AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCardiacTissue.hpp>

Inheritance diagram for AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)
virtual const c_matrix< double, SPACE_DIM, SPACE_DIM > &	rGetExtracellularConductivityTensor (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)
template<class Archive >
void	SaveCardiacCells (Archive &archive, const unsigned int version) const
template<class Archive >
void	LoadCardiacCells (Archive &archive, const unsigned int version)

Protected Member Functions
void	CalculateHaloNodesFromNodeExchange ()
void	SetUpHaloCells (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

Protected Attributes
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

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

Friends
class	boost::serialization::access
class	TestMonodomainTissue

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >

Class containing "tissue-like" functionality used in monodomain and bidomain problems.

Contains the cardiac cells (ODE systems for each node of the mesh) and conductivity tensors (dependent on fibre directions).

Also contains knowledge of parallelisation in the form of the distributed vector factory. This class deals with created a distributed vector of cells, and getting the ionic current and stimuli from these cells and putting them in replicated arrays for the PDE solvers to call.

Template Parameters

ELEMENT_DIM	Dimension of the elements.
SPACE_DIM	Dimension of the space. If not specified, it defaults to ELEMENT_DIM.

Definition at line 85 of file AbstractCardiacTissue.hpp.

Constructor & Destructor Documentation

AbstractCardiacTissue() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue	(	AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *	pCellFactory,
		bool	exchangeHalos = false
	)

This constructor is called from the Initialise() method of the CardiacProblem class. It creates all the cell objects, and sets up the conductivities.

Note that pCellFactory contains a pointer to the mesh

Parameters

pCellFactory	factory to use to create cardiac cells. If this is actually an AbstractPurkinjeCellFactory it creates purkinje cells.
exchangeHalos	used in state-variable interpolation. Defaults to false.

Definition at line 53 of file AbstractCardiacTissue.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreatePurkinjeCellForNode(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FinaliseCellCreation(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::FinalisePurkinjeCellCreation(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), HeartConfig::GetMeshName(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), HeartConfig::Instance(), PetscTools::IsSequential(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mCellsDistributed, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mExchangeHalos, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mFibreFilePathNoExtension, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIionicCacheReplicated, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeCellsDistributed, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeIionicCacheReplicated, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeIntracellularStimulusCacheReplicated, PetscTools::ReplicateBool(), PetscTools::ReplicateException(), ReplicatableVector::Resize(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetUpHaloCells(), and AbstractCardiacCellInterface::SetUsedInTissueSimulation().

AbstractCardiacTissue() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue

(

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *

pMesh

)

This constructor is called by the archiver only.

Parameters

pMesh

a pointer to the AbstractTetrahedral mesh.

Definition at line 181 of file AbstractCardiacTissue.cpp.

References AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ArchiveLocationInfo::GetArchiveDirectory(), ArchiveLocationInfo::GetMeshFilename(), DistributedVectorFactory::GetProblemSize(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mFibreFilePathNoExtension, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIionicCacheReplicated, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, and ReplicatableVector::Resize().

~AbstractCardiacTissue()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Virtual destructor

Definition at line 197 of file AbstractCardiacTissue.cpp.

Member Function Documentation

CalculateHaloNodesFromNodeExchange()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CalculateHaloNodesFromNodeExchange ( )

protected

If the mesh is a tetrahedral mesh then all elements and nodes are known. The halo nodes to the ones which are actually used as cardiac cells must be calculated explicitly.

Definition at line 423 of file AbstractCardiacTissue.cpp.

References PetscTools::GetNumProcs().

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

CreateIntracellularConductivityTensor()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor ( )

private

Convenience method for intracellular conductivity tensor creation

Todo:

#1316 Create a class defining constant tensors to be used when no fibre orientation is provided.

Todo:

#1316 Create a class defining constant tensors to be used when no fibre orientation is provided.

Definition at line 240 of file AbstractCardiacTissue.cpp.

References RelativeTo::AbsoluteOrCwd, GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), FileFinder::Exists(), HeartConfig::GetConductivityHeterogeneities(), HeartConfig::Instance(), NEVER_REACHED, and PetscTools::ReplicateException().

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

GetCardiacCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellInterface * AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell

(

unsigned

globalIndex

)

Returns

a pointer to a cell, indexed by the global node index.

Note

Should only called by the process owning the cell - triggers an assertion otherwise.

Parameters

globalIndex

global node index for which to retrieve a cell

Definition at line 385 of file AbstractCardiacTissue.cpp.

Referenced by CardiacSimulation::CreateAndRun().

GetCardiacCellOrHaloCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellInterface * AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCellOrHaloCell

(

unsigned

globalIndex

)

Returns

a pointer to a halo cell, indexed by the global node index.

Note

Should only called by the process halo owning the cell - triggers an assertion otherwise.

Parameters

globalIndex

global node index for which to retrieve a cell

Definition at line 402 of file AbstractCardiacTissue.cpp.

GetDoCacheReplication()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetDoCacheReplication

(

)

Get whether or not to replicate the caches across all processors.

Returns

mDoCacheReplication - true if the cache needs to be replicated

Definition at line 359 of file AbstractCardiacTissue.cpp.

GetPurkinjeCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCardiacCellInterface * AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetPurkinjeCell

(

unsigned

globalIndex

)

Returns

a pointer to a Purkinje cell, indexed by the global node index.

Note

Should only called by the process owning the cell - triggers an assertion otherwise.

Parameters

globalIndex

global node index for which to retrieve a cell

Definition at line 393 of file AbstractCardiacTissue.cpp.

References EXCEPT_IF_NOT.

HasPurkinje()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::HasPurkinje

(

)

Returns

whether this tissue contains Purkinje fibres.

Definition at line 234 of file AbstractCardiacTissue.cpp.

load()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Unarchive the member variables.

Parameters

archive
version

Definition at line 169 of file AbstractCardiacTissue.hpp.

References AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CalculateHaloNodesFromNodeExchange(), ProcessSpecificArchive< Archive >::Get(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), DistributedVectorFactory::GetProblemSize(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mDoCacheReplication, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mExchangeHalos, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloCellsDistributed, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloGlobalToLocalIndexMap, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mNodesToReceivePerProcess, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mNodesToSendPerProcess, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpConductivityModifier, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeIionicCacheReplicated, and ReplicatableVector::Resize().

LoadCardiacCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inline

Load our tissue from an archive.

Handles the checkpoint migration case, deleting loaded cells immediately if they are not local to this process.

Also loads halo cells if we're doing halo exchange, by using the non-local cells from the archive.

Parameters

archive	the process-specific archive to load from
version	archive version

Definition at line 570 of file AbstractCardiacTissue.hpp.

References DynamicModelLoaderRegistry::GetLoader(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), DistributedVectorFactory::GetOriginalFactory(), DynamicModelLoaderRegistry::Instance(), DistributedVectorFactory::IsGlobalIndexLocal(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mCellsDistributed, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloCellsDistributed, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloGlobalToLocalIndexMap, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeCellsDistributed, and NEVER_REACHED.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

pGetMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::pGetMesh

(

)

const

Returns

a pointer to the mesh object

pointer to mesh object

Definition at line 775 of file AbstractCardiacTissue.cpp.

ReplicateCaches()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::ReplicateCaches

(

)

Replicate the Iionic and intracellular stimulus caches.

Definition at line 745 of file AbstractCardiacTissue.cpp.

rGetCellsDistributed()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< AbstractCardiacCellInterface * > & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetCellsDistributed

(

)

const

Returns

a reference to the vector of distributed cells. Needed for archiving.

Definition at line 762 of file AbstractCardiacTissue.cpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SaveCardiacCells().

rGetExtracellularConductivityTensor()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns

the extracellular conductivity tensor for the given element (this throws an exception in this abstract class since monodomain don't have extracellular ones) it is overridden in the BidomainTissue.

Parameters

elementIndex

index of the element of interest

Reimplemented in BidomainTissue< SPACE_DIM >, BidomainTissue< DIM >, ExtendedBidomainTissue< SPACE_DIM >, and ExtendedBidomainTissue< DIM >.

Definition at line 379 of file AbstractCardiacTissue.cpp.

rGetIionicCacheReplicated()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetIionicCacheReplicated

(

)

Returns

the entire ionic current cache

Definition at line 704 of file AbstractCardiacTissue.cpp.

rGetIntracellularConductivityTensor()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const c_matrix< double, SPACE_DIM, SPACE_DIM > & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetIntracellularConductivityTensor

(

unsigned

elementIndex

)

Returns

the intracellular conductivity tensor for the given element

Parameters

elementIndex

index of the element of interest

Definition at line 365 of file AbstractCardiacTissue.cpp.

rGetIntracellularStimulusCacheReplicated()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetIntracellularStimulusCacheReplicated

(

)

Returns

the entire stimulus current cache

Definition at line 710 of file AbstractCardiacTissue.cpp.

rGetPurkinjeCellsDistributed()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< AbstractCardiacCellInterface * > & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeCellsDistributed

(

)

const

Returns

a reference to the vector of distributed Purkinje cells. Needed for archiving.

Definition at line 768 of file AbstractCardiacTissue.cpp.

References EXCEPT_IF_NOT.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SaveCardiacCells().

rGetPurkinjeIionicCacheReplicated()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeIionicCacheReplicated

(

)

Returns

the entire Purkinje ionic current cache

Definition at line 716 of file AbstractCardiacTissue.cpp.

References EXCEPT_IF_NOT.

rGetPurkinjeIntracellularStimulusCacheReplicated()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeIntracellularStimulusCacheReplicated

(

)

Returns

the entire Purkinje stimulus current cache

Definition at line 723 of file AbstractCardiacTissue.cpp.

References EXCEPT_IF_NOT.

save()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 100 of file AbstractCardiacTissue.hpp.

References RelativeTo::AbsoluteOrCwd, RelativeTo::ChasteTestOutput, FileFinder::CopyTo(), FileFinder::Exists(), ProcessSpecificArchive< Archive >::Get(), ArchiveLocationInfo::GetArchiveRelativePath(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), ArchiveLocationInfo::GetMeshFilename(), HeartConfig::Instance(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mDoCacheReplication, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mExchangeHalos, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mFibreFilePathNoExtension, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpMesh, NEVER_REACHED, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SaveCardiacCells(), and TRY_IF_MASTER.

SaveCardiacCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inline

Save our tissue to an archive.

Writes:

1. mpDistributedVectorFactory
2. number of cells on this process
3. each cell pointer in turn, interleaved with Purkinje cells if present

Parameters

archive	the process-specific archive to write cells to.
version

Definition at line 528 of file AbstractCardiacTissue.hpp.

References AbstractDynamicallyLoadableEntity::GetLoader(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, NEVER_REACHED, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetCellsDistributed(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeCellsDistributed().

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save().

SetCacheReplication()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication

(

bool

doCacheReplication

)

Set whether or not to replicate the caches across all processors.

See also mDoCacheReplication.

Parameters

doCacheReplication

- true if the cache needs to be replicated

Definition at line 353 of file AbstractCardiacTissue.cpp.

Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver(), MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver(), and OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver().

SetConductivityModifier()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetConductivityModifier

(

AbstractConductivityModifier< ELEMENT_DIM, SPACE_DIM > *

pModifier

)

Set a modifier class which will be used to modifier a conductivity obtained from mpIntracellularConductivityTensors when rGetIntracellularConductivityTensor() is called. For example, it is required when conductivities become deformation-dependent.

Parameters

pModifier

Pointer to the concrete modifier class

Definition at line 781 of file AbstractCardiacTissue.cpp.

SetUpHaloCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetUpHaloCells ( AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *  pCellFactory )

protected

If mExchangeHalos is true, this method calls CalculateHaloNodesFromNodeExchange and sets up the halo cell data structures mHaloCellsDistributed and mHaloGlobalToLocalIndexMap.

Parameters

pCellFactory

cell factory to use to create halo cells

Definition at line 436 of file AbstractCardiacTissue.cpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

SolveCellSystems()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems ( Vec  existingSolution, double  time, double  nextTime, bool  updateVoltage = false  )

virtual

Integrate the cell ODEs and update ionic current etc for each of the cells, between the two times provided.

Parameters

existingSolution	the current voltage solution vector
time	the current simulation time
nextTime	when to simulate the cells until
updateVoltage	whether to also solve for the voltage (generally false, true for operator splitting methods). Defaults to false

Todo:

This may want to go to std::cerr ??

Todo:

#2017 This code will be needed in the future, not being covered now. Add a test which covers this, e.g. by doing a simulation with a bad stimulus for one of the Purkinje cells - stimulating with the wrong choice of sign say.

Reimplemented in ExtendedBidomainTissue< SPACE_DIM >, and ExtendedBidomainTissue< DIM >.

Definition at line 464 of file AbstractCardiacTissue.cpp.

UpdateCaches()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::UpdateCaches	(	unsigned	globalIndex,
		unsigned	localIndex,
		double	nextTime
	)

Update the Iionic and intracellular stimulus caches.

Parameters

globalIndex	global index of the entry to update
localIndex	local index of the entry to update
nextTime	the next PDE time point, at which to evaluate the stimulus current

Definition at line 730 of file AbstractCardiacTissue.cpp.

UpdatePurkinjeCaches()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::UpdatePurkinjeCaches	(	unsigned	globalIndex,
		unsigned	localIndex,
		double	nextTime
	)

Update the Iionic and intracellular stimulus caches for Purkinje cells.

Parameters

globalIndex	global index of the entry to update
localIndex	local index of the entry to update
nextTime	the next PDE time point, at which to evaluate the stimulus current

Definition at line 737 of file AbstractCardiacTissue.cpp.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 90 of file AbstractCardiacTissue.hpp.

TestMonodomainTissue

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class TestMonodomainTissue

friend

Definition at line 91 of file AbstractCardiacTissue.hpp.

Member Data Documentation

mCellsDistributed

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< AbstractCardiacCellInterface* > AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mCellsDistributed

protected

The vector of cells. Distributed.

Definition at line 243 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells().

mDoCacheReplication

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mDoCacheReplication

protected

Whether we need to replicate the caches.

When doing matrix-based RHS assembly, we only actually need information from cells/nodes local to the processor, so replicating the caches is an unnecessary communication overhead.

Defaults to true.

Definition at line 310 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save().

mExchangeHalos

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mExchangeHalos

protected

Whether to exchange cell models across the halo boundaries. Used in state variable interpolation.

Definition at line 321 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save().

mFibreFilePathNoExtension

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mFibreFilePathNoExtension

protected

Path to the location of the fibre file without extension.

Definition at line 289 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save().

mHaloCellsDistributed

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< AbstractCardiacCellInterface* > AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloCellsDistributed

protected

The vector of halo cells. Distributed.

Definition at line 327 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells().

mHaloGlobalToLocalIndexMap

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloGlobalToLocalIndexMap

protected

Map of global to local indices for halo nodes.

Definition at line 330 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells().

mHaloNodes

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHaloNodes

protected

Vector of halo node indices for current process

Definition at line 324 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

mHasPurkinje

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mHasPurkinje

protected

Whether this tissue has any Purkinje cells.

Definition at line 299 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SaveCardiacCells().

mIionicCacheReplicated

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIionicCacheReplicated

protected

Cache containing all the ionic currents for each node, replicated over all processes.

Definition at line 253 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

mIntracellularStimulusCacheReplicated

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated

protected

Cache containing all the stimulus currents for each node, replicated over all processes.

Definition at line 265 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

mMeshUnarchived

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mMeshUnarchived

protected

Whether the mesh was unarchived or got from elsewhere.

Definition at line 315 of file AbstractCardiacTissue.hpp.

mNodesToReceivePerProcess

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::vector<unsigned> > AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mNodesToReceivePerProcess

protected

A vector which will be of size GetNumProcs() for information to receive for process i.

Definition at line 343 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

mNodesToSendPerProcess

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::vector<unsigned> > AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mNodesToSendPerProcess

protected

A vector which will be of size GetNumProcs() where each internal vector except i=GetMyRank() contains an ordered list of indices of nodes to send to process i during data exchange

Definition at line 337 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

mpConductivityModifier

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractConductivityModifier<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpConductivityModifier

protected

This class, if not NULL, will be used to modify the conductivity that is obtained from mpIntracellularConductivityTensors when rGetIntracellularConductivityTensor() is called. For example, it is required when conductivities become deformation dependent.

Definition at line 296 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

mpConfig

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

HeartConfig* AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpConfig

protected

Local pointer to the HeartConfig singleton instance, for convenience.

Definition at line 274 of file AbstractCardiacTissue.hpp.

mpDistributedVectorFactory

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedVectorFactory* AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory

protected

Local pointer to the distributed vector factory associated with the mesh object used.

Used to retrieve node ownership range when needed.

NB: This is set from mpMesh->GetDistributedVectorFactory() and thus always equal to that. We never assume ownership of the object.

Definition at line 284 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SaveCardiacCells().

mpIntracellularConductivityTensors

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractConductivityTensors<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpIntracellularConductivityTensors

protected

Intracellular conductivity tensors. Not archived, since it's loaded from the HeartConfig singleton.

Definition at line 240 of file AbstractCardiacTissue.hpp.

mpMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mpMesh

protected

It's handy to keep a pointer to the mesh object

Definition at line 236 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::save().

mPurkinjeCellsDistributed

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< AbstractCardiacCellInterface* > AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeCellsDistributed

protected

The vector of the purkinje cells. Distributed. Empty unless a AbstractPurkinjeCellFactory is given to the constructor.

Definition at line 247 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::LoadCardiacCells().

mPurkinjeIionicCacheReplicated

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeIionicCacheReplicated

protected

Cache containing all the ionic currents for each purkinje node, replicated over all processes.

Definition at line 259 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::load().

mPurkinjeIntracellularStimulusCacheReplicated

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ReplicatableVector AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::mPurkinjeIntracellularStimulusCacheReplicated

protected

Cache containing all the stimulus currents for each Purkinje node, replicated over all processes.

Definition at line 271 of file AbstractCardiacTissue.hpp.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue().

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

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