#include <ExtendedBidomainAssembler.hpp>

Inheritance diagram for ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	ExtendedBidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, ExtendedBidomainTissue< SPACE_DIM > pTissue)

virtual	~ExtendedBidomainAssembler ()

Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 3, true, true, NORMAL >
	AbstractCardiacFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > pTissue)

Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
	AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

virtual	~AbstractFeVolumeIntegralAssembler ()

Public Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
	AbstractFeAssemblerCommon ()

void	SetCurrentSolution (Vec currentSolution)

virtual	~AbstractFeAssemblerCommon ()

Public Member Functions inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
	AbstractFeAssemblerInterface ()

void	SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)

void	SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly)

void	Assemble ()

void	AssembleMatrix ()

void	AssembleVector ()

virtual	~AbstractFeAssemblerInterface ()

Protected Member Functions
virtual c_matrix< double, 3 (ELEMENT_DIM+1), 3 (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 3 > &rU, c_matrix< double, 3, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
void	ComputeTransformedBasisFunctionDerivatives (const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rReturnValue)

void	DoAssemble ()

virtual c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual void	AssembleOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1) > &rAElem, c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> &rBElem)

virtual bool	ElementAssemblyCriterion (Element< ELEMENT_DIM, SPACE_DIM > &rElement)

Protected Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
virtual double	GetCurrentSolutionOrGuessValue (unsigned nodeIndex, unsigned indexOfUnknown)

virtual void	ResetInterpolatedQuantities ()

virtual void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)

virtual void	IncrementInterpolatedGradientQuantities (const c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, unsigned phiIndex, const Node< SPACE_DIM > *pNode)

Protected Attributes
ExtendedBidomainTissue < SPACE_DIM > *	mpExtendedBidomainTissue

Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 3, true, true, NORMAL >
AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	mpCardiacTissue

HeartConfig *	mpConfig

Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh

GaussianQuadratureRule < ELEMENT_DIM > *	mpQuadRule

Protected Attributes inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
ReplicatableVector	mCurrentSolutionOrGuessReplicated

Protected Attributes inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
Vec	mVectorToAssemble

Mat	mMatrixToAssemble

bool	mAssembleMatrix

bool	mAssembleVector

bool	mZeroMatrixBeforeAssembly

bool	mZeroVectorBeforeAssembly

PetscInt	mOwnershipRangeLo

PetscInt	mOwnershipRangeHi

Additional Inherited Members
Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
typedef LinearBasisFunction < ELEMENT_DIM >	BasisFunction

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >

This is a derived class of AbstractCardiacFeVolumeIntegralAssembler and takes care of assembling LHS for solution of the extended bidomain euqations

See Buist ML, Poh YC. An Extended Bidomain Framework Incorporating Multiple Cell Types. Biophysical Journal, Volume 99, Issue 1, 13-18, 7 July 2010.

Major differences with bidomain assembler:

there are two cells (instead of one)
extracellular stimulus is present

Definition at line 70 of file ExtendedBidomainAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ExtendedBidomainAssembler	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		ExtendedBidomainTissue< SPACE_DIM > *	pTissue
	)

Constructor stores the mesh and pde and sets up boundary conditions.

Parameters

pMesh	pointer to the mesh
pTissue	pointer to the tissue

Definition at line 133 of file ExtendedBidomainAssembler.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::~ExtendedBidomainAssembler ( )

virtual

Destructor.

Definition at line 143 of file ExtendedBidomainAssembler.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, 3 (ELEMENT_DIM+1), 3 (ELEMENT_DIM+1)> ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm	(	c_vector< double, ELEMENT_DIM+1 > &	rPhi,
		c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, 3 > &	rU,
		c_matrix< double, 3, SPACE_DIM > &	rGradU,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)

protectedvirtual

ComputeMatrixTerm()

This method is called by AssembleOnElement() and tells the assembler the contribution to add to the element stiffness matrix.

Parameters

rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rX	The point in space
rU	The unknown as a vector, u(i) = u_i
rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElement	Pointer to the element

Returns: stencil matrix

Definition at line 45 of file ExtendedBidomainAssembler.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and PdeSimulationTime::GetPdeTimeStep().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainTissue<SPACE_DIM>* ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainTissue

protected

The tissue for which we assemble the matrix

Definition at line 77 of file ExtendedBidomainAssembler.hpp.

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

heart/src/solver/electrics/extended_bidomain/ExtendedBidomainAssembler.hpp
heart/src/solver/electrics/extended_bidomain/ExtendedBidomainAssembler.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM >