#include <AbstractBidomainSolver.hpp>

Inheritance diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)

virtual	~AbstractBidomainSolver ()

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

void	SetRowForAverageOfPhiZeroed (unsigned rowMeanPhiEZero)

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	GetBoundaryConditions ()

void	ResetBoundaryConditionsContainer (BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc)

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
	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

void	FinaliseForBath (bool computeMatrix, bool computeVector)

Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes
bool	mBathSimulation

BidomainTissue< SPACE_DIM > *	mpBidomainTissue

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	mpBoundaryConditions

bool	mNullSpaceCreated

HeartConfig *	mpConfig

std::vector< unsigned >	mFixedExtracellularPotentialNodes

unsigned	mRowForAverageOfPhiZeroed

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >
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 AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >

Abstract Bidomain class containing some common functionality Inherits from AbstractDynamicLinearPdeSolver so child classes must implement SetupLinearSystem()

Definition at line 49 of file AbstractBidomainSolver.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver	(	bool	bathSimulation,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BidomainTissue< SPACE_DIM > *	pTissue,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *	pBoundaryConditions
	)

Constructor

Parameters

bathSimulation	whether the simulation has a perfusing bath
pMesh	pointer to the mesh
pTissue	pointer to the tissue
pBoundaryConditions	pointer to the boundary conditions container

Definition at line 234 of file AbstractBidomainSolver.cpp.

References HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >::mMatrixIsConstant, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::~AbstractBidomainSolver ( )

virtual

Destructor

Definition at line 257 of file AbstractBidomainSolver.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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=1,3,5,..) 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 = (0,1,0,1....,0,1), so v.b = sum_{i=1,3,5..} b_i.

Definition at line 198 of file AbstractBidomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath	(	bool	computeMatrix,
		bool	computeVector
	)

protected

Apply any changes needed to the linear system for problems that include a bath. Checks the voltage-voltage block of the matrix at bath-nodes is zero, and puts a 1 on the diagonal.

Precondition: This method requires the system matrix to be in assembled state. Call FinaliseLhsMatrix() on your linear system if required.

Parameters

computeMatrix	Whether the LHS matrix of the linear system has been computed
computeVector	Whether the RHS vector of the linear system has been computed

Definition at line 307 of file AbstractBidomainSolver.cpp.

References LinearSystem::GetLhsMatrix(), LinearSystem::GetMatrixElement(), LinearSystem::GetOwnershipRange(), LinearSystem::GetSize(), HeartRegionCode::IsRegionBath(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mBathSimulation, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, LinearSystem::rGetLhsMatrix(), LinearSystem::rGetRhsVector(), PetscMatTools::SetElement(), and PetscVecTools::SetElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protectedvirtual

FinaliseAssembleSystem

Called at the end of SetupLinearSystem(), before the system is solved.

If no dirichlet boundary conditions (i) Check compatibility condition to check we are solving a linear system that can be solved Then either: (a) If not setting average(phi)=0, we are solving a singular system, so set up a null space. (b) Apply average(phi)=0 constraint by altering the last row, to get a non-singular system

Parameters

existingSolution Solution at current time

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 129 of file AbstractBidomainSolver.cpp.

References PetscTools::Destroy().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protectedvirtual

Returns: null basis vector

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

Definition at line 105 of file AbstractBidomainSolver.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,2>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions ( )

inline

Returns: the boundary conditions being used

Definition at line 192 of file AbstractBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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 >.

Reimplemented in BidomainSolver< ELEMENT_DIM, SPACE_DIM >.

Definition at line 43 of file AbstractBidomainSolver.cpp.

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

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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 99 of file AbstractBidomainSolver.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::ResetBoundaryConditionsContainer ( BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * pBcc )

inline

Reset the boundary conditions being used. The caller should deal with deleting the old bcc pointer.

Parameters

pBcc	The new boundary conditions container.

Definition at line 202 of file AbstractBidomainSolver.hpp.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep(), and BidomainProblem< DIM >::OnEndOfTimestep().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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 262 of file AbstractBidomainSolver.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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. Ought to be an odd number...

Definition at line 295 of file AbstractBidomainSolver.cpp.

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

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mBathSimulation

protected

Whether the simulation involves a perfusing bath

Definition at line 53 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> AbstractBidomainSolver< 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 70 of file AbstractBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated

protected

Used when intialising null-space solver to resolve singularity

Definition at line 62 of file AbstractBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainTissue<SPACE_DIM>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue

protected

The PDE to be solved.

Definition at line 56 of file AbstractBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions

protected

Boundary conditions

Definition at line 59 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< DIM, DIM >::GetBoundaryConditions().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig

protected

Local cache of the configuration singleton instance

Definition at line 65 of file AbstractBidomainSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractBidomainSolver< 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 77 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

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

heart/src/solver/electrics/bidomain/AbstractBidomainSolver.hpp
heart/src/solver/electrics/bidomain/AbstractBidomainSolver.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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