#include <MeshCompt.h>

Inheritance diagram for MeshCompt:

Collaboration diagram for MeshCompt:

Public Member Functions
void	addRow (unsigned int index, const vector< double > &entry, const vector< unsigned int > &colIndex)

void	clearExtendedMeshEntryVolume ()
	Inherited virtual function to clear the vector of MeshEntryVolume. More...

double	extendedMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry, including. More...

void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)
	Add boundary voxels to stencil for cross-solver junctions. More...

vector< unsigned int >	getNeighbors (unsigned int fid) const
	Looks up stencil to return vector of indices of coupled voxels. More...

virtual vector< unsigned int >	getParentVoxel () const =0

const SparseMatrix< double > &	getStencil () const
	Returns entire sparse matrix of mesh. Used by diffusion solver. More...

unsigned int	getStencilRow (unsigned int meshIndex, const double entry, const unsigned int colIndex) const

virtual const vector< double > &	getVoxelArea () const =0

virtual const vector< double > &	getVoxelLength () const =0

vector< double >	innerGetStencilRate (unsigned int row) const

void	innerResetStencil ()
	virtual func implemented here. More...

	MeshCompt ()

void	setStencilSize (unsigned int numRows, unsigned int numCols)

	~MeshCompt ()

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

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

	ChemCompt ()

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

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

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

Private Attributes
SparseMatrix< double >	coreStencil_
	Handles the core stencil for own vol. More...

vector< double >	extendedMeshEntryVolume_

SparseMatrix< double >	m_
	Handles stencil for core + abutting voxels. More...

Additional Inherited Members
Static Public Member Functions inherited from ChemCompt
static double	distance (double x, double y, double z)

static const Cinfo *	initCinfo ()

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

Detailed Description

The MeshCompt represents the base class for all compartments which are set up as a meshes. These include CubeMesh, CylMesh and NeuroMesh. The MeshCompt handles the stencil that is the core of all the meshes. The stencil specifies which compartments diffuse into each other, and by how much.

Definition at line 20 of file MeshCompt.h.

Constructor & Destructor Documentation

MeshCompt::MeshCompt ( )

Definition at line 24 of file MeshCompt.cpp.

 {
     ;
 }

MeshCompt::~MeshCompt ( )

Definition at line 29 of file MeshCompt.cpp.

 {
     ;
 }

Member Function Documentation

void MeshCompt::addRow	(	unsigned int	index,
		const vector< double > &	entry,
		const vector< unsigned int > &	colIndex
	)

Definition at line 98 of file MeshCompt.cpp.

References SparseMatrix< T >::addRow(), and coreStencil_.

Referenced by CylMesh::buildStencil(), NeuroMesh::buildStencil(), and CubeMesh::buildStencil().

 {
     coreStencil_.addRow( index, entry, colIndex );
 }

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void MeshCompt::clearExtendedMeshEntryVolume ( )

virtual

Inherited virtual function to clear the vector of MeshEntryVolume.

Implements ChemCompt.

Definition at line 43 of file MeshCompt.cpp.

References extendedMeshEntryVolume_.

 {
     extendedMeshEntryVolume_.clear();
 }

double MeshCompt::extendedMeshEntryVolume ( unsigned int fid ) const

virtual

Virtual function to return volume of mesh Entry, including.

Utility function to return volume of any voxel including those diffusively coupled and aubtting the present volume.

Implements ChemCompt.

Reimplemented in NeuroMesh, SpineMesh, and PsdMesh.

Definition at line 36 of file MeshCompt.cpp.

References extendedMeshEntryVolume_.

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

 {
     assert( index < extendedMeshEntryVolume_.size() );
     return extendedMeshEntryVolume_[ index ];
 }

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

virtual

Add boundary voxels to stencil for cross-solver junctions.

extendStencil adds voxels to the current stencil m_, to build up a monolithic stencil that also handles the entries just past all the boundaries. This function may be called many times to deal with the addition of multiple junctions. Before the first of these calls, the m_ matrix should be set to the coreStencil_.

Organizes vj by voxel, that is, by row.

Implements ChemCompt.

Definition at line 121 of file MeshCompt.cpp.

References SparseMatrix< T >::addRow(), SparseMatrix< T >::clear(), coreStencil_, EMPTY, extendedMeshEntryVolume_, ChemCompt::getMeshEntryVolume(), SparseMatrix< T >::getRow(), m_, SparseMatrix< T >::nRows(), and SparseMatrix< T >::setSize().

Referenced by testCubeMeshExtendStencil().

 {
     // Maps from remote meshIndex (in vj) to local index of proxy voxel.
     map< unsigned int, unsigned int > meshMap;
     map< unsigned int, unsigned int >::iterator mmi;
 
     // Maps from local index of proxy voxel back to remote meshIndex.
     vector< unsigned int > meshBackMap;
 
 
     unsigned int coreSize = coreStencil_.nRows();
     unsigned int oldSize = m_.nRows();
     unsigned int newSize = oldSize;
 
     vector< vector< VoxelJunction > > vvj( coreSize );
 
     for ( vector< VoxelJunction >::const_iterator
                     i = vj.begin(); i != vj.end(); ++i ) {
         mmi = meshMap.find( i->second );
         if ( mmi == meshMap.end() ) {
             assert( i->first < coreSize );
             meshBackMap.push_back( i->second );
             meshMap[i->second] = newSize++;
             vvj[i->first].push_back( *i );
         }
     }
     vector< vector< VoxelJunction > > vvjCol( newSize );
     SparseMatrix< double > oldM = m_;
     m_.clear();
     m_.setSize( newSize, newSize );
     for ( unsigned int i = 0; i < newSize; ++i ) {
         vector< VoxelJunction > temp;
         if ( i < oldSize ) { // Copy over old matrix.
             const double* entry;
             const unsigned int* colIndex;
             unsigned int num = oldM.getRow( i, &entry, &colIndex );
             temp.resize( num );
             for ( unsigned int j = 0; j < num; ++j ) {
                 temp[j].first = colIndex[j];
                 temp[j].diffScale = entry[j];
             }
         }
         if ( i < coreSize ) { // Set up diffusion into proxy voxels.
             for ( vector< VoxelJunction >::const_iterator
                 j = vvj[i].begin(); j != vvj[i].end(); ++j )
             {
                 unsigned int row = j->first;
                 assert( row == i );
                 unsigned int col = meshMap[j->second];
                 assert( col >= oldSize );
                 temp.push_back(
                         VoxelJunction( col, EMPTY, j->diffScale ) );
                 vvjCol[col].push_back(
                         VoxelJunction( row, EMPTY, j->diffScale ) );
             }
         }
         if ( i >= oldSize ) { // Set up diffusion from proxy to old voxels
             for ( vector< VoxelJunction >::const_iterator
                 j = vvjCol[i].begin(); j != vvjCol[i].end(); ++j )
             {
                 temp.push_back( *j );
             }
         }
         // Now we've filled in all the VoxelJunctions for the new row.
         sort( temp.begin(), temp.end() );
         vector< double > e( temp.size() );
         vector< unsigned int > c( temp.size() );
         for ( unsigned int j = 0; j < temp.size(); ++j ) {
             e[j] = temp[j].diffScale;
             c[j] = temp[j].first;
         }
         m_.addRow( i, e, c );
     }
 
     // Fill in the volumes of the external mesh entries
     for ( vector< unsigned int>::const_iterator
             i = meshBackMap.begin(); i != meshBackMap.end(); ++i ) {
         extendedMeshEntryVolume_.push_back( other->getMeshEntryVolume( *i ) );
     }
 }

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vector< unsigned int > MeshCompt::getNeighbors ( unsigned int fid ) const

virtual

Looks up stencil to return vector of indices of coupled voxels.

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

Implements ChemCompt.

Definition at line 69 of file MeshCompt.cpp.

References SparseMatrix< T >::getRow(), and m_.

Referenced by NeuroMesh::getDiffusionArea(), and testCubeMesh().

 {
     const double* entry;
     const unsigned int *colIndex;
 
     unsigned int n = m_.getRow( row, &entry, &colIndex );
 
     vector< unsigned int > ret;
     ret.insert( ret.end(), colIndex, colIndex + n );
 
     return ret;
 }

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virtual vector< unsigned int > MeshCompt::getParentVoxel ( ) const

pure virtual

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

Referenced by Dsolve::build(), and EndoMesh::getParentVoxel().

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const SparseMatrix< double > & MeshCompt::getStencil ( ) const

Returns entire sparse matrix of mesh. Used by diffusion solver.

Definition at line 60 of file MeshCompt.cpp.

References coreStencil_.

 {
         return coreStencil_;
 }

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

virtual

Derived function to return SparseMatrix-style row info for specified mesh entry.

Implements ChemCompt.

Definition at line 54 of file MeshCompt.cpp.

References SparseMatrix< T >::getRow(), and m_.

Referenced by testCubeMeshExtendStencil().

 {
         return m_.getRow( meshIndex, entry, colIndex );
 }

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virtual const vector< double >& MeshCompt::getVoxelArea ( ) const

pure virtual

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

Referenced by Dsolve::build().

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virtual const vector< double >& MeshCompt::getVoxelLength ( ) const

pure virtual

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

Referenced by Dsolve::build(), and EndoMesh::matchMeshEntries().

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

virtual

Looks up stencil to return vector of diffusion coupling to neighbor voxels.

Implements ChemCompt.

Definition at line 85 of file MeshCompt.cpp.

References SparseMatrix< T >::getRow(), and m_.

 {
     const double* entry;
     const unsigned int *colIndex;
 
     unsigned int n = m_.getRow( row, &entry, &colIndex );
 
     vector< double > ret;
     ret.insert( ret.end(), entry, entry + n );
 
     return ret;
 }

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void MeshCompt::innerResetStencil ( )

virtual

virtual func implemented here.

Implements ChemCompt.

Definition at line 49 of file MeshCompt.cpp.

References coreStencil_, and m_.

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

 {
     m_ = coreStencil_;
 }

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void MeshCompt::setStencilSize	(	unsigned int	numRows,
		unsigned int	numCols
	)

Definition at line 106 of file MeshCompt.cpp.

References SparseMatrix< T >::clear(), coreStencil_, and SparseMatrix< T >::setSize().

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

 {
     coreStencil_.clear();
     coreStencil_.setSize( numRows, numCols );
 }

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Member Data Documentation

SparseMatrix< double > MeshCompt::coreStencil_

private

Handles the core stencil for own vol.

Definition at line 74 of file MeshCompt.h.

Referenced by addRow(), extendStencil(), getStencil(), innerResetStencil(), and setStencilSize().

vector< double > MeshCompt::extendedMeshEntryVolume_

private

vector of meshEntryVolumes for abutting surfaces, needed to compute diffusion rates across junctions. Indexed from zero.

Definition at line 85 of file MeshCompt.h.

Referenced by clearExtendedMeshEntryVolume(), extendedMeshEntryVolume(), and extendStencil().

SparseMatrix< double > MeshCompt::m_

private

Handles stencil for core + abutting voxels.

Definition at line 77 of file MeshCompt.h.

Referenced by extendStencil(), getNeighbors(), getStencilRow(), innerGetStencilRate(), and innerResetStencil().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation