Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
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, SPACE_DIM > *pCellFactory, bool exchangeHalos=false)
 
 AbstractCardiacTissue (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
 
virtual ~AbstractCardiacTissue ()
 
bool HasPurkinje ()
 
void SetCacheReplication (bool doCacheReplication)
 
bool GetDoCacheReplication ()
 
const c_matrix< double, SPACE_DIM, SPACE_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, SPACE_DIM > * pGetMesh () const
 
void SetConductivityModifier (AbstractConductivityModifier< ELEMENT_DIM, SPACE_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, SPACE_DIM > *pCellFactory)
 
- Protected Attributes inherited from AbstractCardiacTissue< SPACE_DIM >
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
 
AbstractConductivityTensors< ELEMENT_DIM, SPACE_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, SPACE_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

◆ BidomainTissue() [1/2]

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

Constructor sets up extracellular conductivity tensors.

Parameters
pCellFactoryfactory to pass on to the base class constructor
exchangeHalosused in state-variable interpolation. Defaults to false.

Definition at line 45 of file BidomainTissue.cpp.

References BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

◆ BidomainTissue() [2/2]

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

Archiving constructor

Parameters
pMesha pointer to the AbstractTetrahedral mesh (recovered from archive).

Definition at line 54 of file BidomainTissue.cpp.

References BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

◆ ~BidomainTissue()

template<unsigned SPACE_DIM>
BidomainTissue< SPACE_DIM >::~BidomainTissue ( )

Destructor

Definition at line 167 of file BidomainTissue.cpp.

Member Function Documentation

◆ CreateExtracellularConductivityTensors()

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, and FileFinder::Exists().

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

◆ rGetExtracellularConductivityTensor()

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
elementIndexindex of the element of interest

Reimplemented from AbstractCardiacTissue< SPACE_DIM >.

Definition at line 177 of file BidomainTissue.cpp.

◆ serialize()

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 Symbol Documentation

◆ boost::serialization::access

template<unsigned SPACE_DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 63 of file BidomainTissue.hpp.

◆ TestBidomainTissue

template<unsigned SPACE_DIM>
friend class TestBidomainTissue
friend

Definition at line 60 of file BidomainTissue.hpp.

Member Data Documentation

◆ mpExtracellularConductivityTensors

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.

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