classFieldToSrcIndex_[datasetPath].push_back(ii);
        vars_.push_back(varname);
    }
    data_.resize(numTgt);
}
Example #15
0
void Neutral::setNumField( const Eref& e, unsigned int num )
{
	assert( e.isDataHere() );
	unsigned int rawIndex = e.element()->rawIndex( e.dataIndex() );
	e.element()->resizeField( rawIndex, num );
}
Example #16
0
double MeshEntry::getVolume( const Eref& e ) const
{
	return parent_->getMeshEntryVolume( e.dataIndex() );
	// return parent_->getMeshEntryVolume( e.fieldIndex() );
}
unsigned int Neutral::getIndex( const Eref& e ) const
{
	return e.dataIndex();
}
Example #18
0
unsigned int Neutral::getNumField( const Eref& e ) const
{
	assert( e.isDataHere() );
	unsigned int rawIndex = e.element()->rawIndex( e.dataIndex() );
	return e.element()->numField( rawIndex );
}