#include <ExtendedBidomainTissue.hpp>

Inheritance diagram for ExtendedBidomainTissue< SPACE_DIM >:

Collaboration diagram for ExtendedBidomainTissue< SPACE_DIM >:

Public Member Functions
	ExtendedBidomainTissue (AbstractCardiacCellFactory< SPACE_DIM > pCellFactory, AbstractCardiacCellFactory< SPACE_DIM > pCellFactorySecondCell, AbstractStimulusFactory< SPACE_DIM > *pExtracellularStimulusFactory)

	ExtendedBidomainTissue (std::vector< AbstractCardiacCellInterface * > &rCellsDistributed, std::vector< AbstractCardiacCellInterface * > &rSecondCellsDistributed, std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rExtraStimuliDistributed, std::vector< double > &rGgapsDistributed, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh, c_vector< double, SPACE_DIM > intracellularConductivitiesSecondCell)

virtual	~ExtendedBidomainTissue ()

void	SetIntracellularConductivitiesSecondCell (c_vector< double, SPACE_DIM > conductivities)

AbstractCardiacCellInterface *	GetCardiacSecondCell (unsigned globalIndex)

boost::shared_ptr < AbstractStimulusFunction >	GetExtracellularStimulus (unsigned globalIndex)

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

const std::vector< double > &	rGetGapsDistributed () const

const std::vector < boost::shared_ptr < AbstractStimulusFunction > > &	rGetExtracellularStimulusDistributed () const

c_vector< double, SPACE_DIM >	GetIntracellularConductivitiesSecondCell () const

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

void	CreateIntracellularConductivityTensorSecondCell ()

void	SetGgapHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > > &rGgapHeterogeneityRegions, std::vector< double > rGgapValues)

void	CreateGGapConductivities ()

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

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

ReplicatableVector &	rGetIionicCacheReplicatedSecondCell ()

ReplicatableVector &	rGetIntracellularStimulusCacheReplicatedSecondCell ()

ReplicatableVector &	rGetExtracellularStimulusCacheReplicated ()

ReplicatableVector &	rGetGgapCacheReplicated ()

double	GetAmFirstCell ()

double	GetAmSecondCell ()

double	GetAmGap ()

double	GetCmFirstCell ()

double	GetCmSecondCell ()

double	GetGGap ()

void	SetAmFirstCell (double value)

void	SetAmSecondCell (double value)

void	SetAmGap (double value)

void	SetCmFirstCell (double value)

void	SetCmSecondCell (double value)

void	SetGGap (double value)

bool	HasTheUserSuppliedExtracellularStimulus ()

void	SetUserSuppliedExtracellularStimulus (bool flag)

template<class Archive >
void	SaveExtendedBidomainCells (Archive &archive, const unsigned int version) const

template<class Archive >
void	SaveExtracellularStimulus (Archive &archive, const unsigned int version) const

template<class Archive >
void	LoadExtracellularStimulus (Archive &archive, const unsigned int version, std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuli, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)

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)

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)

Static Public Member Functions
template<class Archive >
static void	LoadExtendedBidomainCells (Archive &archive, const unsigned int version, std::vector< AbstractCardiacCellInterface * > &rCells, std::vector< AbstractCardiacCellInterface * > &rSecondCells, std::vector< double > &rGgaps, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)

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

void	CreateExtracellularConductivityTensors ()

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

void	ReplicateAdditionalCaches ()

Private Attributes
AbstractConductivityTensors < SPACE_DIM, SPACE_DIM > *	mpIntracellularConductivityTensorsSecondCell

c_vector< double, SPACE_DIM >	mIntracellularConductivitiesSecondCell

AbstractConductivityTensors < SPACE_DIM, SPACE_DIM > *	mpExtracellularConductivityTensors

ReplicatableVector	mExtracellularStimulusCacheReplicated

ReplicatableVector	mGgapCacheReplicated

ReplicatableVector	mIionicCacheReplicatedSecondCell

ReplicatableVector	mIntracellularStimulusCacheReplicatedSecondCell

std::vector < AbstractCardiacCellInterface * >	mCellsDistributedSecondCell

std::vector< boost::shared_ptr < AbstractStimulusFunction > >	mExtracellularStimuliDistributed

std::vector< double >	mGgapDistributed

double	mAmFirstCell

double	mAmSecondCell

double	mAmGap

double	mCmFirstCell

double	mCmSecondCell

double	mGGap

bool	mUserSuppliedExtracellularStimulus

std::vector< boost::shared_ptr < AbstractChasteRegion < SPACE_DIM > > >	mGgapHeterogeneityRegions

std::vector< double >	mGgapValues

Friends
class	TestExtendedBidomainTissue

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 ExtendedBidomainTissue< SPACE_DIM >

Class that provides functionalities to specify a tissue within the context of the extended bidomain framework.

