#include <MonodomainSolver.hpp>

Inheritance diagram for MonodomainSolver< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainSolver< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
void	PrepareForSetupLinearSystem (Vec currentSolution)

virtual void	InitialiseForSolve (Vec initialSolution)

	MonodomainSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, MonodomainTissue< ELEMENT_DIM, SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBoundaryConditions)

virtual	~MonodomainSolver ()

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
	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)

Private Attributes
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	mpMonodomainTissue

BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 1 > *	mpBoundaryConditions

MonodomainAssembler < ELEMENT_DIM, SPACE_DIM > *	mpMonodomainAssembler

NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, 1 > *	mpNeumannSurfaceTermsAssembler

MonodomainCorrectionTermAssembler < ELEMENT_DIM, SPACE_DIM > *	mpMonodomainCorrectionTermAssembler

Mat	mMassMatrix

Vec	mVecForConstructingRhs

Additional Inherited Members
Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
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 MonodomainSolver< ELEMENT_DIM, SPACE_DIM >

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

The discretised monodomain equation leads to the linear system (see FEM implementations document)

( (chi*C/dt) M + K ) V^{n+1} = (chi*C/dt) M V^{n} + M F^{n} + c_surf

where chi is the surface-area to volume ratio, C the capacitance, dt the timestep M the mass matrix, K the stiffness matrix, V^{n} the vector of voltages at time n, F^{n} the vector of (chi*Iionic + Istim) at each node, and c_surf a vector arising from any surface stimuli (usually zero).

This solver uses two assemblers, MonodomainAssembler to assemble the LHS matrix, [(chi*C/dt) M + K], and also to compute c_surf, and MassMatrixAssembler to assemble the mass matrix M used on the RHS. Note that MonodomainAssembler itself calls: MassMatrixAssembler for M (as this class does directly for RHS), and MonodomainStiffnessMatrixAssembler for K.

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 wiki page ChasteGuides/StateVariableInterpolation for more details on this. In this case the equation is ( (chi*C/dt) M + K ) V^{n+1} = (chi*C/dt) M V^{n} + M F^{n} + c_surf + c_correction and another assembler is used to create the c_correction.

Definition at line 74 of file MonodomainSolver.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *	pBoundaryConditions
	)

Constructor

Parameters

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

Definition at line 183 of file MonodomainSolver.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor

Definition at line 217 of file MonodomainSolver.cpp.

References PetscTools::Destroy().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< 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 137 of file MonodomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< 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 176 of file MonodomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< 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 42 of file MonodomainSolver.cpp.

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

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Mat MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mMassMatrix

private

The mass matrix, used to computing the RHS vector

Definition at line 98 of file MonodomainSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,1>* MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions

private

Boundary conditions

Definition at line 83 of file MonodomainSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>* MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainAssembler

private

The monodomain assembler, used to set up the LHS matrix

Definition at line 86 of file MonodomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM>* MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainCorrectionTermAssembler

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 95 of file MonodomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue

private

Monodomain tissue class (collection of cells, and conductivities)

Definition at line 80 of file MonodomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

NaturalNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM,1>* MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler

private

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

Definition at line 89 of file MonodomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs

private

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

Definition at line 103 of file MonodomainSolver.hpp.

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

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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