#include <BidomainTissue.hpp>

Inheritance diagram for BidomainTissue< SPACE_DIM >:

Collaboration diagram for BidomainTissue< SPACE_DIM >:

Public Member Functions
	BidomainTissue (AbstractCardiacCellFactory< SPACE_DIM > *pCellFactory, bool exchangeHalos=false)

	BidomainTissue (AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)

	~BidomainTissue ()

const c_matrix< double, SPACE_DIM, SPACE_DIM > &	rGetExtracellularConductivityTensor (unsigned elementIndex)

Public Member Functions inherited from AbstractCardiacTissue< SPACE_DIM >
	AbstractCardiacTissue (AbstractCardiacCellFactory< ELEMENT_DIM, ELEMENT_DIM > *pCellFactory, bool exchangeHalos=false)

	AbstractCardiacTissue (AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > *pMesh)

virtual	~AbstractCardiacTissue ()

bool	HasPurkinje ()

void	SetCacheReplication (bool doCacheReplication)

bool	GetDoCacheReplication ()

const c_matrix< double, ELEMENT_DIM, ELEMENT_DIM > &	rGetIntracellularConductivityTensor (unsigned elementIndex)

AbstractCardiacCellInterface *	GetCardiacCell (unsigned globalIndex)

AbstractCardiacCellInterface *	GetPurkinjeCell (unsigned globalIndex)

AbstractCardiacCellInterface *	GetCardiacCellOrHaloCell (unsigned globalIndex)

virtual void	SolveCellSystems (Vec existingSolution, double time, double nextTime, bool updateVoltage=false)

ReplicatableVector &	rGetIionicCacheReplicated ()

ReplicatableVector &	rGetIntracellularStimulusCacheReplicated ()

ReplicatableVector &	rGetPurkinjeIionicCacheReplicated ()

ReplicatableVector &	rGetPurkinjeIntracellularStimulusCacheReplicated ()

void	UpdateCaches (unsigned globalIndex, unsigned localIndex, double nextTime)

void	UpdatePurkinjeCaches (unsigned globalIndex, unsigned localIndex, double nextTime)

void	ReplicateCaches ()

const std::vector < AbstractCardiacCellInterface * > &	rGetCellsDistributed () const

const std::vector < AbstractCardiacCellInterface * > &	rGetPurkinjeCellsDistributed () const

const AbstractTetrahedralMesh < ELEMENT_DIM, ELEMENT_DIM > *	pGetMesh () const

void	SetConductivityModifier (AbstractConductivityModifier< ELEMENT_DIM, ELEMENT_DIM > *pModifier)

void	SaveCardiacCells (Archive &archive, const unsigned int version) const

void	LoadCardiacCells (Archive &archive, const unsigned int version)

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

void	CreateExtracellularConductivityTensors ()

Private Attributes
AbstractConductivityTensors < SPACE_DIM, SPACE_DIM > *	mpExtracellularConductivityTensors

Friends
class	TestBidomainTissue

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractCardiacTissue< SPACE_DIM >
void	CalculateHaloNodesFromNodeExchange ()

void	SetUpHaloCells (AbstractCardiacCellFactory< ELEMENT_DIM, ELEMENT_DIM > *pCellFactory)

Protected Attributes inherited from AbstractCardiacTissue< SPACE_DIM >
AbstractTetrahedralMesh < ELEMENT_DIM, ELEMENT_DIM > *	mpMesh

AbstractConductivityTensors < ELEMENT_DIM, ELEMENT_DIM > *	mpIntracellularConductivityTensors

std::vector < AbstractCardiacCellInterface * >	mCellsDistributed

std::vector < AbstractCardiacCellInterface * >	mPurkinjeCellsDistributed

ReplicatableVector	mIionicCacheReplicated

ReplicatableVector	mPurkinjeIionicCacheReplicated

ReplicatableVector	mIntracellularStimulusCacheReplicated

ReplicatableVector	mPurkinjeIntracellularStimulusCacheReplicated

HeartConfig *	mpConfig

DistributedVectorFactory *	mpDistributedVectorFactory

std::string	mFibreFilePathNoExtension

AbstractConductivityModifier < ELEMENT_DIM, ELEMENT_DIM > *	mpConductivityModifier

bool	mHasPurkinje

bool	mDoCacheReplication

bool	mMeshUnarchived

bool	mExchangeHalos

std::vector< unsigned >	mHaloNodes

std::vector < AbstractCardiacCellInterface * >	mHaloCellsDistributed

std::map< unsigned, unsigned >	mHaloGlobalToLocalIndexMap

std::vector< std::vector < unsigned > >	mNodesToSendPerProcess

std::vector< std::vector < unsigned > >	mNodesToReceivePerProcess

Detailed Description

template<unsigned SPACE_DIM>
class BidomainTissue< SPACE_DIM >

BidomainTissue class.

See documentation for AbstractCardiacTissue. This class also has extracellular conductivity tensors.

Definition at line 60 of file BidomainTissue.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>

BidomainTissue< SPACE_DIM >::BidomainTissue	(	AbstractCardiacCellFactory< SPACE_DIM > *	pCellFactory,
		bool	exchangeHalos = `false`
	)

Constructor sets up extracellular conductivity tensors.

Parameters

pCellFactory	factory to pass on to the base class constructor
exchangeHalos	used in state-variable interpolation. Defaults to false.

Definition at line 45 of file BidomainTissue.cpp.

References BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

template<unsigned SPACE_DIM>

BidomainTissue< SPACE_DIM >::BidomainTissue ( AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > * pMesh )

Archiving constructor

Parameters

pMesh a pointer to the AbstractTetrahedral mesh (recovered from archive).

Definition at line 54 of file BidomainTissue.cpp.

References BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

template<unsigned SPACE_DIM>

BidomainTissue< SPACE_DIM >::~BidomainTissue ( )

Destructor

Definition at line 166 of file BidomainTissue.cpp.

Member Function Documentation

template<unsigned SPACE_DIM>

void BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors ( )

private

Convenience method for extracellular conductivity tensors creation

Definition at line 61 of file BidomainTissue.cpp.

References RelativeTo::AbsoluteOrCwd, FileFinder::Exists(), HeartConfig::GetConductivityHeterogeneities(), HeartConfig::Instance(), NEVER_REACHED, and PetscTools::ReplicateException().

Referenced by BidomainTissue< SPACE_DIM >::BidomainTissue().

template<unsigned SPACE_DIM>

const c_matrix< double, SPACE_DIM, SPACE_DIM > & BidomainTissue< SPACE_DIM >::rGetExtracellularConductivityTensor ( unsigned elementIndex )

virtual

Returns: the extracellular conductivity tensor for the given element

Parameters

elementIndex index of the element of interest

Reimplemented from AbstractCardiacTissue< SPACE_DIM >.

Definition at line 176 of file BidomainTissue.cpp.

template<unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 74 of file BidomainTissue.hpp.

Friends And Related Function Documentation

template<unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 66 of file BidomainTissue.hpp.

Member Data Documentation

template<unsigned SPACE_DIM>

AbstractConductivityTensors<SPACE_DIM,SPACE_DIM>* BidomainTissue< SPACE_DIM >::mpExtracellularConductivityTensors

private

Extracellular conductivity tensors.

Definition at line 81 of file BidomainTissue.hpp.

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

heart/src/tissue/BidomainTissue.hpp
heart/src/tissue/BidomainTissue.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned SPACE_DIM> class BidomainTissue< SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned SPACE_DIM>
class BidomainTissue< SPACE_DIM >