The extended bidomain equations are of the form:

div ( sigma_i1 grad Phi_1 ) + Am1*Cm1*d(phi_1)/dt - Am2*Cm2*d(phi_e)/dt + Am1*I_ion1 - Am1*I_stim1 + Amgap*G_gap*(phi_1 - phi_2)
div ( sigma_i2 grad Phi_2 ) + Am2*Cm2*d(phi_2)/dt - Am2*Cm2*d(phi_e)/dt + Am2*I_ion2 - Am2*I_stim2 - Amgap*G_gap*(phi_1 - phi_2) div ( sigma_e grad Phi_e ) + div ( sigma_i1 grad Phi_1 ) + div ( sigma_i2 grad Phi_2 ) = I_stim

The unknowns are:
- Phi_1 (intracellular potential of the first cell).
- Phi_2 (intracellular potential of the second cell).
- Phi_e (extracellular potential).
Am1, Am2 and Amgap are surface-to-volume ratios for first cell, second cell and gap junction. User can set their values. Cm1 and cm2 are capaciatnce values of first and second cell respectively sigma_i1 and sigma_i2 are intracellular conductivity tensors of first and second cell respectively sigma_e is the conductivity tensor for the extracellular space G_gap is the conductance (in ms/cm2) of the gap junction channel.

Definition at line 77 of file ExtendedBidomainTissue.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>

ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue	(	AbstractCardiacCellFactory< SPACE_DIM > *	pCellFactory,
		AbstractCardiacCellFactory< SPACE_DIM > *	pCellFactorySecondCell,
		AbstractStimulusFactory< SPACE_DIM > *	pExtracellularStimulusFactory
	)

Constructor sets up extracellular conductivity tensors.

Parameters

pCellFactory	factory to pass on to the base class constructor
pCellFactorySecondCell	factory to pass on to the base class constructor for the second cell
pExtracellularStimulusFactory	factory for creating extracellular stimuli

Definition at line 47 of file ExtendedBidomainTissue.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::CreateStimulusForNode(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FinaliseCellCreation(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), ExtendedBidomainTissue< SPACE_DIM >::mCellsDistributedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimuliDistributed, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimulusCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapDistributed, ExtendedBidomainTissue< SPACE_DIM >::mIionicCacheReplicatedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mIntracellularStimulusCacheReplicatedSecondCell, AbstractCardiacTissue< SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacTissue< SPACE_DIM >::mpMesh, PetscTools::ReplicateException(), and ReplicatableVector::Resize().

template<unsigned SPACE_DIM>

ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue	(	std::vector< AbstractCardiacCellInterface * > &	rCellsDistributed,
		std::vector< AbstractCardiacCellInterface * > &	rSecondCellsDistributed,
		std::vector< boost::shared_ptr< AbstractStimulusFunction > > &	rExtraStimuliDistributed,
		std::vector< double > &	rGgapsDistributed,
		AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *	pMesh,
		c_vector< double, SPACE_DIM >	intracellularConductivitiesSecondCell
	)

Archiving constructor

Parameters

rCellsDistributed	local cell models (recovered from archive)
rSecondCellsDistributed	local cell models for second cells (recovered from archive)
rExtraStimuliDistributed	local extracellular stimuli (recovered from archive)
rGgapsDistributed	distributed Ggaps (recovered from archive)
pMesh	a pointer to the AbstractTetrahedral mesh (recovered from archive).
intracellularConductivitiesSecondCell	a vector with the orthotropic conductivities for the second cell (this is needed because the second cell values may not be taken from HeartConfig as the the ones for the first cell are).

Definition at line 117 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

ExtendedBidomainTissue< SPACE_DIM >::~ExtendedBidomainTissue ( )

virtual

Destructor

Definition at line 438 of file ExtendedBidomainTissue.cpp.

Member Function Documentation

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors ( )

private

Convenience method for extracellular conductivity tensors creation

Definition at line 334 of file ExtendedBidomainTissue.cpp.

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

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

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::CreateGGapConductivities ( )

Create the pattern of Ggap across the mesh based upon mCellHeterogeneityRegions, mGgapValues and mGgap. This will fill in mGgapDistributed. It will set mGgap everywhere except in the areas mCellHeterogeneityRegions[i] where it will put mGgapValues[i] instead. If mCellHeterogeneityRegions (and mGgapValues) are empty, mGgap will be set everywhere.

