#include <ChemCompt.h>

Inheritance diagram for ChemCompt:

Collaboration diagram for ChemCompt:

Public Member Functions
void	buildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)

void	buildJunction (ChemCompt *other, vector< VoxelJunction > &ret)

	ChemCompt ()

virtual void	clearExtendedMeshEntryVolume ()=0
	clear out extended mesh entries for rebuilding. More...

virtual double	extendedMeshEntryVolume (unsigned int fid) const =0
	Volume of mesh Entry including abutting diff-coupled voxels. More...

virtual void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)=0

void	flipRet (vector< VoxelJunction > &ret) const
	Utility function for swapping first and second in VoxelJunctions. More...

void	getChildConcs (const Eref &e, vector< double > &childConcs) const

virtual vector< double >	getCoordinates (unsigned int fid) const =0
	Virtual function to return coords of mesh Entry. More...

virtual vector< double >	getDiffusionArea (unsigned int fid) const =0
	Virtual function to return diffusion X-section area per neighbor. More...

virtual vector< double >	getDiffusionScaling (unsigned int fid) const =0
	Virtual function to return scale factor for diffusion. 1 here. More...

unsigned int	getDimensions () const

double	getEntireVolume (const Eref &e) const

bool	getIsMembraneBound () const

virtual unsigned int	getMeshDimensions (unsigned int fid) const =0
	Virtual function to return dimensions of specified entry. More...

virtual double	getMeshEntryVolume (unsigned int fid) const =0
	Virtual function to return volume of mesh Entry. More...

virtual unsigned int	getMeshType (unsigned int fid) const =0
	Virtual function to return MeshType of specified entry. More...

string	getMethod () const

virtual vector< unsigned int >	getNeighbors (unsigned int fid) const =0
	Virtual function to return info on Entries connected to this one. More...

unsigned int	getNumEntries () const

double	getOneVoxelVolume (const Eref &e, unsigned int voxel) const

vector< unsigned int >	getStencilIndex (unsigned int row) const

vector< double >	getStencilRate (unsigned int row) const

virtual unsigned int	getStencilRow (unsigned int meshIndex, const double entry, const unsigned int colIndex) const =0

vector< double >	getVoxelMidpoint () const
	Returns vector of all voxel midpoints in compartment. More...

vector< double >	getVoxelVolume () const
	Returns vector of all voxel volumes in compartment. More...

void	handleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)

virtual void	indexToSpace (unsigned int index, double &x, double &y, double &z) const =0

virtual void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)=0

virtual unsigned int	innerGetDimensions () const =0

virtual unsigned int	innerGetNumEntries () const =0

virtual vector< double >	innerGetStencilRate (unsigned int row) const =0
	Virtual func for getting stencil rates for the derived classes. More...

virtual void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)=0

virtual void	innerResetStencil ()=0

virtual void	innerSetNumEntries (unsigned int n)=0

MeshEntry *	lookupEntry (unsigned int index)

virtual void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const =0

virtual double	nearest (double x, double y, double z, unsigned int &index) const =0

void	resetStencil ()

unsigned int	setChildConcs (const Eref &e, const vector< double > &childConcs, unsigned int start) const

void	setEntireVolume (const Eref &e, double volume)

void	setIsMembraneBound (bool v)

virtual void	setMeshEntryVolume (unsigned int fid, double volume)

void	setMethod (string method)

void	setNumEntries (unsigned int num)

void	setOneVoxelVolume (const Eref &e, unsigned int voxel, double volume)

void	setVolumeNotRates (double volume)

virtual double	vGetEntireVolume () const =0

virtual const vector< double > &	vGetVoxelMidpoint () const =0
	Virtual func so that derived classes can return voxel midpoint. More...

virtual const vector< double > &	vGetVoxelVolume () const =0
	Virtual func so that derived classes can pass voxel volume back. More...

virtual bool	vSetVolumeNotRates (double volume)=0
	Virtual function for actually doing this. More...

virtual	~ChemCompt ()

Static Public Member Functions
static double	distance (double x, double y, double z)

static const Cinfo *	initCinfo ()

static SrcFinfo1< vector < double > > *	voxelVolOut ()

Private Attributes
vector< Boundary >	boundaries_
	Wrapper for self ptr. More...

