#include <MonodomainProblem.hpp>

Inheritance diagram for MonodomainProblem< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainProblem< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	CreateCardiacTissue ()

AbstractDynamicLinearPdeSolver < ELEMENT_DIM, SPACE_DIM, 1 > *	CreateSolver ()

	MonodomainProblem (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

	MonodomainProblem ()

virtual	~MonodomainProblem ()

MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	GetMonodomainTissue ()

void	WriteInfo (double time)

virtual void	DefineWriterColumns (bool extending)

virtual void	WriteOneStep (double time, Vec voltageVec)

Public Member Functions inherited from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >
	AbstractCardiacProblem (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

	AbstractCardiacProblem ()

virtual	~AbstractCardiacProblem ()

void	Initialise ()

void	SetNodesPerProcessorFilename (const std::string &rFilename)

void	SetBoundaryConditionsContainer (BccType pBcc)

virtual void	PreSolveChecks ()

virtual Vec	CreateInitialCondition ()

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 ()

virtual void	AtBeginningOfTimestep (double time)

virtual void	OnEndOfTimestep (double time)

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

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

void	LoadExtraArchive (Archive &archive, unsigned version)

virtual bool	GetHasBath ()

virtual void	SetElectrodes ()

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

Public Member Functions inherited from AbstractUntemplatedCardiacProblem
virtual	~AbstractUntemplatedCardiacProblem ()

Protected Attributes
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *	mpMonodomainTissue

Protected Attributes inherited from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >
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	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >
virtual void	CreateMeshFromHeartConfig ()

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MonodomainProblem< ELEMENT_DIM, SPACE_DIM >

Class which specifies and solves a monodomain problem.

Definition at line 54 of file MonodomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::MonodomainProblem ( AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > * pCellFactory )

Constructor

Parameters

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

Definition at line 80 of file MonodomainProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::MonodomainProblem ( )

Constructor just used for archiving

Definition at line 87 of file MonodomainProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor

Definition at line 94 of file MonodomainProblem.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateCardiacTissue ( )

virtual

Returns: Created monodomain tissue.

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >.

Definition at line 45 of file MonodomainProblem.cpp.

References HeartConfig::GetUseStateVariableInterpolation(), and HeartConfig::Instance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 > * MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateSolver ( )

virtual

Returns: Created suitable solver for monodomain problems.

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >.

Definition at line 52 of file MonodomainProblem.cpp.

References HeartConfig::Instance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::DefineWriterColumns ( bool extending )

virtual

Define what variables are written to the primary results file.

Parameters

extending whether we are extending an existing results file

Reimplemented from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >.

Definition at line 125 of file MonodomainProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::GetMonodomainTissue ( )

Returns: the monodomain PDE

Definition at line 99 of file MonodomainProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 66 of file MonodomainProblem.hpp.

References MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteInfo ( double time )

virtual

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

Parameters

time	the current time

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >.

Definition at line 106 of file MonodomainProblem.cpp.

References PetscTools::AmMaster().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)

virtual

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

Parameters

time	the current time
voltageVec	the solution vector to write

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 1 >.

Definition at line 132 of file MonodomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 58 of file MonodomainProblem.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue

protected

The monodomain tissue object.

Definition at line 74 of file MonodomainProblem.hpp.

Referenced by MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::serialize().

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

heart/src/problem/MonodomainProblem.hpp
heart/src/problem/MonodomainProblem.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class MonodomainProblem< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MonodomainProblem< ELEMENT_DIM, SPACE_DIM >