#include <BidomainProblem.hpp>

Inheritance diagram for BidomainProblem< DIM >:

Collaboration diagram for BidomainProblem< DIM >:

Public Member Functions
	BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false)

	BidomainProblem ()

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

void	SetNodeForAverageOfPhiZeroed (unsigned node)

BidomainTissue< DIM > *	GetBidomainTissue ()

void	WriteInfo (double time)

virtual void	DefineWriterColumns (bool extending)

virtual void	WriteOneStep (double time, Vec voltageVec)

void	PreSolveChecks ()

void	AtBeginningOfTimestep (double time)

void	OnEndOfTimestep (double time)

void	SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes)

template<class Archive >
void	LoadExtraArchiveForBidomain (Archive &archive, unsigned version)

bool	GetHasBath ()

void	SetElectrodes ()

Public Member Functions inherited from AbstractCardiacProblem< DIM, DIM, 2 >
	AbstractCardiacProblem (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

	AbstractCardiacProblem ()

virtual	~AbstractCardiacProblem ()

void	Initialise ()

void	SetNodesPerProcessorFilename (const std::string &rFilename)

void	SetBoundaryConditionsContainer (BccType pBcc)

void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

void	PrintOutput (bool rPrintOutput)

void	SetWriteInfo (bool writeInfo=true)

Vec	GetSolution ()

DistributedVector	GetSolutionDistributedVector ()

double	GetCurrentTime ()

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > *	GetTissue ()

void	Solve ()

void	CloseFilesAndPostProcess ()

void	DefineExtraVariablesWriterColumns (bool extending)

void	WriteExtraVariablesOneStep ()

bool	InitialiseWriter ()

void	SetUseHdf5DataWriterCache (bool useCache=true)

void	SetHdf5DataWriterTargetChunkSizeAndAlignment (hsize_t size)

void	SetOutputNodes (std::vector< unsigned > &rNodesToOutput)

Hdf5DataReader	GetDataReader ()

void	SetUseTimeAdaptivityController (bool useAdaptivity, AbstractTimeAdaptivityController *pController=NULL)

void	LoadExtraArchive (Archive &archive, unsigned version)

void	AddOutputModifier (boost::shared_ptr< AbstractOutputModifier > pOutputModifier)

Public Member Functions inherited from AbstractUntemplatedCardiacProblem
virtual	~AbstractUntemplatedCardiacProblem ()

Protected Member Functions
Vec	CreateInitialCondition ()

void	AnalyseMeshForBath ()

virtual AbstractCardiacTissue< DIM > *	CreateCardiacTissue ()

virtual AbstractDynamicLinearPdeSolver< DIM, DIM, 2 > *	CreateSolver ()

Protected Member Functions inherited from AbstractCardiacProblem< DIM, DIM, 2 >
virtual void	CreateMeshFromHeartConfig ()

Protected Attributes
BidomainTissue< DIM > *	mpBidomainTissue

std::vector< unsigned >	mFixedExtracellularPotentialNodes

unsigned	mExtracelluarColumnId

unsigned	mRowForAverageOfPhiZeroed

bool	mHasBath

boost::shared_ptr< Electrodes< DIM > >	mpElectrodes

AbstractBidomainSolver< DIM, DIM > *	mpSolver

Protected Attributes inherited from AbstractCardiacProblem< DIM, DIM, 2 >
std::string	mMeshFilename

bool	mAllocatedMemoryForMesh

bool	mWriteInfo

bool	mPrintOutput

std::vector< unsigned >	mNodesToOutput

unsigned	mVoltageColumnId

std::vector< unsigned >	mExtraVariablesId

unsigned	mTimeColumnId

unsigned	mNodeColumnId

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > *	mpCardiacTissue

BccType	mpBoundaryConditionsContainer

BccType	mpDefaultBoundaryConditionsContainer

AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpSolver

AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *	mpCellFactory

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

Vec	mSolution

double	mCurrentTime

AbstractTimeAdaptivityController *	mpTimeAdaptivityController

Hdf5DataWriter *	mpWriter

bool	mUseHdf5DataWriterCache

hsize_t	mHdf5DataWriterChunkSizeAndAlignment

std::vector< boost::shared_ptr< AbstractOutputModifier > >	mOutputModifiers

Private Member Functions
template<class Archive >
void	save (Archive &archive, const unsigned int version) const

template<class Archive >
void	load (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

class	TestPCTwoLevelsBlockDiagonal

class	TestBidomainWithBathProblem

class	TestCardiacSimulationArchiver

Detailed Description

template<unsigned DIM>
class BidomainProblem< DIM >

Class which specifies and solves a bidomain problem.

The solution vector is of the form: (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j.

Definition at line 65 of file BidomainProblem.hpp.

Constructor & Destructor Documentation

◆ BidomainProblem() [1/2]

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem	(	AbstractCardiacCellFactory< DIM > *	pCellFactory,
		bool	hasBath = `false`
	)

Constructor

Parameters

pCellFactory	User defined cell factory which shows how the pde should create cells.
hasBath	Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).

Definition at line 164 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

◆ BidomainProblem() [2/2]

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem ( )

Constructor just used for archiving

Definition at line 175 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

Member Function Documentation

◆ AnalyseMeshForBath()

template<unsigned DIM>

void BidomainProblem< DIM >::AnalyseMeshForBath ( )

protected

Annotate bath nodes with the correct region code, if a bath is present. Will throw if mHasBath is set but no bath is present in the mesh.

Definition at line 45 of file BidomainProblem.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetUnsignedAttribute(), HeartRegionCode::GetValidBathId(), HeartRegionCode::GetValidTissueId(), HeartConfig::Instance(), HeartRegionCode::IsRegionBath(), HeartRegionCode::IsRegionTissue(), PetscTools::ReplicateBool(), and HeartConfig::rGetBathIdentifiers().

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

◆ AtBeginningOfTimestep()

template<unsigned DIM>

void BidomainProblem< DIM >::AtBeginningOfTimestep ( double time )

virtual

Called at beginning of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch on the electrodes (if there are any).

Parameters

time	the current time

Todo:: #1159 #1324 heart/src/problem/AbstractCardiacProblem.hpp:657 expects both pointing at the same place when unarchiving

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 296 of file BidomainProblem.cpp.

◆ CreateCardiacTissue()

template<unsigned DIM>

AbstractCardiacTissue< DIM > * BidomainProblem< DIM >::CreateCardiacTissue ( )

protectedvirtual

Returns: a newly created bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 125 of file BidomainProblem.cpp.

References HeartConfig::Instance().

◆ CreateInitialCondition()

template<unsigned DIM>

Vec BidomainProblem< DIM >::CreateInitialCondition ( )

protectedvirtual

Create normal initial condition but overwrite V to zero for bath nodes, if there are any.

Returns: the newly created intial conditions vector

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 100 of file BidomainProblem.cpp.

References DistributedVector::Begin(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), DistributedVector::End(), HeartRegionCode::IsRegionBath(), and DistributedVector::Restore().

◆ CreateSolver()

template<unsigned DIM>

AbstractDynamicLinearPdeSolver< DIM, DIM, 2 > * BidomainProblem< DIM >::CreateSolver ( )

protectedvirtual

Returns: a newly created suitable bidomain solver

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 133 of file BidomainProblem.cpp.

◆ DefineWriterColumns()

template<unsigned DIM>

void BidomainProblem< DIM >::DefineWriterColumns ( bool extending )

virtual

Define what variables are written to the primary results file. Adds the extracellular potential.

Parameters

extending whether we are extending an existing results file

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 233 of file BidomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().

◆ GetBidomainTissue()

template<unsigned DIM>

BidomainTissue< DIM > * BidomainProblem< DIM >::GetBidomainTissue ( )

Returns: the pde. Can only be called after Initialise()

Definition at line 202 of file BidomainProblem.cpp.

◆ GetHasBath()

template<unsigned DIM>

bool BidomainProblem< DIM >::GetHasBath ( )

virtual

Returns: whether this is a bidomain problem with bath or not

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 383 of file BidomainProblem.cpp.

◆ load()

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Load the member variables from an archive.

Parameters

archive
version

Definition at line 97 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainTissue, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

◆ LoadExtraArchiveForBidomain()

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::LoadExtraArchiveForBidomain	(	Archive &	archive,
		unsigned	version
	)

Used when loading a set of archives written by a parallel simulation onto a single process. Loads data from the given process-specific archive (written by a non-master process) and merges it into our data.

Parameters

archive	the archive to load
version	the archive file version

Note: The process-specific archives currently contain the following data. If the layout changes, then this method will need to be altered, since it hard-codes knowledge of the order in which things are archived.

Stuff known by AbstractCardiacProblem
mpElectrodes->mpBoundaryConditionsContainer

This gets called by AbstractCardiacProblem::LoadExtraArchive when it's done the generic stuff.

Todo:: #1159 sanity check that the contents of p_bcc and mpElectrodes->GetBoundaryConditionsContainer() match.

Definition at line 299 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::mpElectrodes, and AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive().

◆ OnEndOfTimestep()

template<unsigned DIM>

void BidomainProblem< DIM >::OnEndOfTimestep ( double time )

virtual

Called at end of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch off the electrodes (if there are any).

Parameters

time	the current time

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 337 of file BidomainProblem.cpp.

References HeartConfig::Instance().

◆ PreSolveChecks()

template<unsigned DIM>

void BidomainProblem< DIM >::PreSolveChecks ( )

virtual

Performs a series of checks before solving. Checks that a suitable method of resolving the singularity is being used.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 259 of file BidomainProblem.cpp.

References EXCEPTION, HeartConfig::Instance(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().

◆ save()

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Save the member variables to an archive.

Parameters

archive
version

Definition at line 80 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainTissue, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

◆ SetElectrodes()

template<unsigned DIM>

void BidomainProblem< DIM >::SetElectrodes ( )

virtual

Set an electrode object (which provides boundary conditions). Only valid if there is a bath.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 279 of file BidomainProblem.cpp.

References HeartConfig::Instance().

◆ SetFixedExtracellularPotentialNodes()

template<unsigned DIM>

void BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned > nodes )

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

nodes 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 184 of file BidomainProblem.cpp.

◆ SetNodeForAverageOfPhiZeroed()

template<unsigned DIM>

void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned node )

Set which row of the linear system should be used to enforce the condition that the average of phi_e is zero. If not called, this condition will not be used.

Parameters

node	the mesh node index giving the row at which to impose the constraint

Definition at line 196 of file BidomainProblem.cpp.

◆ SetUpAdditionalStoppingTimes()

template<unsigned DIM>

void BidomainProblem< DIM >::SetUpAdditionalStoppingTimes ( std::vector< double > & rAdditionalStoppingTimes )

virtual

Method to fill in a vector of additional stopping times consisting of the times when the electrodes are to be turned on and off

Parameters

rAdditionalStoppingTimes reference to vector that will contain the on and off times for the electrodes

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 373 of file BidomainProblem.cpp.

◆ WriteInfo()

template<unsigned DIM>

void BidomainProblem< DIM >::WriteInfo ( double time )

virtual

Print out time and max/min voltage/phi_e values at current time.

Parameters

time	current time.

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 209 of file BidomainProblem.cpp.

References PetscTools::AmMaster(), and CHASTE_PETSC_NULLPTR.

◆ WriteOneStep()

template<unsigned DIM>

void BidomainProblem< DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)

virtual

Write one timestep of output data to the primary results file. Adds the extracellular potential to the results.

Parameters

time	the current time
voltageVec	the solution vector to write

friend

Definition at line 115 of file BidomainProblem.hpp.

◆ TestPCTwoLevelsBlockDiagonal

protected

We need to save the solver that is being used to be able to switch off the electrodes (by adding default boundary conditions to the solver)

Definition at line 155 of file BidomainProblem.hpp.

◆ mRowForAverageOfPhiZeroed

template<unsigned DIM>

unsigned BidomainProblem< DIM >::mRowForAverageOfPhiZeroed

protected

Another method of resolving the singularity in the bidomain equations. Specifies a row of the matrix at which to impose an extra condition.

Definition at line 129 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::load(), and BidomainProblem< DIM >::save().

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

heart/src/problem/AbstractCardiacProblem.hpp
heart/src/problem/BidomainProblem.hpp
heart/src/problem/BidomainProblem.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ BidomainProblem() [1/2]

◆ BidomainProblem() [2/2]

Member Function Documentation

◆ AnalyseMeshForBath()

◆ AtBeginningOfTimestep()

◆ CreateCardiacTissue()

◆ CreateInitialCondition()

◆ CreateSolver()

◆ DefineWriterColumns()

◆ GetBidomainTissue()

◆ GetHasBath()

◆ load()

◆ LoadExtraArchiveForBidomain()

◆ OnEndOfTimestep()

◆ PreSolveChecks()

◆ save()

◆ SetElectrodes()

◆ SetFixedExtracellularPotentialNodes()

◆ SetNodeForAverageOfPhiZeroed()

◆ SetUpAdditionalStoppingTimes()

◆ WriteInfo()

◆ WriteOneStep()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestBidomainWithBathProblem

◆ TestCardiacSimulationArchiver

◆ TestPCTwoLevelsBlockDiagonal

Member Data Documentation

◆ mExtracelluarColumnId

◆ mFixedExtracellularPotentialNodes

◆ mHasBath

◆ mpBidomainTissue

◆ mpElectrodes

◆ mpSolver

◆ mRowForAverageOfPhiZeroed