Definition at line 156 of file ExtendedBidomainTissue.cpp.

References Node< SPACE_DIM >::GetPoint(), and PetscTools::ReplicateException().

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell ( )

Convenience method for intracellular conductivity tensors creation for the second cell

Definition at line 194 of file ExtendedBidomainTissue.cpp.

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

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

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetAmFirstCell ( )

Returns: Am for the first cell

Definition at line 606 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetAmGap ( )

Returns: Am for the gap junction

Definition at line 618 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetAmSecondCell ( )

Returns: Am for the second cell

Definition at line 612 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

AbstractCardiacCellInterface * ExtendedBidomainTissue< SPACE_DIM >::GetCardiacSecondCell ( unsigned globalIndex )

Returns: a pointer to the second cell

Parameters

globalIndex the global index in the mesh

Definition at line 503 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetCmFirstCell ( )

Returns: Cm for the first cell

Definition at line 624 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetCmSecondCell ( )

Returns: Cm for the second cell

Definition at line 630 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

boost::shared_ptr< AbstractStimulusFunction > ExtendedBidomainTissue< SPACE_DIM >::GetExtracellularStimulus ( unsigned globalIndex )

Returns: a pointer to the extracellular stimulus. Useful for testing

Parameters

globalIndex the global index in the mesh

Definition at line 509 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::GetGGap ( )

Returns: the conducatnce of the gap junction (mGGap)

Definition at line 636 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > ExtendedBidomainTissue< SPACE_DIM >::GetIntracellularConductivitiesSecondCell ( ) const

Returns: the intracellular conductivities of the second cell

Definition at line 469 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

bool ExtendedBidomainTissue< SPACE_DIM >::HasTheUserSuppliedExtracellularStimulus ( )

This method gives access to the member variable mUserSuppliedExtracellularStimulus, which is false by default but turned true if the user supplies an extracellular stimulus in any form.

Returns: true if the user supplied an extracellular stimulus.

Definition at line 303 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

template<class Archive >

static void ExtendedBidomainTissue< SPACE_DIM >::LoadExtendedBidomainCells	(	Archive &	archive,
		const unsigned int	version,
		std::vector< AbstractCardiacCellInterface * > &	rCells,
		std::vector< AbstractCardiacCellInterface * > &	rSecondCells,
		std::vector< double > &	rGgaps,
		AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *	pMesh
	)

inlinestatic

Load our tissue from an archive. This is the equivalent of LoadCardiacCells in the abstract class. it loads the two cells instead of only one.

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

Parameters

archive	the process-specific archive to load from
version	archive version
rCells	vector to fill in with pointers to local cells
rSecondCells	vector to fill in with pointers to the second cells
rGgaps	vector of values of gap junctions
pMesh	the mesh, so we can get at the node permutation, if any

Definition at line 472 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

template<class Archive >

void ExtendedBidomainTissue< SPACE_DIM >::LoadExtracellularStimulus	(	Archive &	archive,
		const unsigned int	version,
		std::vector< boost::shared_ptr< AbstractStimulusFunction > > &	rStimuli,
		AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *	pMesh
	)

inline

This method is the equivalent of LoadCardiacCells but Load the extracellular stimulus instead

Parameters

archive	the master archive; cells will actually be written to the process-specific archive.
version
rStimuli	the extracellular stimuli (will be filled from the archive).
pMesh	the mesh (needed to work out number of nodes). Here it is assumed we have already unarchived the mesh somewhere and the pointer passed in is not NULL.

Definition at line 580 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::ReplicateAdditionalCaches ( )

private

The parent class AbstractCardiacTissue has a method ReplicateCaches that replicates some caches of general use. This method replicates more caches that are specific to extended bidomain problems, namely:

Iionic and intracellular stimulus for the second cell
Extracellular stimulus
Gap junction conductivities (Ggap)

It is typically called right after the ReplicateCaches method in the parent class.

Definition at line 573 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

const c_matrix< double, SPACE_DIM, SPACE_DIM > & ExtendedBidomainTissue< 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 475 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetExtracellularStimulusCacheReplicated ( )

Returns: the extracellular stimulus

Definition at line 594 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

const std::vector< boost::shared_ptr< AbstractStimulusFunction > > & ExtendedBidomainTissue< SPACE_DIM >::rGetExtracellularStimulusDistributed ( ) const

Returns: a reference to the vector of distributed extracellular stimuli. Needed for archiving.

Definition at line 327 of file ExtendedBidomainTissue.cpp.

