#include <MonodomainCorrectionTermAssembler.hpp>

Inheritance diagram for MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >:

Public Member Functions
	MonodomainCorrectionTermAssembler (AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > pMesh, MonodomainTissue< ELEM_DIM, SPACE_DIM > pTissue)

Public Member Functions inherited from AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 1 >
	AbstractCorrectionTermAssembler (AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > pMesh, AbstractCardiacTissue< ELEM_DIM, SPACE_DIM > pTissue)

Public Member Functions inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM, true, false, 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
c_vector< double, 1 *(ELEM_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEM_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEM_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEM_DIM, SPACE_DIM > *pElement)

Protected Member Functions inherited from AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 1 >
void	ResetInterpolatedQuantities (void)

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

bool	ElementAssemblyCriterion (Element< ELEM_DIM, SPACE_DIM > &rElement)

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	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 AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 1 >
double	mIionicInterp

std::vector< double >	mStateVariablesAtQuadPoint

std::vector< bool >	mElementsCanDoSvi

Protected Attributes inherited from AbstractCardiacFeVolumeIntegralAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM, true, false, 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 ELEM_DIM, unsigned SPACE_DIM>
class MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >

An assembler which computes the correction term to add to the RHS vector if using state variable interpolation (SVI), as well as determining which elements should be corrected on. The formula to determine which elements SVI is used is delta Iionic > TOL, where delta Iionic is the max difference between nodal ionic values, and TOL is chosen conservatively to be 1uA/cm^2^. See wiki page ChasteGuides/StateVariableInterpolation for more details.

Definition at line 54 of file MonodomainCorrectionTermAssembler.hpp.

Constructor & Destructor Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::MonodomainCorrectionTermAssembler	(	AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > *	pMesh,
		MonodomainTissue< ELEM_DIM, SPACE_DIM > *	pTissue
	)

Constructor.

Parameters

pMesh	pointer to the mesh
pTissue	pointer to the cardiac tissue

Definition at line 40 of file MonodomainCorrectionTermAssembler.cpp.

References HeartConfig::GetUseStateVariableInterpolation(), and AbstractCardiacFeVolumeIntegralAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM, true, false, CARDIAC >::mpConfig.

Member Function Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

c_vector< double, 1 *(ELEM_DIM+1)> MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::ComputeVectorTerm	(	c_vector< double, ELEM_DIM+1 > &	rPhi,
		c_matrix< double, SPACE_DIM, ELEM_DIM+1 > &	rGradPhi,
		ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, SPACE_DIM > &	rGradU,
		Element< ELEM_DIM, SPACE_DIM > *	pElement
	)

protected

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

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, rU(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 49 of file MonodomainCorrectionTermAssembler.cpp.

References AbstractCardiacCellInterface::GetIIonic(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), HeartConfig::GetSurfaceAreaToVolumeRatio(), AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 1 >::mIionicInterp, AbstractCardiacFeVolumeIntegralAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM, true, false, CARDIAC >::mpCardiacTissue, AbstractCardiacFeVolumeIntegralAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM, true, false, CARDIAC >::mpConfig, and AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 1 >::mStateVariablesAtQuadPoint.

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

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

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<unsigned ELEM_DIM, unsigned SPACE_DIM> class MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM>
class MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >