ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM > Class Template Reference

#include <ExtendedBidomainSolver.hpp>

Inherits AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

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List of all members.

Public Member Functions

 ExtendedBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > *pMesh, ExtendedBidomainTissue< SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, 3 > *pBoundaryConditions, unsigned numQuadPoints=2)
 ~ExtendedBidomainSolver ()

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

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 53 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,
unsigned  numQuadPoints = 2 
) [inline]

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
numQuadPoints number of quadrature points (defaults to 2)

Definition at line 181 of file ExtendedBidomainSolver.cpp.

References EXCEPTION, AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mBathSimulation, AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mNumQuadPoints, 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 (  )  [inline]

Destructor

Definition at line 209 of file ExtendedBidomainSolver.cpp.

References ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mMassMatrix, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainAssembler, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpExtendedBidomainNeumannSurfaceTermAssembler, and ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mVecForConstructingRhs.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve ( Vec  initialSolution  )  [inline, private, virtual]

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

Parameters:
initialSolution initial solution

Reimplemented from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

Definition at line 35 of file ExtendedBidomainSolver.cpp.

References ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mMassMatrix, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mVecForConstructingRhs, LinearSystem::rGetRhsVector(), and PetscTools::SetupMat().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver< 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

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 58 of file ExtendedBidomainSolver.cpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::Assemble(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::AssembleMatrix(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::AssembleVector(), DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedVectorFactory::CreateDistributedVector(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), PetscMatTools::Finalise(), LinearSystem::FinaliseLhsMatrix(), LinearSystem::FinaliseRhsVector(), PdeSimulationTime::GetPdeTimeStep(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mMassMatrix, AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mpBoundaryConditions, 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 >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::mVecForConstructingRhs, AbstractFeSurfaceIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ResetBoundaryConditionsContainer(), DistributedVector::Restore(), LinearSystem::rGetLhsMatrix(), LinearSystem::rGetRhsVector(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetVectorToAssemble(), and LinearSystem::SwitchWriteModeLhsMatrix().

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 60 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::InitialiseForSolve(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::SetupLinearSystem(), and ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::~ExtendedBidomainSolver().

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

Reimplemented from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

Definition at line 69 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::SetupLinearSystem(), and 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 72 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::SetupLinearSystem(), and 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 66 of file ExtendedBidomainSolver.hpp.

Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::InitialiseForSolve(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::SetupLinearSystem(), and ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::~ExtendedBidomainSolver().

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