AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractBidomainSolver.hpp>

Inheritance diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:

List of all members.

Public Member Functions

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

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)

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 Attributes

bool mBathSimulation

BidomainTissue< SPACE_DIM > * mpBidomainTissue

BoundaryConditionsContainer
< ELEMENT_DIM, SPACE_DIM, 2 > * mpBoundaryConditions

BidomainAssembler< ELEMENT_DIM,
SPACE_DIM > * mpBidomainAssembler

unsigned mNumQuadPoints

bool mNullSpaceCreated

HeartConfig * mpConfig

std::vector< unsigned > mFixedExtracellularPotentialNodes

unsigned mRowForAverageOfPhiZeroed

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 43 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,
		unsigned	numQuadPoints = `2`
	)			`[inline]`

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
	numQuadPoints	number of Gaussian quadrature points in each dimension

Definition at line 242 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 >::mpBidomainAssembler, 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 ( ) [inline, virtual]

Destructor

Definition at line 269 of file AbstractBidomainSolver.cpp.

References AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainAssembler.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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

Todo:: : block preconditioners only make sense in Bidomain... Add some warning/error message

Todo:: : #1082 only works if you know about the whole mesh.

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Reimplemented in MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >.

Definition at line 35 of file AbstractBidomainSolver.cpp.

References PetscTools::AmMaster(), HeartRegionCode::BATH, HeartConfig::GetAbsoluteTolerance(), HeartConfig::GetRelativeTolerance(), AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), PetscTools::IsSequential(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpLinearSystem, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed, LinearSystem::SetAbsoluteTolerance(), LinearSystem::SetKspType(), LinearSystem::SetMatrixIsSymmetric(), LinearSystem::SetPcType(), LinearSystem::SetRelativeTolerance(), and TERMINATE.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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=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.

Todo:: #1327 This could be a collective MPI-like operation

Definition at line 212 of file AbstractBidomainSolver.cpp.

References EXCEPTION, and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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 112 of file AbstractBidomainSolver.cpp.

References PdeSimulationTime::GetTime(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >::mDt, and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 144 of file AbstractBidomainSolver.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec AbstractBidomainSolver< 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 bidomain equations used.

Definition at line 119 of file AbstractBidomainSolver.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath	(	bool	computeMatrix,
		bool	computeVector
	)			`[inline, 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.

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

Todo:: : #1215 #1328 this seems not to be an issue anymore. Document and remove code.

Todo:: #1328 This code may no longer be needed since all the operations in the following loop may apply only to local elements. MatSetValue and VecSetValue are not collective...

Definition at line 324 of file AbstractBidomainSolver.cpp.

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

Referenced by MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractBidomainSolver< 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 278 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 ) [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. Ought to be an odd number...

Definition at line 311 of file AbstractBidomainSolver.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions ( ) [inline]

Get the boundary conditions being used

Definition at line 196 of file AbstractBidomainSolver.hpp.

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

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 206 of file AbstractBidomainSolver.hpp.

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

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 47 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath(), BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseAssembler(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

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 50 of file AbstractBidomainSolver.hpp.

Referenced by BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseAssembler(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem(), and MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

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 53 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< DIM, DIM >::GetBoundaryConditions(), AbstractBidomainSolver< DIM, DIM >::ResetBoundaryConditionsContainer(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BidomainAssembler<ELEMENT_DIM,SPACE_DIM>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainAssembler [protected]

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

Definition at line 59 of file AbstractBidomainSolver.hpp.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver(), BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseAssembler(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::~AbstractBidomainSolver().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractBidomainSolver< 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 65 of file AbstractBidomainSolver.hpp.

Referenced by BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseAssembler(), and MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

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 68 of file AbstractBidomainSolver.hpp.

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

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 71 of file AbstractBidomainSolver.hpp.

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

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 76 of file AbstractBidomainSolver.hpp.

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

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 83 of file AbstractBidomainSolver.hpp.

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

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

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


Public Member Functions
	AbstractBidomainSolver (bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BidomainTissue< SPACE_DIM > pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions, unsigned numQuadPoints=2)
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)
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 Attributes
bool	mBathSimulation
BidomainTissue< SPACE_DIM > *	mpBidomainTissue
BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 2 > *	mpBoundaryConditions
BidomainAssembler< ELEMENT_DIM, SPACE_DIM > *	mpBidomainAssembler
unsigned	mNumQuadPoints
bool	mNullSpaceCreated
HeartConfig *	mpConfig
std::vector< unsigned >	mFixedExtracellularPotentialNodes
unsigned	mRowForAverageOfPhiZeroed

AbstractBidomainSolver< 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 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 >