Referenced by ExtendedBidomainTissue< DIM >::SaveExtracellularStimulus().

template<unsigned SPACE_DIM>

const std::vector< double > & ExtendedBidomainTissue< SPACE_DIM >::rGetGapsDistributed ( ) const

Returns: a reference to the vector of distributed values of Ggaps. Needed for archiving.

Definition at line 321 of file ExtendedBidomainTissue.cpp.

Referenced by ExtendedBidomainTissue< DIM >::SaveExtendedBidomainCells().

template<unsigned SPACE_DIM>

ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetGgapCacheReplicated ( )

Returns: the values of ggap

Definition at line 600 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetIionicCacheReplicatedSecondCell ( )

Returns: the entire ionic current cache for the second cell

Definition at line 582 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

const c_matrix< double, SPACE_DIM, SPACE_DIM > & ExtendedBidomainTissue< SPACE_DIM >::rGetIntracellularConductivityTensorSecondCell ( unsigned elementIndex )

Returns: the intracellular conductivity tensor for the given element for tehs econd cell

Parameters

elementIndex index of the element of interest

Definition at line 489 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetIntracellularStimulusCacheReplicatedSecondCell ( )

Returns: the entire stimulus current cache for the second cell

Definition at line 588 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

const std::vector< AbstractCardiacCellInterface * > & ExtendedBidomainTissue< SPACE_DIM >::rGetSecondCellsDistributed ( ) const

Returns: a reference to the vector of distributed cells (second cell). Needed for archiving.

Definition at line 315 of file ExtendedBidomainTissue.cpp.

Referenced by ExtendedBidomainTissue< DIM >::SaveExtendedBidomainCells().

template<unsigned SPACE_DIM>

template<class Archive >

void ExtendedBidomainTissue< SPACE_DIM >::SaveExtendedBidomainCells	(	Archive &	archive,
		const unsigned int	version
	)		const

inline

This method is the equivalent of SaveCardiacCells in the abstract class but save both cells of the extended bidomain tissue

Parameters

archive	the master archive; cells will actually be written to the process-specific archive.
version

Definition at line 425 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

template<class Archive >

void ExtendedBidomainTissue< SPACE_DIM >::SaveExtracellularStimulus	(	Archive &	archive,
		const unsigned int	version
	)		const

inline

This method is the equivalent of SaveCardiacCells but Saves the extracellular stimulus instead

Parameters

archive	the master archive; cells will actually be written to the process-specific archive.
version

Definition at line 558 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive
version

Definition at line 91 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetAmFirstCell ( double value )

Parameters

value Am for the first cell

Definition at line 642 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetAmGap ( double value )

Parameters

value Am for the gap junction

Definition at line 654 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetAmSecondCell ( double value )

Parameters

value Am for the second cell

Definition at line 648 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetCmFirstCell ( double value )

Parameters

value Cm for the first cell

Definition at line 666 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetCmSecondCell ( double value )

Parameters

value Cm for the first cell

Definition at line 672 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetGGap ( double value )

Parameters

value conductance, in mS of the gap junction

Definition at line 660 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetGgapHeterogeneities	(	std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > > &	rGgapHeterogeneityRegions,
		std::vector< double >	rGgapValues
	)

Set the values of mCellHeterogeneityRegions and mGgapValues for the heterogeneities of Ggap.

Parameters

rGgapHeterogeneityRegions	a vector of (pointers to) heterogeneity regions for gap junctions
rGgapValues	a vector (of the same size as rGgapHeterogeneityRegions) with the respective values of Ggap for every region.

Definition at line 147 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetIntracellularConductivitiesSecondCell ( c_vector< double, SPACE_DIM > conductivities )

Sets the value of the conductivities for the second cell.

Parameters

conductivities the conductivities to be set.

Definition at line 460 of file ExtendedBidomainTissue.cpp.

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::SetUserSuppliedExtracellularStimulus ( bool flag )

This method allows modifications of the mUserSuppliedExtracellularStimulus flag (false by default). Other classes (e.g., Problem classes) can use this method to tell the Tissue that the user specified an extracellular stimulus.

Parameters

flag	; true if you want to tell the Tissue object that the user supplied an extracellular stimulus explicitly

Definition at line 309 of file ExtendedBidomainTissue.cpp.

Referenced by ExtendedBidomainProblem< DIM >::CreateCardiacTissue().

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< 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. This is a re-implementation from the version in the base class.

Parameters

existingSolution	the current voltage solution vector
time	the current simulation time
nextTime	when to simulate the cells until
updateVoltage	(unused here)

Reimplemented from AbstractCardiacTissue< SPACE_DIM >.

