#include <MonodomainAssembler.hpp>

Inheritance diagram for MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
c_matrix< double, 1 (ELEMENT_DIM+1), 1 (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, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

	MonodomainAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, MonodomainTissue< ELEMENT_DIM, SPACE_DIM > pTissue)

Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 1, 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 Attributes
MassMatrixAssembler < ELEMENT_DIM, SPACE_DIM >	mMassMatrixAssembler

MonodomainStiffnessMatrixAssembler < ELEMENT_DIM, SPACE_DIM >	mStiffnessMatrixAssembler

Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 1, 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

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 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)

Detailed Description

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

Assembler, mainly used for assembling the LHS matrix of the linear system that arises when the monodomain equations are discretised.

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

( (chi*C/dt) M + K ) V^{n+1} = (chi*C/dt) M V^{n} + M F^{n} + c_surf

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

This assembler is used for assembling the matrix A :=(chi*C/dt) M + K. Hence, this class inherits from AbstractCardiacFeVolumeIntegralAssembler and implements the method ComputeMatrixTerm().

Definition at line 64 of file MonodomainAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainAssembler	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	pTissue
	)

Constructor

Parameters

pMesh	pointer to the mesh
pTissue	pointer to the tissue

Definition at line 58 of file MonodomainAssembler.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, 1 (ELEMENT_DIM+1), 1 (ELEMENT_DIM+1)> MonodomainAssembler< 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, 1 > &	rU,
		c_matrix< double, 1, SPACE_DIM > &	rGradU,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)

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

Am and Cm are set as scaling factors for the mass matrix in its constructor.

Definition at line 43 of file MonodomainAssembler.cpp.

References PdeSimulationTime::GetPdeTimeStepInverse().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MassMatrixAssembler<ELEMENT_DIM, SPACE_DIM> MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::mMassMatrixAssembler

protected

This assembler uses another assembler, though just for calling the ComputeMatrixTerm() method.

Definition at line 70 of file MonodomainAssembler.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainStiffnessMatrixAssembler<ELEMENT_DIM, SPACE_DIM> MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::mStiffnessMatrixAssembler

protected

This assembler uses another assembler, though just for calling the ComputeMatrixTerm() method.

Definition at line 74 of file MonodomainAssembler.hpp.

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

heart/src/solver/electrics/monodomain/MonodomainAssembler.hpp
heart/src/solver/electrics/monodomain/MonodomainAssembler.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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