MeshEntry	entry_

bool	isMembraneBound_

string	method_

Detailed Description

The ChemCompt represents a chemically identified compartment. This may be spatially extended, and may even be discontinuous. The same set of reactions and molecules populates any given compartment. Examples of compartments might be: nucleus, cell membrane, early endosomes, spine heads. Connects to one or more 'Geometry' elements to define its boundaries.

Definition at line 23 of file ChemCompt.h.

Constructor & Destructor Documentation

ChemCompt::ChemCompt ( )

Definition at line 198 of file ChemCompt.cpp.

Referenced by initCinfo().

     :
         entry_( this ),
         isMembraneBound_( false )
 {
     ;
 }

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ChemCompt::~ChemCompt ( )

virtual

Definition at line 206 of file ChemCompt.cpp.

 {
         /*
     for ( unsigned int i = 0; i < stencil_.size(); ++i ) {
         if ( stencil_[i] )
             delete stencil_[i];
     }
     */
 }

Member Function Documentation

void ChemCompt::buildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)

buildDefaultMesh tells the ChemCompt to make a standard mesh partitioning with the specified total volume and the specified number of subdivisions. For example, a CubeMesh of volume 8 and subdivisions 8 would make a 2x2x2 mesh. This function is specialized in each derived class.

Definition at line 220 of file ChemCompt.cpp.

References innerBuildDefaultMesh().

Referenced by initCinfo().

 {
     this->innerBuildDefaultMesh( e, volume, numEntries );
 }

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void ChemCompt::buildJunction	(	ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)

Wrapper function to buld junction between two meshes, and to extend the meshes so that their stencils also handle update to the voxels abutting the boundary on the neighbor mesh.

Definition at line 400 of file ChemCompt.cpp.

References extendStencil(), and matchMeshEntries().

 {
     matchMeshEntries( other, ret );
     extendStencil( other, ret );
 }

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virtual void ChemCompt::clearExtendedMeshEntryVolume ( )

pure virtual

clear out extended mesh entries for rebuilding.

Implemented in MeshCompt.

double ChemCompt::distance	(	double	x,
		double	y,
		double	z
	)

static

Definition at line 422 of file ChemCompt.cpp.

Referenced by CylMesh::matchCylMeshEntries(), CylMesh::nearest(), and CubeMesh::nearest().

 {
     return sqrt( x * x + y * y + z * z );
 }

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virtual double ChemCompt::extendedMeshEntryVolume ( unsigned int fid ) const

pure virtual

Volume of mesh Entry including abutting diff-coupled voxels.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, EndoMesh, and MeshCompt.

virtual void ChemCompt::extendStencil	(	const ChemCompt *	other,
		const vector< VoxelJunction > &	vj
	)

pure virtual

Function to add voxels for boundaries. This is done so that the solver can do reaction-diffusion computations on the entire mesh including voxels of neighboring solvers abutting the boundary. It uses these to stitch together the computations that span multiple solvers and compartments.

Implemented in MeshCompt.

Referenced by buildJunction().

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void ChemCompt::flipRet ( vector< VoxelJunction > & ret ) const

Utility function for swapping first and second in VoxelJunctions.

Definition at line 406 of file ChemCompt.cpp.

Referenced by CubeMesh::matchCubeMeshEntries(), CubeMesh::matchCylMeshEntries(), CylMesh::matchMeshEntries(), SpineMesh::matchMeshEntries(), CubeMesh::matchMeshEntries(), and NeuroMesh::matchMeshEntries().

 {
    vector< VoxelJunction >::iterator i;
    for ( i = ret.begin(); i != ret.end(); ++i ) {
           unsigned int temp = i->first;
           i->first = i->second;
           i->second = temp;
           double vol = i->firstVol;
           i->firstVol = i->secondVol;
           i->secondVol = vol;
    }
 }

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void ChemCompt::getChildConcs	(	const Eref &	e,
		vector< double > &	childConcs
	)		const

Recursively traverses all children, depth_first, scooping up concentration terms: conc and concInit for pools, Kf and Kb for Reacs, and Km for enzymes. These are inserted in order into the vector of childConcs. Does not traverse into children of other ChemCompts

Definition at line 264 of file ChemCompt.cpp.

References Neutral::children().

Referenced by CylMesh::innerSetCoords(), CylMesh::setDiffLength(), setEntireVolume(), CylMesh::setR0(), CylMesh::setR1(), CylMesh::setX0(), CylMesh::setX1(), CylMesh::setY0(), CylMesh::setY1(), CylMesh::setZ0(), and CylMesh::setZ1().

 {
     vector< Id > kids;
     Neutral::children( e, kids );
     for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
     {
         if ( i->element()->cinfo()->isA( "PoolBase" ) ) {
             childConcs.push_back( Field< double >::get( *i, "conc" ) );
             childConcs.push_back( Field< double >::get( *i, "concInit" ) );
         } else if ( i->element()->cinfo()->isA( "ReacBase" ) ) {
             childConcs.push_back( Field< double >::get( *i, "Kf" ) );
             childConcs.push_back( Field< double >::get( *i, "Kb" ) );
         } else if ( i->element()->cinfo()->isA( "EnzBase" ) ) {
             childConcs.push_back( Field< double >::get( *i, "Km" ) );
         } else if ( i->element()->cinfo()->isA( "ChemCompt" ) ) {
             // Do NOT traverse into child ChemCompts, they look after their
             // own volumes.
             continue;
         }
         getChildConcs( i->eref(), childConcs );
     }
 }

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virtual vector< double > ChemCompt::getCoordinates ( unsigned int fid ) const

pure virtual

Virtual function to return coords of mesh Entry.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by EndoMesh::getCoordinates(), and MeshEntry::getCoordinates().

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virtual vector< double > ChemCompt::getDiffusionArea ( unsigned int fid ) const

pure virtual

Virtual function to return diffusion X-section area per neighbor.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by MeshEntry::getDiffusionArea().

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virtual vector< double > ChemCompt::getDiffusionScaling ( unsigned int fid ) const

pure virtual

Virtual function to return scale factor for diffusion. 1 here.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by MeshEntry::getDiffusionScaling().

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unsigned int ChemCompt::getDimensions ( ) const

Returns # of dimensions of mesh. This is 3 for cube, and 1 for cylinder or neurons.

Definition at line 340 of file ChemCompt.cpp.

References innerGetDimensions().

Referenced by initCinfo(), testCubeMesh(), and testCubeMeshExtendStencil().

 {
     return this->innerGetDimensions();
 }

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double ChemCompt::getEntireVolume ( const Eref & e ) const

Returns volume, area, or length of compartment, depending on dimensionality.

Definition at line 259 of file ChemCompt.cpp.

References vGetEntireVolume().

Referenced by initCinfo().

 {
     return vGetEntireVolume();
 }

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bool ChemCompt::getIsMembraneBound ( ) const

Definition at line 355 of file ChemCompt.cpp.

References isMembraneBound_.

Referenced by initCinfo().

 {
     return isMembraneBound_;
 }

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virtual unsigned int ChemCompt::getMeshDimensions ( unsigned int fid ) const

pure virtual

Virtual function to return dimensions of specified entry.

Implemented in NeuroMesh, CubeMesh, SpineMesh, CylMesh, PsdMesh, and EndoMesh.

Referenced by MeshEntry::getDimensions().

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virtual double ChemCompt::getMeshEntryVolume ( unsigned int fid ) const

pure virtual

Virtual function to return volume of mesh Entry.

Implemented in NeuroMesh, CubeMesh, SpineMesh, CylMesh, PsdMesh, and EndoMesh.

Referenced by MeshCompt::extendStencil(), EndoMesh::getMeshEntryVolume(), getOneVoxelVolume(), and MeshEntry::getVolume().

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virtual unsigned int ChemCompt::getMeshType ( unsigned int fid ) const

pure virtual

Virtual function to return MeshType of specified entry.

Implemented in NeuroMesh, CubeMesh, SpineMesh, CylMesh, PsdMesh, and EndoMesh.

Referenced by MeshEntry::getMeshType().

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string ChemCompt::getMethod ( ) const

virtual vector< unsigned int > ChemCompt::getNeighbors ( unsigned int fid ) const

pure virtual

Virtual function to return info on Entries connected to this one.

Implemented in MeshCompt.

Referenced by MeshEntry::getNeighbors(), and getStencilIndex().

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unsigned int ChemCompt::getNumEntries ( ) const

Returns the number of MeshEntries on this ChemCompt

Definition at line 390 of file ChemCompt.cpp.

References innerGetNumEntries().

Referenced by Dsolve::build(), EndoMesh::getDiffusionArea(), EndoMesh::getDiffusionScaling(), initCinfo(), EndoMesh::innerHandleRequestMeshStats(), CylBase::matchCubeMeshEntries(), CylMesh::matchCubeMeshEntries(), and MeshEntry::triggerRemesh().

 {
     return this->innerGetNumEntries();
 }

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double ChemCompt::getOneVoxelVolume	(	const Eref &	e,
		unsigned int	voxel
	)		const

Returns volume of specified voxel

Definition at line 323 of file ChemCompt.cpp.

References getMeshEntryVolume().

Referenced by initCinfo().

 {
     return this->getMeshEntryVolume( dataIndex );
 }

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vector< unsigned int > ChemCompt::getStencilIndex ( unsigned int row ) const

Function to return the stencil indices used in the diffusion calculations for voxelized compartments. Refers to the getNeighbors virtual function.

Definition at line 350 of file ChemCompt.cpp.

References getNeighbors().

Referenced by initCinfo().

 {
     return this->getNeighbors( row );
 }

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vector< double > ChemCompt::getStencilRate ( unsigned int row ) const

Function to return the stencil values used in the diffusion calculations for voxelized compartments.

Definition at line 345 of file ChemCompt.cpp.

References innerGetStencilRate().

Referenced by initCinfo().

 {
     return this->innerGetStencilRate( row );
 }

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virtual unsigned int ChemCompt::getStencilRow	(	unsigned int	meshIndex,
		const double **	entry,
		const unsigned int **	colIndex
	)		const

pure virtual

Function to look up scale factor derived from area and length of compartment junction, for all the mesh entries connected to the specified one. Modeled on equivalent function in SparseMatrix. meshIndex: index of reference mesh entry entry: array of values of scale factor colIndex: array of relative indices for each entry. The values returned here are the offset from the meshIndex. Returns number of entries and colIndexes. For a 1-D mesh, there will be 2 except at boundaries For a 2-D mesh, there will be 4 except at boundaries For a 3-D mesh, there will be 6 except at boundaries For a neuromesh, there will be a variable number depending on branching. For a CylMesh there are 2 except at boundaries.

Implemented in MeshCompt.

vector< double > ChemCompt::getVoxelMidpoint ( ) const

Returns vector of all voxel midpoints in compartment.

Definition at line 318 of file ChemCompt.cpp.

References vGetVoxelMidpoint().

Referenced by initCinfo().

 {
     return this->vGetVoxelMidpoint();
 }

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vector< double > ChemCompt::getVoxelVolume ( ) const

Returns vector of all voxel volumes in compartment.

Definition at line 313 of file ChemCompt.cpp.

References vGetVoxelVolume().

Referenced by Dsolve::build(), initCinfo(), and mapVoxelsBetweenMeshes().

 {
     return this->vGetVoxelVolume();
 }

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void ChemCompt::handleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)

Definition at line 226 of file ChemCompt.cpp.

References innerHandleNodeInfo().

Referenced by initCinfo().

 {
     // Pass it down to derived classes along with the SrcFinfo
     innerHandleNodeInfo( e, numNodes, numThreads );
 }

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virtual void ChemCompt::indexToSpace	(	unsigned int	index,
		double &	x,
		double &	y,
		double &	z
	)		const

pure virtual

Converts specified index to xyz coords of middle of voxel Values out of range return original xyz

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by EndoMesh::indexToSpace().

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const Cinfo * ChemCompt::initCinfo ( )

static

Definition at line 25 of file ChemCompt.cpp.

References buildDefaultMesh(), ChemCompt(), chemMeshCinfo, getDimensions(), getEntireVolume(), getIsMembraneBound(), getNumEntries(), getOneVoxelVolume(), getStencilIndex(), getStencilRate(), getVoxelMidpoint(), getVoxelVolume(), handleNodeInfo(), MeshEntry::initCinfo(), Neutral::initCinfo(), lookupEntry(), resetStencil(), setEntireVolume(), setIsMembraneBound(), setNumEntries(), setOneVoxelVolume(), setVolumeNotRates(), and voxelVolOut().

