#include <ExtendedBidomainSolver.hpp>

Inheritance diagram for ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >:

Collaboration diagram for ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >:

Public Member Functions
	ExtendedBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > pMesh, ExtendedBidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, 3 > *pBoundaryConditions)

	~ExtendedBidomainSolver ()

Public Member Functions inherited from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >
	AbstractExtendedBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, ExtendedBidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *pBcc)

virtual	~AbstractExtendedBidomainSolver ()

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

void	SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)

BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 3 > *	GetBoundaryConditions ()

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
	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	InitialiseForSolve (Vec initialSolution)

void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)

Private Attributes
Mat	mMassMatrix

Vec	mVecForConstructingRhs

ExtendedBidomainAssembler < ELEM_DIM, SPACE_DIM > *	mpExtendedBidomainAssembler

ExtendedBidomainNeumannSurfaceTermAssembler < ELEM_DIM, SPACE_DIM > *	mpExtendedBidomainNeumannSurfaceTermAssembler

Additional Inherited Members
Protected Member Functions inherited from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >
void	InitialiseForSolve (Vec initialSolution)

virtual void	CheckCompatibilityCondition ()

void	PrepareForSetupLinearSystem (Vec existingSolution)

virtual void	FinaliseLinearSystem (Vec existingSolution)

virtual Vec	GenerateNullBasis () const

Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes inherited from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >
bool	mBathSimulation

ExtendedBidomainTissue < SPACE_DIM > *	mpExtendedBidomainTissue

BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 3 > *	mpBoundaryConditions

ExtendedBidomainAssembler < ELEMENT_DIM, SPACE_DIM > *	mpExtendedBidomainAssembler

HeartConfig *	mpConfig

bool	mNullSpaceCreated

std::vector< unsigned >	mFixedExtracellularPotentialNodes

unsigned	mRowForAverageOfPhiZeroed

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
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 ELEM_DIM, unsigned SPACE_DIM>
class ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >

An extended bidomain solver, which computes the right-hand-side (RHS) vector of the linear system to be solved using matrix-vector products.

Definition at line 59 of file ExtendedBidomainSolver.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::ExtendedBidomainSolver	(	bool	bathSimulation,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		ExtendedBidomainTissue< SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *	pBoundaryConditions
	)

Constructor

Parameters

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

Definition at line 184 of file ExtendedBidomainSolver.cpp.

References EXCEPTION, AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mBathSimulation, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainAssembler, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainNeumannSurfaceTermAssembler, AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainTissue, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< SPACE_DIM >::SetCacheReplication().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Destructor

Definition at line 211 of file ExtendedBidomainSolver.cpp.

References PetscTools::Destroy().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

privatevirtual

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

Parameters

initialSolution initial solution

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 42 of file ExtendedBidomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void ExtendedBidomainSolver< 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

Todo:: turn these into exceptions somewhere else

The following line should also have

intracellular_stimulus_first_cell - intracellular_stimulus_second_cell in the summation, but they are zero...

Implements AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 64 of file ExtendedBidomainSolver.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(), PdeSimulationTime::GetPdeTimeStep(), DistributedVector::Restore(), and AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble().

Member Data Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

Mat ExtendedBidomainSolver< ELEM_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 66 of file ExtendedBidomainSolver.hpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

ExtendedBidomainAssembler<ELEM_DIM,SPACE_DIM>* ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainAssembler

private

The bidomain assembler, used to set up the LHS matrix

Definition at line 75 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

ExtendedBidomainNeumannSurfaceTermAssembler<ELEM_DIM,SPACE_DIM>* ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainNeumannSurfaceTermAssembler

private

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

Definition at line 78 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

Vec ExtendedBidomainSolver< ELEM_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 72 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver().

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

heart/src/solver/electrics/extended_bidomain/ExtendedBidomainSolver.hpp
heart/src/solver/electrics/extended_bidomain/ExtendedBidomainSolver.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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