Chaste Release::3.1
Public Member Functions | Private Member Functions | Private Attributes
ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM > Class Template Reference

#include <ExtendedBidomainSolver.hpp>

Inheritance diagram for ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >:
Collaboration diagram for ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >:

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 60 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 
)

Constructor

Parameters:
bathSimulationWhether the simulation involves a perfusing bath
pMeshpointer to the mesh
pTissuepointer to the PDE
pBoundaryConditionspointer to the boundary conditions
numQuadPointsnumber of quadrature points (defaults to 2)

Definition at line 188 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 ( )

Destructor

Definition at line 216 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) [private, virtual]

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

Parameters:
initialSolutioninitial solution

Reimplemented from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_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 
) [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:
currentSolutionSolution at current time
computeMatrixWhether 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 65 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 67 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

Reimplemented from AbstractExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

Definition at line 76 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 79 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 73 of file ExtendedBidomainSolver.hpp.

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

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