#include <AbstractExtendedBidomainSolver.hpp>

Inheritance diagram for AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

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)

virtual	~AbstractExtendedBidomainSolver ()

void	SetFixedExtracellularPotentialNodes (std::vector< unsigned > fixedExtracellularPotentialNodes)

void	SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *	GetBoundaryConditions ()

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
	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	FollowingSolveLinearSystem (Vec currentSolution)

virtual void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)=0

LinearSystem *	GetLinearSystem ()

Protected Member Functions
void	InitialiseForSolve (Vec initialSolution)

virtual void	CheckCompatibilityCondition ()

void	PrepareForSetupLinearSystem (Vec existingSolution)

virtual void	FinaliseLinearSystem (Vec existingSolution)

virtual Vec	GenerateNullBasis () const

Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes
bool	mBathSimulation

ExtendedBidomainTissue< SPACE_DIM > *	mpExtendedBidomainTissue

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *	mpBoundaryConditions

ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM > *	mpExtendedBidomainAssembler

HeartConfig *	mpConfig

bool	mNullSpaceCreated

std::vector< unsigned >	mFixedExtracellularPotentialNodes

unsigned	mRowForAverageOfPhiZeroed

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >
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 AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >

Abstract class with shared functionalities for different extended bidomain solvers.

Definition at line 50 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
	)

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

Definition at line 202 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 ( )

virtual

Destructor.

Definition at line 227 of file AbstractExtendedBidomainSolver.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition ( )

protectedvirtual

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 166 of file AbstractExtendedBidomainSolver.cpp.

References DistributedVector::Begin(), DistributedVector::End(), and EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem ( Vec existingSolution )

protectedvirtual

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 111 of file AbstractExtendedBidomainSolver.cpp.

References PetscTools::Destroy().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis ( ) const

protectedvirtual

Returns: vector for null basis

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

Definition at line 86 of file AbstractExtendedBidomainSolver.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), and DistributedVector::Restore().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

inline

Returns: the boundary conditions being used

Definition at line 186 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 )

protectedvirtual

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 >.

Definition at line 39 of file AbstractExtendedBidomainSolver.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem ( Vec existingSolution )

protectedvirtual

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 80 of file AbstractExtendedBidomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 232 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 )

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 264 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 57 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 82 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 76 of file AbstractExtendedBidomainSolver.hpp.

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

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 64 of file AbstractExtendedBidomainSolver.hpp.

Referenced by 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 73 of file AbstractExtendedBidomainSolver.hpp.

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

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)

Definition at line 70 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 61 of file AbstractExtendedBidomainSolver.hpp.

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 90 of file AbstractExtendedBidomainSolver.hpp.

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

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 >