Referenced by EndoMesh::initCinfo(), CylMesh::initCinfo(), PsdMesh::initCinfo(), SpineMesh::initCinfo(), NeuroMesh::initCinfo(), and CubeMesh::initCinfo().

 {
         // Field Definitions
         static ElementValueFinfo< ChemCompt, double > volume(
             "volume",
             "Volume of entire chemical domain."
             "Assigning this only works if the chemical compartment has"
             "only a single voxel. Otherwise ignored."
             "This function goes through all objects below this on the"
             "tree, and rescales their molecule #s and rates as per the"
             "volume change. This keeps concentration the same, and also"
             "maintains rates as expressed in volume units.",
             &ChemCompt::setEntireVolume,
             &ChemCompt::getEntireVolume
         );
 
         static ReadOnlyValueFinfo< ChemCompt, vector< double > >
                 voxelVolume(
             "voxelVolume",
             "Vector of volumes of each of the voxels.",
             &ChemCompt::getVoxelVolume
         );
 
         static ReadOnlyValueFinfo< ChemCompt, vector< double > >
                 voxelMidpoint(
             "voxelMidpoint",
             "Vector of midpoint coordinates of each of the voxels. The "
             "size of this vector is 3N, where N is the number of voxels. "
             "The first N entries are for x, next N for y, last N are z. ",
             &ChemCompt::getVoxelMidpoint
         );
 
         static LookupElementValueFinfo<
                 ChemCompt, unsigned int, double >
             oneVoxelVolume(
             "oneVoxelVolume",
             "Volume of specified voxel.",
             &ChemCompt::setOneVoxelVolume,
             &ChemCompt::getOneVoxelVolume
         );
 
         static ReadOnlyValueFinfo< ChemCompt, unsigned int > numDimensions(
             "numDimensions",
             "Number of spatial dimensions of this compartment. Usually 3 or 2",
             &ChemCompt::getDimensions
         );
 
         static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< double > > stencilRate(
             "stencilRate",
             "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.",
             &ChemCompt::getStencilRate
         );
 
         static ReadOnlyLookupValueFinfo< ChemCompt, unsigned int, vector< unsigned int > > stencilIndex(
             "stencilIndex",
             "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.",
             &ChemCompt::getStencilIndex
         );
 
         static ValueFinfo< ChemCompt, bool > isMembraneBound(
             "isMembraneBound",
             "Flag, set to True for meshes where each voxel is membrane "
             "bound. \n"
             "NeuroMesh and SpineMesh are false. \n"
             "CubeMesh, CylMesh, and EndoMesh can be either. If they are "
             "membrane bound they can still interact via channels and "
             "cross-compartment reactions. ",
             &ChemCompt::setIsMembraneBound,
             &ChemCompt::getIsMembraneBound
         );
 
         // MsgDest Definitions
 
         static DestFinfo buildDefaultMesh( "buildDefaultMesh",
             "Tells ChemCompt derived class to build a default mesh with the"
             "specified volume and number of meshEntries.",
             new EpFunc2< ChemCompt, double, unsigned int >(
                 &ChemCompt::buildDefaultMesh )
         );
 
         static DestFinfo setVolumeNotRates( "setVolumeNotRates",
             "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 in"
             "the model. If you don't know why you would want to do this,"
             "then you shouldn't use this function.",
             new OpFunc1< ChemCompt, double >(
                 &ChemCompt::setVolumeNotRates )
         );
 
         static DestFinfo handleNodeInfo( "handleNodeInfo",
             "Tells ChemCompt how many nodes and threads per node it is "
             "allowed to use. Triggers a return meshSplitOut message.",
             new EpFunc2< ChemCompt, unsigned int, unsigned int >(
                 &ChemCompt::handleNodeInfo )
         );
 
         static DestFinfo resetStencil( "resetStencil",
             "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.",
             new OpFunc0< ChemCompt >(
                 &ChemCompt::resetStencil )
         );
 
