#include <MonodomainPurkinjeProblem.hpp>

Inheritance diagram for MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	MonodomainPurkinjeProblem (AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

	MonodomainPurkinjeProblem ()

virtual	~MonodomainPurkinjeProblem ()

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, 2 >
	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 ()

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

AbstractDynamicLinearPdeSolver < ELEMENT_DIM, SPACE_DIM, 2 > *	CreateSolver ()

virtual void	CreateMeshFromHeartConfig ()

Vec	CreateInitialCondition ()

Protected Attributes
unsigned	mPurkinjeVoltageColumnId

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

Friends
class	boost::serialization::access

Detailed Description

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

Class which specifies and solves a monodomain problem with Purkinje fibres.

Definition at line 51 of file MonodomainPurkinjeProblem.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeProblem ( AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM > * pCellFactory )

Constructor

Parameters

pCellFactory user defined cell factory which shows how the tissue should create cells.

Definition at line 93 of file MonodomainPurkinjeProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeProblem ( )

Constructor just used for archiving

Definition at line 102 of file MonodomainPurkinjeProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor

Definition at line 110 of file MonodomainPurkinjeProblem.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protectedvirtual

Returns: newly created our tissue object.

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >.

Definition at line 43 of file MonodomainPurkinjeProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Vec MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::CreateInitialCondition ( )

protectedvirtual

Overridden method which creates initial condition using Purkinje initial voltages as well.

Returns: newly created initial condition

Reimplemented from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >.

Definition at line 70 of file MonodomainPurkinjeProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::CreateMeshFromHeartConfig ( )

protectedvirtual

Returns: newly created suitable (MixedDimensionMesh) mesh for monodomain problems with Purkinje.

Reimplemented from AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >.

Definition at line 63 of file MonodomainPurkinjeProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 > * MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::CreateSolver ( )

protectedvirtual

Returns: newly created suitable solver for monodomain problems with Purkinje.

Todo:: #2017 give a nice error

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >.

Definition at line 50 of file MonodomainPurkinjeProblem.cpp.

References EXCEPT_IF_NOT, and HeartConfig::Instance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeProblem< 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, 2 >.

Definition at line 153 of file MonodomainPurkinjeProblem.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 = ELEMENT_DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Todo:: Serialization of Purkinje problems is untested

Definition at line 63 of file MonodomainPurkinjeProblem.hpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MonodomainPurkinjeProblem< 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, 2 >.

Definition at line 116 of file MonodomainPurkinjeProblem.cpp.

References PetscTools::AmMaster().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

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

Parameters

time	the current time
voltageVec	the solution vector to write

Implements AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, 2 >.

Definition at line 169 of file MonodomainPurkinjeProblem.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 55 of file MonodomainPurkinjeProblem.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

unsigned MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::mPurkinjeVoltageColumnId

protected

Used by the writer.

Definition at line 75 of file MonodomainPurkinjeProblem.hpp.

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

heart/src/problem/MonodomainPurkinjeProblem.hpp
heart/src/problem/MonodomainPurkinjeProblem.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

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