#include <AbstractCorrectionTermAssembler.hpp>

Inheritance diagram for AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >:

Collaboration diagram for AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >:

Public Member Functions
	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
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)

Protected Attributes
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

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 ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >

A parent class for MonodomainCorrectionTermAssembler and BidomainCorrectionTermAssembler, used for state variable interpolation (SVI).

Definition at line 49 of file AbstractCorrectionTermAssembler.hpp.

Constructor & Destructor Documentation

◆ AbstractCorrectionTermAssembler()

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler	(	AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > *	pMesh,
		AbstractCardiacTissue< ELEM_DIM, SPACE_DIM > *	pTissue
	)

Constructor.

Parameters

pMesh	pointer to the mesh
pTissue	pointer to the cardiac tissue

Definition at line 40 of file AbstractCorrectionTermAssembler.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetOwnership(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetUnsignedAttribute(), HeartRegionCode::IsRegionBath(), and AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mElementsCanDoSvi.

Member Function Documentation

◆ ElementAssemblyCriterion()

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ElementAssemblyCriterion ( Element< ELEM_DIM, SPACE_DIM > & rElement )

protected

Returns: true if we should assemble the correction term for this element. Checks if there is a sufficiently steep ionic current gradient to make the expense worthwhile, by checking if the maximum difference between nodal ionic currents is greater than 1 uA/cm^2^.

Parameters

rElement the element to test

Definition at line 109 of file AbstractCorrectionTermAssembler.cpp.

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

◆ IncrementInterpolatedQuantities()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::IncrementInterpolatedQuantities	(	double	phiI,
		const Node< SPACE_DIM > *	pNode
	)

protectedvirtual

Interpolates state variables and ionic current.

Parameters

phiI
pNode

Reimplemented from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >.

Definition at line 94 of file AbstractCorrectionTermAssembler.cpp.

◆ ResetInterpolatedQuantities()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ResetInterpolatedQuantities ( void )

protectedvirtual

Resets interpolated state variables and ionic current.

Reimplemented from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >.

Definition at line 83 of file AbstractCorrectionTermAssembler.cpp.

Member Data Documentation

◆ mElementsCanDoSvi

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::vector<bool> AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mElementsCanDoSvi

protected

Vector of bools, one bool per element, representing whether each element can do SVI. If the element has different cell models at each node, or has been designated a bath element, then it cannot do SVI.

Definition at line 70 of file AbstractCorrectionTermAssembler.hpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), and AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, 2 >::ResetInterpolatedQuantities().