Chaste  Release::2017.1
AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#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
 
LinearSystemGetLinearSystem ()
 

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
 
HeartConfigmpConfig
 
bool mNullSpaceCreated
 
std::vector< unsignedmFixedExtracellularPotentialNodes
 
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
 
AbstractTimeAdaptivityControllermpTimeAdaptivityController
 
bool mOutputToVtk
 
bool mOutputToParallelVtk
 
bool mOutputToTxt
 
std::string mOutputDirectory
 
std::string mFilenamePrefix
 
unsigned mPrintingTimestepMultiple
 
Hdf5DataWritermpHdf5Writer
 
std::vector< int > mVariableColumnIds
 
- Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
LinearSystemmpLinearSystem
 
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 
)
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
existingSolutionSolution 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
initialSolutionan 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
existingSolutionis 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
fixedExtracellularPotentialNodesthe 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
rowMeanPhiEZeroindicates 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
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: