#include <MonodomainPurkinjeSolver.hpp>

Inheritance diagram for MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
void	PrepareForSetupLinearSystem (Vec currentSolution)

virtual void	InitialiseForSolve (Vec initialSolution)

	MonodomainPurkinjeSolver (MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > pMesh, MonodomainTissue< ELEMENT_DIM, SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)

virtual	~MonodomainPurkinjeSolver ()

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	FinaliseLinearSystem (Vec currentSolution)

virtual void	FollowingSolveLinearSystem (Vec currentSolution)

LinearSystem *	GetLinearSystem ()

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

void	SetIdentityBlockToLhsMatrix ()

Private Attributes
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	mpMixedMesh

MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	mpMonodomainTissue

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	mpBoundaryConditions

MonodomainPurkinjeVolumeAssembler< ELEMENT_DIM, SPACE_DIM > *	mpVolumeAssembler

MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM > *	mpCableAssembler

NaturalNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM, 2 > *	mpNeumannSurfaceTermsAssembler

Mat	mMassMatrix

Vec	mVecForConstructingRhs

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

void	WriteOneStep (double time, Vec solution)

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 MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >

Solver class for Monodomain problems on tissues containing Purkinje fibres.

In such problems, there are a subset of nodes of the mesh which are labelled as Purkinje nodes (and 1D elements connecting them). There are two variables to be computed, the (normal, myocardium) transmembrane voltage (V), defined at ALL nodes of the mesh, and the Purkinje voltage (Vp), defined at the purkinje nodes. Hence, the Purkinje nodes have two variables defined on them.

For parallelisation/implementation reasons, we choose to have two variables to be defined at ALL nodes, introducing dummy variables Vp for non-Purkinje nodes. We set Vp = 0 at non-Purkinje nodes. Hence we solve for {V,Vp} at every node in the mesh, and PROBLEM_DIM=2. The linear system to be assembled, written as usual in block form but actually in striped form in the code, is:

[ A1 0 ][V ] = [b1] [ 0 A2 ][Vp] = [b2]

where each block is of size num_nodes.

A1 and b1 are obtained by integrating over 3D myocardium elements and are therefore exactly the same as in a normal monodomain problem.

Suppose the nodes are ordered such that all the Purkinje nodes are last. Then the matrix A2 needs to be of the form A2 = [I 0 ] [0 Ap] where the first block is of size num_non_purkinje_nodes, and the second is of size num_purkinje_nodes. Ap is obtained by assembling over 1D purkinje elements. After assembly we add in the identity block, which is just represents the equations Vp=0 for the dummy variables (non-purkinje nodes). Finally, we similarly have b2 = [0 ] [bp] where bp involves a loop over 1D purkinje elements.

This class implements the above, and is based on (but doesn't inherit from, as the PROBLEM_DIMENSION is different) MonodomainSolver.

Definition at line 89 of file MonodomainPurkinjeSolver.hpp.

Constructor & Destructor Documentation

◆ MonodomainPurkinjeSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver	(	MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	pBoundaryConditions
	)

Constructor

Parameters

pMesh	pointer to the mesh
pTissue	pointer to the tissue
pBoundaryConditions	pointer to the boundary conditions

Definition at line 210 of file MonodomainPurkinjeSolver.cpp.

References EXCEPTION, HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >::mMatrixIsConstant, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpCableAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpMixedMesh, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpVolumeAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication().

◆ ~MonodomainPurkinjeSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor

Definition at line 238 of file MonodomainPurkinjeSolver.cpp.

References PetscTools::Destroy().

Member Function Documentation

◆ InitialiseForSolve()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Overloaded InitialiseForSolve

Parameters

initialSolution initial solution

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 164 of file MonodomainPurkinjeSolver.cpp.

References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), NEVER_REACHED, and PetscTools::SetupMat().

◆ PrepareForSetupLinearSystem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem ( Vec currentSolution )

virtual

Overloaded PrepareForSetupLinearSystem() methods which gets the cell models to solve themselves

Parameters

currentSolution solution at current time

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 203 of file MonodomainPurkinjeSolver.cpp.

References PdeSimulationTime::GetNextTime(), and PdeSimulationTime::GetTime().

◆ SetIdentityBlockToLhsMatrix()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetIdentityBlockToLhsMatrix ( )

private

For the block in the LHS matrix corresponding to the Purkinje voltage at myocardium nodes: this block is zero after all elements are assembled so, so we set it to be the identity block. This is done by just checking which rows of the matrix has zero diagonal values.

Definition at line 140 of file MonodomainPurkinjeSolver.cpp.

References PetscTools::Destroy(), PetscVecTools::GetElement(), PetscMatTools::SetElement(), and PetscMatTools::SwitchWriteMode().

◆ SetupLinearSystem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeSolver< 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 44 of file MonodomainPurkinjeSolver.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::GetPurkinjeCapacitance(), HeartConfig::GetPurkinjeSurfaceAreaToVolumeRatio(), HeartConfig::GetSurfaceAreaToVolumeRatio(), HeartConfig::Instance(), DistributedVector::Restore(), and AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble().

Member Data Documentation

◆ mMassMatrix

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Mat MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mMassMatrix

private

The mass matrix, used to computing the RHS vector

Definition at line 123 of file MonodomainPurkinjeSolver.hpp.

◆ mpBoundaryConditions

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions

private

Boundary conditions

Definition at line 103 of file MonodomainPurkinjeSolver.hpp.

◆ mpCableAssembler

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainPurkinjeCableAssembler<ELEMENT_DIM,SPACE_DIM>* MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpCableAssembler

private

The cable element assembler, used to set up cable integral parts of the LHS matrix

Definition at line 114 of file MonodomainPurkinjeSolver.hpp.

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

◆ mpMixedMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpMixedMesh

private

Saved pointer to the mesh in this class, as the pointer saved in the parent class (AbstractDynamicLinearPdeSolver::mpMesh) is not declared to be a pointer to a mixed mesh

Definition at line 97 of file MonodomainPurkinjeSolver.hpp.

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