Definition at line 515 of file ExtendedBidomainTissue.cpp.

References DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), and PetscTools::ReplicateException().

template<unsigned SPACE_DIM>

void ExtendedBidomainTissue< SPACE_DIM >::UpdateAdditionalCaches	(	unsigned	globalIndex,
		unsigned	localIndex,
		double	nextTime
	)

private

The parent class AbstractCardiacTissue has a method UpdateCaches that updates some caches of general use. This method updates more caches that are specific to extended bidomain problems, namely:

Iionic and intracellular stimulus for the second cell
Extracellular stimulus
Gap junction conductivities (Ggap)

It is typically called right after the UpdateCaches method in the parent class.

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 564 of file ExtendedBidomainTissue.cpp.

Friends And Related Function Documentation

template<unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 83 of file ExtendedBidomainTissue.hpp.

Member Data Documentation

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mAmFirstCell

private

the Am for the first cell, set by the problem class and picked up by the assembler

Definition at line 152 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mAmGap

private

the Am for the gap junction, set by the problem class and picked up by the assembler

Definition at line 156 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mAmSecondCell

private

the Am for the second cell, set by the problem class and picked up by the assembler

Definition at line 154 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

std::vector< AbstractCardiacCellInterface* > ExtendedBidomainTissue< SPACE_DIM >::mCellsDistributedSecondCell

private

The vector of cells (the second one). Distributed.

Definition at line 143 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mCmFirstCell

private

the Cm for the first cell, set by the problem class and picked up by the assembler

Definition at line 158 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mCmSecondCell

private

the Cm for the second cell, set by the problem class and picked up by the assembler

Definition at line 160 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

std::vector<boost::shared_ptr<AbstractStimulusFunction> > ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimuliDistributed

private

The vector of stimuli for the extracellular stimulus. Distributed.

Definition at line 146 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimulusCacheReplicated

private

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

Definition at line 122 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

double ExtendedBidomainTissue< SPACE_DIM >::mGGap

private

the conductance of the gap junction, in mS/cm2. Set by the problem class and picked up by the assembler

Definition at line 162 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

template<unsigned SPACE_DIM>

ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mGgapCacheReplicated

private

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

Definition at line 128 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

std::vector<double> ExtendedBidomainTissue< SPACE_DIM >::mGgapDistributed

private

The vector of gap junction conductances. Distributed

Definition at line 149 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > ExtendedBidomainTissue< SPACE_DIM >::mGgapHeterogeneityRegions

private

vector of regions for Ggap heterogeneities

Definition at line 204 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

std::vector<double> ExtendedBidomainTissue< SPACE_DIM >::mGgapValues

private

values of heterogeneous Ggaps corresponding to mGgapHeterogeneityRegions. This has the same size as mGgapHeterogeneityRegions

Definition at line 206 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mIionicCacheReplicatedSecondCell

private

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

Definition at line 134 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

c_vector<double, SPACE_DIM> ExtendedBidomainTissue< SPACE_DIM >::mIntracellularConductivitiesSecondCell

private

Stores the values of the conductivities for the second cell. Accessible via get and set methods. The problem class will set it This variable is a convenient interface for other classes. It is used to fill in mpIntracellularConductivityTensorsSecondCell.

Definition at line 112 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mIntracellularStimulusCacheReplicatedSecondCell

private

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

Definition at line 140 of file ExtendedBidomainTissue.hpp.

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

template<unsigned SPACE_DIM>

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

private

Extracellular conductivity tensors.

Definition at line 116 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

AbstractConductivityTensors<SPACE_DIM, SPACE_DIM>* ExtendedBidomainTissue< SPACE_DIM >::mpIntracellularConductivityTensorsSecondCell

private

Intracellular conductivity tensors for the second cell.

Definition at line 106 of file ExtendedBidomainTissue.hpp.

template<unsigned SPACE_DIM>

bool ExtendedBidomainTissue< SPACE_DIM >::mUserSuppliedExtracellularStimulus

private

Whether the extracellular stimulus that is passed in was supplied by the user or not (it could be the default zero implementation). Initialise to false (user did not pass in anything).

Definition at line 168 of file ExtendedBidomainTissue.hpp.

Referenced by ExtendedBidomainTissue< DIM >::serialize().

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

heart/src/tissue/ExtendedBidomainTissue.hpp
heart/src/tissue/ExtendedBidomainTissue.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned SPACE_DIM> class ExtendedBidomainTissue< SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned SPACE_DIM>
class ExtendedBidomainTissue< SPACE_DIM >