 
         // Field Elements
 
         static FieldElementFinfo< ChemCompt, MeshEntry > entryFinfo(
             "mesh",
             "Field Element for mesh entries",
             MeshEntry::initCinfo(),
             &ChemCompt::lookupEntry,
             &ChemCompt::setNumEntries,
             &ChemCompt::getNumEntries,
             false
         );
 
     static Finfo* chemMeshFinfos[] = {
         &volume,            // Value
         &voxelVolume,       // ReadOnlyLookupValue
         &voxelMidpoint,     // ReadOnlyLookupValue
         &oneVoxelVolume,    // ReadOnlyLookupValue
         &numDimensions, // ReadOnlyValue
         &stencilRate,   // ReadOnlyLookupValue
         &stencilIndex,  // ReadOnlyLookupValue
         &isMembraneBound,   // Value
         voxelVolOut(),  // SrcFinfo
         &buildDefaultMesh,  // DestFinfo
         &setVolumeNotRates,     // DestFinfo
         &resetStencil,  // DestFinfo
         &entryFinfo,    // FieldElementFinfo
     };
 
     static string doc[] = {
         "Name", "ChemCompt",
         "Author", "Upi Bhalla",
         "Description", "Pure virtual base class for chemical compartments"
 
     };
     static Dinfo< short > dinfo;
     static Cinfo chemMeshCinfo (
         "ChemCompt",
         Neutral::initCinfo(),
         chemMeshFinfos,
         sizeof( chemMeshFinfos ) / sizeof ( Finfo* ),
         &dinfo,
         doc,
         sizeof(doc)/sizeof( string ),
         true // This is a base class, not be be created directly.
     );
 
     return &chemMeshCinfo;
 }

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virtual void ChemCompt::innerBuildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)

pure virtual

Implemented in NeuroMesh, CubeMesh, PsdMesh, SpineMesh, CylMesh, and EndoMesh.

Referenced by buildDefaultMesh().

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virtual unsigned int ChemCompt::innerGetDimensions ( ) const

pure virtual

Implemented in SpineMesh, NeuroMesh, PsdMesh, CubeMesh, CylMesh, and EndoMesh.

Referenced by getDimensions().

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virtual unsigned int ChemCompt::innerGetNumEntries ( ) const

pure virtual

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by getNumEntries(), EndoMesh::getParentVoxel(), and EndoMesh::innerGetNumEntries().

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virtual vector< double > ChemCompt::innerGetStencilRate ( unsigned int row ) const

pure virtual

Virtual func for getting stencil rates for the derived classes.

Implemented in MeshCompt.

Referenced by getStencilRate().

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virtual void ChemCompt::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)

pure virtual

Implemented in NeuroMesh, SpineMesh, PsdMesh, CylMesh, CubeMesh, and EndoMesh.

Referenced by handleNodeInfo().

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virtual void ChemCompt::innerResetStencil ( )

pure virtual

Implemented in MeshCompt.

Referenced by resetStencil().

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virtual void ChemCompt::innerSetNumEntries ( unsigned int n )

pure virtual

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by setNumEntries().

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MeshEntry * ChemCompt::lookupEntry ( unsigned int index )

Returns the matched lookupEntry

Definition at line 379 of file ChemCompt.cpp.

References entry_.

Referenced by PsdMesh::handlePsdList(), SpineMesh::handleSpineList(), and initCinfo().

 {
     return &entry_;
 }

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virtual void ChemCompt::matchMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)		const

pure virtual

Returns the meshIndices (NOT spatial indices) of all adjacent mesh entry pairs on ether side of the (self, other) junction. meshIndices are the indices that look up entries in the vector of pools. spatialIndices are (iz * ny + iy) * nx + ix, that is, a linear conversion of cartesian spatial indices. So, for two touching cubes, the return vector is the paired meshIndices on either side of the plane of contact. If one mesh has a finer mesh than the other, or if there are more than one contact points from self to other (for example, at a corner), then we just have multiple pairs using the same meshIndex of the repeated voxel.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by buildJunction(), mapVoxelsBetweenMeshes(), and CubeMesh::matchCylMeshEntries().

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virtual double ChemCompt::nearest	(	double	x,
		double	y,
		double	z,
		unsigned int &	index
	)		const

pure virtual

Returns distance and index of nearest mesh entry. Computes each mesh entry position as its geometric centre. If the current location is not inside a valid mesh entry, distance returned is negative.

Implemented in NeuroMesh, CubeMesh, SpineMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by EndoMesh::nearest().

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void ChemCompt::resetStencil ( )

Reset stencil m_ to coreStencil_. This is needed as a prelude to rebuilding the junctions using extendStencil.

