#include <BidomainSolver.hpp>

Inheritance diagram for BidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for BidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	BidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)

void	InitialiseForSolve (Vec initialSolution)

Public Member Functions inherited from AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
	AbstractBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)

virtual	~AbstractBidomainSolver ()

void	SetFixedExtracellularPotentialNodes (std::vector< unsigned > fixedExtracellularPotentialNodes)

void	SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	GetBoundaryConditions ()

void	ResetBoundaryConditionsContainer (BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc)

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
	AbstractDynamicLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

void	SetTimes (double tStart, double tEnd)

void	SetTimeStep (double dt)

void	SetInitialCondition (Vec initialCondition)

virtual Vec	Solve ()

void	SetMatrixIsNotAssembled ()

void	SetTimeAdaptivityController (AbstractTimeAdaptivityController *pTimeAdaptivityController)

void	SetOutputToVtk (bool output)

void	SetOutputToParallelVtk (bool output)

void	SetOutputToTxt (bool output)

void	SetOutputDirectoryAndPrefix (std::string outputDirectory, std::string prefix)

void	SetPrintingTimestepMultiple (unsigned multiple)

Public Member Functions inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
	AbstractLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

virtual	~AbstractLinearPdeSolver ()

virtual void	FollowingSolveLinearSystem (Vec currentSolution)

LinearSystem *	GetLinearSystem ()

Private Member Functions
void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)

Private Attributes
Mat	mMassMatrix

Vec	mVecForConstructingRhs

BidomainAssembler< ELEMENT_DIM, SPACE_DIM > *	mpBidomainAssembler

BidomainNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM > *	mpBidomainNeumannSurfaceTermAssembler

BidomainCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM > *	mpBidomainCorrectionTermAssembler

Additional Inherited Members
Protected Member Functions inherited from AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
virtual void	CheckCompatibilityCondition ()

void	PrepareForSetupLinearSystem (Vec existingSolution)

virtual void	FinaliseLinearSystem (Vec existingSolution)

virtual Vec	GenerateNullBasis () const

void	FinaliseForBath (bool computeMatrix, bool computeVector)

Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes inherited from AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
bool	mBathSimulation

BidomainTissue< SPACE_DIM > *	mpBidomainTissue

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	mpBoundaryConditions

bool	mNullSpaceCreated

HeartConfig *	mpConfig

std::vector< unsigned >	mFixedExtracellularPotentialNodes

unsigned	mRowForAverageOfPhiZeroed

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
double	mTstart

double	mTend

bool	mTimesSet

Vec	mInitialCondition

bool	mMatrixIsAssembled

bool	mMatrixIsConstant

double	mIdealTimeStep

double	mLastWorkingTimeStep

AbstractTimeAdaptivityController *	mpTimeAdaptivityController

bool	mOutputToVtk

bool	mOutputToParallelVtk

bool	mOutputToTxt

std::string	mOutputDirectory

std::string	mFilenamePrefix

unsigned	mPrintingTimestepMultiple

Hdf5DataWriter *	mpHdf5Writer

std::vector< int >	mVariableColumnIds

Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
LinearSystem *	mpLinearSystem

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

Detailed Description

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

A bidomain solver, which uses various assemblers to set up the bidomain FEM linear system.

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 solver uses two assemblers, one to assemble the whole LHS matrix, and also to compute c1_surf and c2_surf, and one to assemble the mass matrix M.

Also allows state variable interpolation (SVI) to be used on elements for which it will be needed, if the appropriate HeartConfig boolean is set. See https://chaste.github.io/docs/user-guides/state-variable-interpolation/ for more details on this. In this case the vector [c_correction, 0] is added to the above, and another assembler is used to create the c_correction.

Definition at line 80 of file BidomainSolver.hpp.

Constructor & Destructor Documentation

◆ BidomainSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver	(	bool	bathSimulation,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BidomainTissue< SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	pBoundaryConditions
	)

Constructor

Parameters

bathSimulation	Whether the simulation involves a perfusing bath
pMesh	pointer to the mesh
pTissue	pointer to the tissue
pBoundaryConditions	pointer to the boundary conditions

Definition at line 200 of file BidomainSolver.cpp.

References HeartConfig::Instance(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainAssembler, BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainCorrectionTermAssembler, BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainNeumannSurfaceTermAssembler, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication().

◆ ~BidomainSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Definition at line 238 of file BidomainSolver.cpp.

Member Function Documentation

◆ InitialiseForSolve()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve ( Vec initialSolution )

virtual

Overloaded InitialiseForSolve() which calls base version but also initialises mMassMatrix and mVecForConstructingRhs

Parameters

initialSolution initial solution

Reimplemented from AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >.

Definition at line 43 of file BidomainSolver.cpp.

References AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and PetscTools::SetupMat().

◆ SetupLinearSystem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem	(	Vec	currentSolution,
		bool	computeMatrix
	)

privatevirtual

Implementation of SetupLinearSystem() which uses the assembler to compute the LHS matrix, but sets up the RHS vector using the mass-matrix (constructed using a separate assembler) multiplied by a vector

Parameters

currentSolution	Solution at current time
computeMatrix	Whether to compute the matrix of the linear system

Implements AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 65 of file BidomainSolver.cpp.

References AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::Assemble(), DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedVectorFactory::CreateDistributedVector(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), PetscMatTools::Finalise(), HeartConfig::GetCapacitance(), PdeSimulationTime::GetPdeTimeStepInverse(), HeartConfig::GetSurfaceAreaToVolumeRatio(), HeartConfig::Instance(), HeartRegionCode::IsRegionBath(), DistributedVector::Restore(), and AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble().

Member Data Documentation

◆ mMassMatrix

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Mat BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mMassMatrix

private

Mass matrix, used to computing the RHS vector (actually: mass-matrix in voltage-voltage block, zero elsewhere)

Definition at line 86 of file BidomainSolver.hpp.

◆ mpBidomainAssembler

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainAssembler<ELEMENT_DIM,SPACE_DIM>* BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainAssembler

private

The bidomain assembler, used to set up the LHS matrix

Definition at line 95 of file BidomainSolver.hpp.

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().

◆ mpBidomainCorrectionTermAssembler

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM>* BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainCorrectionTermAssembler

private

If using state variable interpolation, points to an assembler to use in computing the correction term to apply to the RHS.

Definition at line 104 of file BidomainSolver.hpp.

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().

◆ mpBidomainNeumannSurfaceTermAssembler

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM>* BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainNeumannSurfaceTermAssembler

private

Assembler for surface integrals coming from any non-zero Neumann boundary conditions

Definition at line 98 of file BidomainSolver.hpp.

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().

◆ mVecForConstructingRhs

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec BidomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs

private

The vector multiplied by the mass matrix. Ie, if the linear system to be solved is Ax=b, this vector is z where b=Mz.

Definition at line 92 of file BidomainSolver.hpp.

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BidomainSolver()

◆ ~BidomainSolver()

Member Function Documentation

◆ InitialiseForSolve()

◆ SetupLinearSystem()

Member Data Documentation

◆ mMassMatrix

◆ mpBidomainAssembler

◆ mpBidomainCorrectionTermAssembler

◆ mpBidomainNeumannSurfaceTermAssembler

◆ mVecForConstructingRhs