AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractExtendedBidomainSolver.hpp>

Inherits AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >.

Collaboration diagram for AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractExtendedBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, ExtendedBidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *pBcc, unsigned numQuadPoints=2)
virtual	~AbstractExtendedBidomainSolver ()
void	SetFixedExtracellularPotentialNodes (std::vector< unsigned > fixedExtracellularPotentialNodes)
void	SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)
BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 3 > *	GetBoundaryConditions ()
Protected Member Functions
void	InitialiseForSolve (Vec initialSolution)
virtual void	CheckCompatibilityCondition ()
void	PrepareForSetupLinearSystem (Vec existingSolution)
virtual void	FinaliseLinearSystem (Vec existingSolution)
virtual Vec	GenerateNullBasis () const
Protected Attributes
bool	mBathSimulation
ExtendedBidomainTissue < SPACE_DIM > *	mpExtendedBidomainTissue
BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 3 > *	mpBoundaryConditions
unsigned	mNumQuadPoints
ExtendedBidomainAssembler < ELEMENT_DIM, SPACE_DIM > *	mpExtendedBidomainAssembler
HeartConfig *	mpConfig
bool	mNullSpaceCreated
std::vector< unsigned >	mFixedExtracellularPotentialNodes
unsigned	mRowForAverageOfPhiZeroed

Detailed Description

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

Abstract class with shared functionalities for different extended bidomain solvers.

Definition at line 43 of file AbstractExtendedBidomainSolver.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver	(	bool	bathSimulation,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		ExtendedBidomainTissue< SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *	pBcc,
		unsigned	numQuadPoints = `2`
	)			`[inline]`

Constructor stores the mesh and pde and sets up boundary conditions.

Parameters:

	bathSimulation	Whether the simulation has a perfusing bath
	pMesh	pointer to the mesh
	pTissue	pointer to the PDE
	pBcc	pointer to the boundary conditions container
	numQuadPoints	number of quadrature points (defaults to 2)

Definition at line 198 of file AbstractExtendedBidomainSolver.cpp.

References HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >::mMatrixIsConstant, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainAssembler, and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Destructor.

Definition at line 225 of file AbstractExtendedBidomainSolver.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition ( ) [inline, protected, virtual]

Checks whether the linear system will have a solution (if so, infinite solutions) instead of zero solutions. The condition is, if the linear system is Ax=b, that sum b_i over for all the PHI_E components (ie i=2,5,8,..) is zero.

This check is not made if running in parallel, or in debug mode.

The reason why the sum must be zero: the Fredholm alternative states that a singular system Ax=b has a solution if and only if v.b=0 for all v in ker(A) (ie all v such that Av=b). The nullspace ker(A) is one dimensional with basis vector v = (0,0,1,0,0,1....0,0,1), so v.b = sum_{i=2,5,8..} b_i.

Definition at line 162 of file AbstractExtendedBidomainSolver.cpp.

References DistributedVector::Begin(), DistributedVector::End(), EXCEPTION, AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryConditions(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed, and LinearSystem::rGetRhsVector().

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem ( Vec existingSolution ) [inline, protected, virtual]

FinaliseAssembleSystem

Called at the end of SetupLinearSystem(), before the system is solver Here, used to avoid problems with phi_e drifting by one of 3 methods: pinning nodes, using a null space, or using an "average phi_e = 0" row.

Parameters:

existingSolution

Solution at current time

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 108 of file AbstractExtendedBidomainSolver.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis ( ) const [inline, protected, virtual]

GenerateNullBasis

Called by FinaliseAssembleSystem to get the null basis to use for the particular formulation of the extended idomain equations used.

Definition at line 82 of file AbstractExtendedBidomainSolver.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and DistributedVector::Restore().

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions ( ) [inline]

Get the boundary conditions being used

Definition at line 187 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Create the linear system object if it hasn't been already. Can use an initial solution as PETSc template, or base it on the mesh size.

Parameters:

initialSolution

an initial guess

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Reimplemented in ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

Definition at line 32 of file AbstractExtendedBidomainSolver.cpp.

References HeartConfig::GetAbsoluteTolerance(), HeartConfig::GetRelativeTolerance(), HeartConfig::Instance(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed, LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetMatrixIsSymmetric(), LinearSystem::SetPcType(), and LinearSystem::SetRelativeTolerance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem ( Vec existingSolution ) [inline, protected, virtual]

PrepareForSetupLinearSystem

Called at the beginning of SetupLinearSystem(). Here, used to integrate cell model odes.

Parameters:

existingSolution

is the voltage to feed into the cell models

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 74 of file AbstractExtendedBidomainSolver.cpp.

References PdeSimulationTime::GetPdeTimeStep(), PdeSimulationTime::GetTime(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainTissue.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned > fixedExtracellularPotentialNodes ) [inline]

Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.

Parameters:

fixedExtracellularPotentialNodes

the nodes to be fixed.

NOTE: currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.

Definition at line 230 of file AbstractExtendedBidomainSolver.cpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), EXCEPTION, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mFixedExtracellularPotentialNodes, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ResetDirichletCommunication().

Referenced by ExtendedBidomainProblem< DIM >::CreateSolver().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed ( unsigned rowMeanPhiEZero ) [inline]

Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. It is set from the problem class.

Parameters:

rowMeanPhiEZero

indicates the row of the matrix to be replaced.

Definition at line 262 of file AbstractExtendedBidomainSolver.cpp.

References EXCEPTION, and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.

Referenced by ExtendedBidomainProblem< DIM >::CreateSolver().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mBathSimulation [protected]

Whether the simulation involves a perfusing bath

Definition at line 50 of file AbstractExtendedBidomainSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mFixedExtracellularPotentialNodes [protected]

Used when pinning nodes to resolve singularity. This vector indicates the global indices of the nodes to be pinned

Definition at line 81 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated [protected]

Used when intialising null-space solver to resolve singularity

Definition at line 75 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNumQuadPoints [protected]

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

Definition at line 63 of file AbstractExtendedBidomainSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions [protected]

Boundary conditions

Definition at line 57 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractExtendedBidomainSolver< DIM, DIM >::GetBoundaryConditions(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected]

Local cache of the configuration singleton instance

Definition at line 72 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainAssembler<ELEMENT_DIM,SPACE_DIM>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainAssembler [protected]

The extended bidomain assembler, used to set up the LHS matrix, (but not used to set uo the RHS)

Reimplemented in ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.

Definition at line 69 of file AbstractExtendedBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ExtendedBidomainTissue<SPACE_DIM>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainTissue [protected]

The tissue object over which to solve the equation

Definition at line 54 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed [protected]

Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. This number indicates the row of the matrix to be replaced. This is INT_MAX if unset. It is set from the problem class.

Definition at line 89 of file AbstractExtendedBidomainSolver.hpp.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

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

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

AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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