MonodomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <MonodomainSolver.hpp>

Inherits AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >.

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, unsigned numQuadPoints=2)
	~MonodomainSolver ()
Private Member Functions
void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)
Private Attributes
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	mpMonodomainTissue
unsigned	mNumQuadPoints
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

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, one to assemble the LHS matrix, (chi*C/dt) M + K, and also to compute c_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 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 64 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,
		unsigned	numQuadPoints = `2`
	)			`[inline]`

Constructor

Parameters:

	pMesh	pointer to the mesh
	pTissue	pointer to the tissue
	pBoundaryConditions	pointer to the boundary conditions
	numQuadPoints	number of quadrature points (defaults to 2)

Definition at line 178 of file MonodomainSolver.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::~MonodomainSolver ( ) [inline]

Destructor

Definition at line 214 of file MonodomainSolver.cpp.

References MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mMassMatrix, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainAssembler, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainCorrectionTermAssembler, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler, and MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve ( Vec initialSolution ) [inline, virtual]

Overloaded InitialiseForSolve

Parameters:

initialSolution

initial solution

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 130 of file MonodomainSolver.cpp.

References HeartConfig::Instance(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mMassMatrix, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, LinearSystem::rGetRhsVector(), LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetMatrixIsSymmetric(), LinearSystem::SetPcType(), LinearSystem::SetRelativeTolerance(), PetscTools::SetupMat(), and LinearSystem::SetUseFixedNumberIterations().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem ( Vec currentSolution ) [inline, 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 169 of file MonodomainSolver.cpp.

References PdeSimulationTime::GetPdeTimeStep(), PdeSimulationTime::GetTime(), and MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem	(	Vec	currentSolution,
		bool	computeMatrix
	)			`[inline, private, virtual]`

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 35 of file MonodomainSolver.cpp.

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 94 of file MonodomainSolver.hpp.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::~MonodomainSolver().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mNumQuadPoints [private]

Number of quadrature points per dimension (only saved so it can be passed to the assembler)

Definition at line 76 of file MonodomainSolver.hpp.

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

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 79 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 82 of file MonodomainSolver.hpp.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and 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 91 of file MonodomainSolver.hpp.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and 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 70 of file MonodomainSolver.hpp.

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

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 85 of file MonodomainSolver.hpp.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and 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 99 of file MonodomainSolver.hpp.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and 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

MonodomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

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 >