Definition at line 233 of file ChemCompt.cpp.

References innerResetStencil().

Referenced by initCinfo().

 {
     this->innerResetStencil();
 }

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unsigned int ChemCompt::setChildConcs	(	const Eref &	e,
		const vector< double > &	childConcs,
		unsigned int	start
	)		const

Recursively traverses all children, depth_first, restoring concentration terms as scooped up by getChildConcs. Does conc and concInit for pools, Kf and Kb for Reacs, and Km for enzymes. These are restored in order into the vector of childConcs. Does not traverse into children of other ChemCompts.

Definition at line 288 of file ChemCompt.cpp.

References Neutral::children(), and Field< A >::set().

Referenced by setEntireVolume(), and CylMesh::updateCoords().

 {
     vector< Id > kids;
     Neutral::children( e, kids );
     for ( vector < Id >::iterator i = kids.begin(); i != kids.end(); ++i )
     {
         if ( i->element()->cinfo()->isA( "PoolBase" ) ) {
             Field< double >::set( *i, "conc", conc[ start++ ] );
             Field< double >::set( *i, "concInit", conc[start++] );
         } else if ( i->element()->cinfo()->isA( "ReacBase" ) ) {
             Field< double >::set( *i, "Kf", conc[ start++ ] );
             Field< double >::set( *i, "Kb", conc[ start++ ] );
         } else if ( i->element()->cinfo()->isA( "EnzBase" ) ) {
             Field< double >::set( *i, "Km", conc[ start++ ] );
         } else if ( i->element()->cinfo()->isA( "ChemCompt" ) ) {
             // Do NOT traverse into child ChemCompts, they look after their
             // own volumes.
             continue;
         }
         start = setChildConcs( i->eref(), conc, start );
     }
     return start;
 }

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void ChemCompt::setEntireVolume	(	const Eref &	e,
		double	volume
	)

This is a little nasty. It calls buildDefaultMesh with the current numEntries. Should not be used if the mesh has been changed to something more interesting. Perhaps I need to do something like changeVolOfExistingMesh.

Definition at line 242 of file ChemCompt.cpp.

References Eref::dataIndex(), Eref::element(), getChildConcs(), Element::getMsgTargets(), setChildConcs(), vGetVoxelVolume(), voxelVolOut(), and vSetVolumeNotRates().

Referenced by initCinfo().

 {
     // If the reac system is not solved, then explicitly do scaling
     vector< ObjId > tgtVec =
             e.element()->getMsgTargets( e.dataIndex(), voxelVolOut() );
     if ( tgtVec.size() == 0 ) {
         vector< double > childConcs;
         getChildConcs( e, childConcs );
         if ( vSetVolumeNotRates( volume ) ) {
             setChildConcs( e, childConcs, 0 );
         }
     } else {
         vSetVolumeNotRates( volume );
         voxelVolOut()->send( e, this->vGetVoxelVolume() );
     }
 }

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void ChemCompt::setIsMembraneBound ( bool v )

Definition at line 360 of file ChemCompt.cpp.

References isMembraneBound_.

Referenced by initCinfo().

 {
     isMembraneBound_ = v;
 }

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void ChemCompt::setMeshEntryVolume	(	unsigned int	fid,
		double	volume
	)

virtual

Virtual function to assign volume of mesh Entry. Does nothing in most cases, but is operational in SpineMesh and PsdMesh.

Reimplemented in SpineMesh, and PsdMesh.

Definition at line 335 of file ChemCompt.cpp.

Referenced by setOneVoxelVolume().

 {
     cout << "Warning: ChemCompt::setMeshEntryVolume: Undefined except for PSD and spine mesh.\n";
 }

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void ChemCompt::setMethod ( string method )

Hint to system indicating method to be used on this compartment. Defaults to blank, which then leaves the decision to the calling function. Doesn't do anything unless the ChemCompt is parsed by the SimManager.

void ChemCompt::setNumEntries ( unsigned int num )

Dummy function. The numEntries is only set by other functions that define compartment decomposition.

Definition at line 384 of file ChemCompt.cpp.

References innerSetNumEntries().

Referenced by initCinfo().

 {
     this->innerSetNumEntries( num );
     // cout << "Warning: ChemCompt::setNumEntries: No effect. Use subclass-specific functions\nto build or resize mesh.\n";
 }

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void ChemCompt::setOneVoxelVolume	(	const Eref &	e,
		unsigned int	voxel,
		double	volume
	)

Definition at line 328 of file ChemCompt.cpp.

References setMeshEntryVolume().

Referenced by initCinfo().

 {
     this->setMeshEntryVolume( dataIndex, volume );
 }

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void ChemCompt::setVolumeNotRates ( double volume )

Returns true on success. Changes volume but does not notify any child objects. For some classes, this only works if the ChemCompt has just one voxel. It will return false if it can't handle it. This function will invalidate any concentration term in the model. If you don't know why you would want to do this, then you shouldn't use this function.",

Definition at line 370 of file ChemCompt.cpp.

References vSetVolumeNotRates().

Referenced by initCinfo().

 {
     vSetVolumeNotRates( volume ); // Pass on to derived classes.
 }

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virtual double ChemCompt::vGetEntireVolume ( ) const

pure virtual

Implemented in NeuroMesh, CubeMesh, PsdMesh, SpineMesh, CylMesh, and EndoMesh.

Referenced by getEntireVolume().

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virtual const vector< double >& ChemCompt::vGetVoxelMidpoint ( ) const

pure virtual

Virtual func so that derived classes can return voxel midpoint.

Implemented in CubeMesh, SpineMesh, NeuroMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by getVoxelMidpoint(), and EndoMesh::vGetVoxelMidpoint().

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virtual const vector< double >& ChemCompt::vGetVoxelVolume ( ) const

pure virtual

Virtual func so that derived classes can pass voxel volume back.

Implemented in CubeMesh, SpineMesh, NeuroMesh, PsdMesh, CylMesh, and EndoMesh.

Referenced by EndoMesh::getVoxelArea(), EndoMesh::getVoxelLength(), getVoxelVolume(), EndoMesh::matchMeshEntries(), setEntireVolume(), and EndoMesh::vGetVoxelVolume().

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SrcFinfo1< vector< double > > * ChemCompt::voxelVolOut ( )

static

Definition at line 17 of file ChemCompt.cpp.

Referenced by initCinfo(), CubeMesh::setCoords(), and setEntireVolume().

                                                       {
     static SrcFinfo1< vector< double > > voxelVolOut( "voxelVolOut",
     "Sends updated voxel volume out to Ksolve, Gsolve, and Dsolve."
     "Used to request a recalculation of rates and of initial numbers."
     );
     return &voxelVolOut;
 }

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virtual bool ChemCompt::vSetVolumeNotRates ( double volume )

pure virtual

Virtual function for actually doing this.

Implemented in NeuroMesh, CubeMesh, PsdMesh, SpineMesh, CylMesh, and EndoMesh.

Referenced by setEntireVolume(), and setVolumeNotRates().

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Member Data Documentation

vector< Boundary > ChemCompt::boundaries_

private

Wrapper for self ptr.

The Boundaries are Element Fields. They appear as distinct Elements, though they are controlled by the ChemCompt. These are the interfaces between compartments, or just the boundaries of the current one. Each Boundary can be diffusive, reflective, or an interface where molecules in different compartments can talk to each other. All boundaries have a message to a Geometry. The Geometries may be shared, which is why the boundary isn't a Geometry itself. If it is an interface (diffusive or other) then the boundary also contains a message to the adjacent compartment.

Definition at line 347 of file ChemCompt.h.

MeshEntry ChemCompt::entry_

private

Definition at line 333 of file ChemCompt.h.

Referenced by lookupEntry().

bool ChemCompt::isMembraneBound_

private

Flag, set to True for meshes where each voxel is membrane bound. NeuroMesh and SpineMesh are false CubeMesh, CylMesh, and EndoMesh can be either. If they are membrane bound they can still interact via channels and cross-compartment reactions.

Definition at line 363 of file ChemCompt.h.

Referenced by getIsMembraneBound(), and setIsMembraneBound().

string ChemCompt::method_

private

Hint to system indicating method to be used on this compartment. Defaults to blank, which then leaves the decision to the calling function.

Definition at line 354 of file ChemCompt.h.

The documentation for this class was generated from the following files:

moose-core/mesh/ChemCompt.h
moose-core/mesh/ChemCompt.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation