#include <BidomainWithBathProblem.hpp>

Inheritance diagram for BidomainWithBathProblem< DIM >:

Collaboration diagram for BidomainWithBathProblem< DIM >:

Public Member Functions
	BidomainWithBathProblem (AbstractCardiacCellFactory< DIM > *pCellFactory)

	BidomainWithBathProblem ()

	~BidomainWithBathProblem ()

Public Member Functions inherited from BidomainProblem< DIM >
	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 ()

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from BidomainProblem< DIM >
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 inherited from BidomainProblem< DIM >
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

Detailed Description

template<unsigned DIM>
class BidomainWithBathProblem< 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 55 of file BidomainWithBathProblem.hpp.

Constructor & Destructor Documentation

◆ BidomainWithBathProblem() [1/2]

template<unsigned DIM>

BidomainWithBathProblem< DIM >::BidomainWithBathProblem ( AbstractCardiacCellFactory< DIM > * pCellFactory )

Constructor

Parameters

pCellFactory User defined cell factory which shows how the pde should create cells.

Definition at line 40 of file BidomainWithBathProblem.cpp.

◆ BidomainWithBathProblem() [2/2]

template<unsigned DIM>

BidomainWithBathProblem< DIM >::BidomainWithBathProblem ( )

Constructor just used for archiving

Definition at line 47 of file BidomainWithBathProblem.cpp.

◆ ~BidomainWithBathProblem()

template<unsigned DIM>

BidomainWithBathProblem< DIM >::~BidomainWithBathProblem ( )

Destructor

Definition at line 53 of file BidomainWithBathProblem.cpp.

Member Function Documentation

◆ serialize()

template<unsigned DIM>

template<class Archive >

void BidomainWithBathProblem< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize this class

Parameters

archive	the archive
version	the current version of this class

Definition at line 66 of file BidomainWithBathProblem.hpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 58 of file BidomainWithBathProblem.hpp.

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

heart/src/problem/BidomainWithBathProblem.hpp
heart/src/problem/BidomainWithBathProblem.cpp

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BidomainWithBathProblem() [1/2]

◆ BidomainWithBathProblem() [2/2]

◆ ~BidomainWithBathProblem()

Member Function Documentation

◆ serialize()

Friends And Related Symbol Documentation

◆ boost::serialization::access