BidomainTissue< SPACE_DIM > Class Template Reference

#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 57 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 167 of file BidomainTissue.cpp.

References BidomainTissue< SPACE_DIM >::mpExtracellularConductivityTensors.

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::GetConductivityHeterogeneitiesProvided(), HeartConfig::GetConductivityMedia(), HeartConfig::GetExtracellularConductivities(), HeartConfig::GetLoadMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements(), AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::Init(), HeartConfig::Instance(), HeartConfig::IsMeshProvided(), AbstractCardiacTissue< SPACE_DIM >::mFibreFilePathNoExtension, AbstractCardiacTissue< SPACE_DIM >::mpConfig, BidomainTissue< SPACE_DIM >::mpExtracellularConductivityTensors, AbstractCardiacTissue< SPACE_DIM >::mpMesh, NEVER_REACHED, PetscTools::ReplicateException(), AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetFibreOrientationFile(), and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetNonConstantConductivities().

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 177 of file BidomainTissue.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, AbstractCardiacTissue< SPACE_DIM >::mpConductivityModifier, BidomainTissue< SPACE_DIM >::mpExtracellularConductivityTensors, and AbstractConductivityModifier< ELEMENT_DIM, SPACE_DIM >::rGetModifiedConductivityTensor().

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 71 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 63 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 78 of file BidomainTissue.hpp.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::rGetExtracellularConductivityTensor(), and BidomainTissue< SPACE_DIM >::~BidomainTissue().

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

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