#include <BidomainAssembler.hpp>

Inheritance diagram for BidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for BidomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	BidomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue)

virtual	~BidomainAssembler ()

Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, true, CARDIAC >
	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, 2 (ELEMENT_DIM+1), 2 (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, 2 > &rU, c_matrix< double, 2, 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)

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

Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 2, false, true, CARDIAC >
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

Detailed Description

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

Assembler, used for assembling the LHS matrix of the linear system that arises when the bidomain equations are discretised, and for assembling the contribution to the RHS vector that comes from a surface integral.

The discretised bidomain equation leads to the linear system (see FEM implementations document)

[ (chi*C/dt) M + K1 K1 ] [ V^{n+1} ] = [ (chi*C/dt) M V^{n} + M F^{n} + c1_surf ] [ K1 K2 ] [ PhiE^{n+1}] [ c2_surf ]

where chi is the surface-area to volume ratio, C the capacitance, dt the timestep M the mass matrix, K1 and K2 stiffness matrices, V^{n} and PhiE^{n} the vector of voltages and phi_e at time n, F^{n} the vector of (chi*Iionic + Istim) at each node, and c1_surf and c2_surf vectors arising from any surface stimuli (usually zero).

This assembler is used to assemble the LHS matrix, ie

[ (chi*C/dt) M + K1 K1 ] [ K1 K2 ]

Hence, this class inherits from AbstractCardiacFeVolumeIntegralAssembler and implements the methods ComputeMatrixTerm()

Definition at line 70 of file BidomainAssembler.hpp.

Constructor & Destructor Documentation

◆ BidomainAssembler()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainAssembler	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BidomainTissue< 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 98 of file BidomainAssembler.cpp.

◆ ~BidomainAssembler()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

virtual BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::~BidomainAssembler ( )

inlinevirtual

Destructor.

Definition at line 109 of file BidomainAssembler.hpp.

Member Function Documentation

◆ ComputeMatrixTerm()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, 2 (ELEMENT_DIM+1), 2 (ELEMENT_DIM+1)> BidomainAssembler< 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, 2 > &	rU,
		c_matrix< double, 2, 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 LHS 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

Reimplemented in BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >.

Definition at line 44 of file BidomainAssembler.cpp.

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

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().

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

heart/src/solver/electrics/bidomain/BidomainAssembler.hpp
heart/src/solver/electrics/bidomain/BidomainAssembler.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BidomainAssembler()

◆ ~BidomainAssembler()

Member Function Documentation

◆ ComputeMatrixTerm()