MeshCompt Class Reference

#include <MeshCompt.h>

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List of all members.

Public Member Functions
	MeshCompt ()
	~MeshCompt ()
double	extendedMeshEntryVolume (unsigned int fid) const
	Virtual function to return volume of mesh Entry, including.
void	clearExtendedMeshEntryVolume ()
	Inherited virtual function to clear the vector of MeshEntryVolume.
void	innerResetStencil ()
	virtual func implemented here.
unsigned int	getStencilRow (unsigned int meshIndex, const double **entry, const unsigned int **colIndex) const
const SparseMatrix< double > &	getStencil () const
	Returns entire sparse matrix of mesh. Used by diffusion solver.
vector< unsigned int >	getNeighbors (unsigned int fid) const
	Looks up stencil to return vector of indices of coupled voxels.
vector< double >	innerGetStencilRate (unsigned int row) const
void	addRow (unsigned int index, const vector< double > &entry, const vector< unsigned int > &colIndex)
void	setStencilSize (unsigned int numRows, unsigned int numCols)
void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)
	Add boundary voxels to stencil for cross-solver junctions.
virtual vector< unsigned int >	getParentVoxel () const =0
virtual const vector< double > &	getVoxelArea () const =0
virtual const vector< double > &	getVoxelLength () const =0

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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.

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Constructor & Destructor Documentation

MeshCompt::MeshCompt

(

)

MeshCompt::~MeshCompt

(

)

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Member Function Documentation

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

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

void MeshCompt::clearExtendedMeshEntryVolume

(

)

[virtual]

Inherited virtual function to clear the vector of MeshEntryVolume.

Implements ChemCompt.

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 CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

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

Add boundary voxels to stencil for cross-solver junctions.

Referenced by testCubeMeshExtendStencil().

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.

References SparseMatrix< T >::getRow().

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

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virtual vector< unsigned int > MeshCompt::getParentVoxel

(

)

const [pure virtual]

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

const SparseMatrix< double > & MeshCompt::getStencil

(

)

const

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

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.

References SparseMatrix< T >::getRow().

Referenced by testCubeMeshExtendStencil().

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virtual const vector< double >& MeshCompt::getVoxelArea

(

)

const [pure virtual]

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

virtual const vector< double >& MeshCompt::getVoxelLength

(

)

const [pure virtual]

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

vector< double > MeshCompt::innerGetStencilRate

(

unsigned int

row

)

const [virtual]

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

Implements ChemCompt.

References SparseMatrix< T >::getRow().

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void MeshCompt::innerResetStencil

(

)

[virtual]

virtual func implemented here.

Implements ChemCompt.

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

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

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

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

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

• mesh/MeshCompt.h
• mesh/MeshCompt.cpp