AbstractCardiacPde< ELEM_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCardiacPde.hpp>

Inheritance diagram for AbstractCardiacPde< ELEM_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCardiacPde< ELEM_DIM, SPACE_DIM >:

List of all members.

Public Member Functions

AbstractCardiacPde (AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > *pCellFactory, const unsigned stride=1)

AbstractCardiacPde (std::vector< AbstractCardiacCell * > &rCellsDistributed, const unsigned stride=1)

virtual ~AbstractCardiacPde ()

void SetCacheReplication (bool doCacheReplication)

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

AbstractCardiacCell * GetCardiacCell (unsigned globalIndex)

virtual void SolveCellSystems (Vec existingSolution, double time, double nextTime)

ReplicatableVector & rGetIionicCacheReplicated ()

ReplicatableVector & rGetIntracellularStimulusCacheReplicated ()

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

void ReplicateCaches ()

const std::vector
< AbstractCardiacCell * > & GetCellsDistributed () const

Protected Attributes

AbstractConductivityTensors
< SPACE_DIM > * mpIntracellularConductivityTensors

std::vector
< AbstractCardiacCell * > mCellsDistributed

ReplicatableVector mIionicCacheReplicated

ReplicatableVector mIntracellularStimulusCacheReplicated

const unsigned mStride

HeartConfig * mpConfig

bool mDoCacheReplication

bool mDoOneCacheReplication

DistributedVectorFactory * mpDistributedVectorFactory

bool mpFactoryWasUnarchived

Private Member Functions

template<class Archive>

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

Friends

class boost::serialization::access

Detailed Description

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>
class AbstractCardiacPde< ELEM_DIM, SPACE_DIM >

Class containing common functionality to monodomain and bidomain PDEs.

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

Also contains knowledge of parallelisation in the form of the distributed vector factory.

Definition at line 77 of file AbstractCardiacPde.hpp.

Constructor & Destructor Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde	(	AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > *	pCellFactory,
		const unsigned	stride = `1`
	)			`[inline]`

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

Todo:: tidy up using extract method refactoring

Parameters:

	pCellFactory	factory to use to create cells.
	stride	determines how to access in the solution vector (1 for monodomain, 2 for bidomain).

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

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

Definition at line 42 of file AbstractCardiacPde.cpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde	(	std::vector< AbstractCardiacCell * > &	rCellsDistributed,
		const unsigned	stride = `1`
	)			`[inline]`

This constructor is called by the archiver

Parameters:

	rCellsDistributed	pointers to the cardiac cells.
	stride	determines how to access in the solution vector (1 for monodomain, 2 for bidomain).

Todo:: : #98: The state of the object is inconsistent since mpIntracellularConductivityTensors has not been set.

Definition at line 150 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpIntracellularConductivityTensors.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::~AbstractCardiacPde ( ) [inline, virtual]

Virtual destructor

Todo:: : #98 once the archiving constructor is creating the conductivity tensors properly we won't need this if statement

Definition at line 164 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpFactoryWasUnarchived, and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpIntracellularConductivityTensors.

Member Function Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

template<class Archive>

void AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive
	version

Todo:: #98 Check that mpIntracellularConductivityTensors is archived properly here.

Reimplemented in BidomainPde< SPACE_DIM >, MonodomainPde< ELEM_DIM, SPACE_DIM >, BidomainPde< DIM >, MonodomainPde< ELEM_DIM, ELEM_DIM >, and MonodomainPde< ELEMENT_DIM, SPACE_DIM >.

Definition at line 90 of file AbstractCardiacPde.hpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

void AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SetCacheReplication ( bool doCacheReplication ) [inline]

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 192 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mDoCacheReplication.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

const c_matrix< double, SPACE_DIM, SPACE_DIM > & AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIntracellularConductivityTensor ( unsigned elementIndex ) [inline]

Get the intracellular conductivity tensor for the given element

Parameters:

elementIndex

index of the element of interest

Definition at line 198 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpIntracellularConductivityTensors.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

AbstractCardiacCell * AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::GetCardiacCell ( unsigned globalIndex ) [inline]

Get 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 205 of file AbstractCardiacPde.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed, and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpDistributedVectorFactory.

Referenced by CardiacElectroMechanicsProblem< DIM >::WriteWatchedLocationData().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

void AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems	(	Vec	existingSolution,
		double	time,
		double	nextTime
	)			`[inline, virtual]`

SolveCellSystems()

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

Note:: This used to be called PrepareForAssembleSystem, but that method is now a virtual method in the assemblers not the pdes.

Parameters:

	existingSolution	the current voltage solution vector
	time	the current simulation time
	nextTime	when to simulate the cells until

Definition at line 214 of file AbstractCardiacPde.cpp.

References DistributedVector::Begin(), GenericEventHandler< 11, HeartEventHandler >::BeginEvent(), DistributedVectorFactory::CreateDistributedVector(), DistributedVector::End(), GenericEventHandler< 11, HeartEventHandler >::EndEvent(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mDoCacheReplication, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mDoOneCacheReplication, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpDistributedVectorFactory, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::ReplicateCaches(), PetscTools::ReplicateException(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::UpdateCaches().

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::PrepareForAssembleSystem().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIionicCacheReplicated ( ) [inline]

Get the entire ionic current cache

Definition at line 256 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIionicCacheReplicated.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

ReplicatableVector & AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIntracellularStimulusCacheReplicated ( ) [inline]

Get the entire stimulus current cache

Definition at line 262 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated.

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

void AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::UpdateCaches	(	unsigned	globalIndex,
		unsigned	localIndex,
		double	nextTime
	)			`[inline]`

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 268 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIionicCacheReplicated, and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

void AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::ReplicateCaches ( ) [inline]

Replicate the Iionic and intracellular stimulus caches.

Definition at line 275 of file AbstractCardiacPde.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIionicCacheReplicated, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated, AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpDistributedVectorFactory, and ReplicatableVector::Replicate().

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems().

template<unsigned ELEM_DIM, unsigned SPACE_DIM>

const std::vector< AbstractCardiacCell * > & AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::GetCellsDistributed ( ) const [inline]

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

Definition at line 282 of file AbstractCardiacPde.cpp.

References AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed.

Friends And Related Function Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in BidomainPde< SPACE_DIM >, MonodomainPde< ELEM_DIM, SPACE_DIM >, BidomainPde< DIM >, MonodomainPde< ELEM_DIM, ELEM_DIM >, and MonodomainPde< ELEMENT_DIM, SPACE_DIM >.

Definition at line 82 of file AbstractCardiacPde.hpp.

Member Data Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

AbstractConductivityTensors<SPACE_DIM>* AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpIntracellularConductivityTensors [protected]

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

Definition at line 104 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeDiffusionTerm(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIntracellularConductivityTensor(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::~AbstractCardiacPde().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

std::vector< AbstractCardiacCell* > AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mCellsDistributed [protected]

The vector of cells. Distributed.

Definition at line 107 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::GetCardiacCell(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::GetCellsDistributed(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::UpdateCaches(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::~AbstractCardiacPde().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

ReplicatableVector AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIionicCacheReplicated [protected]

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

Definition at line 113 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeNonlinearSourceTermAtNode(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::ReplicateCaches(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIionicCacheReplicated(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::UpdateCaches().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

ReplicatableVector AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mIntracellularStimulusCacheReplicated [protected]

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

Definition at line 119 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeNonlinearSourceTermAtNode(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::ReplicateCaches(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::rGetIntracellularStimulusCacheReplicated(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::UpdateCaches().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

const unsigned AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mStride [protected]

Constant set to 1 in monodomain and 2 in bidomain. Used when accessing the voltage components in the solution vector (because the solution vector is of the form (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j.

Definition at line 127 of file AbstractCardiacPde.hpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

HeartConfig* AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpConfig [protected]

Local pointer to the HeartConfig singleton instance, for convenience.

Definition at line 130 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeDuDtCoefficientFunction(), and MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeNonlinearSourceTermAtNode().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

bool AbstractCardiacPde< ELEM_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 141 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SetCacheReplication(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

bool AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mDoOneCacheReplication [protected]

This is to mark the conventional assembly on the first time step.

Todo:: maybe we don't want the conventional assembly even in the first time step.

Definition at line 148 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

DistributedVectorFactory* AbstractCardiacPde< ELEM_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.

Definition at line 155 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::GetCardiacCell(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::ReplicateCaches(), AbstractCardiacPde< SPACE_DIM >::serialize(), AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::SolveCellSystems(), and AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::~AbstractCardiacPde().

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>

bool AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::mpFactoryWasUnarchived [protected]

Wether the distributed vector factory was unarchived or got from the cell factory.

Definition at line 160 of file AbstractCardiacPde.hpp.

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::~AbstractCardiacPde().

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

/tmp/release_1.1/heart/src/pdes/AbstractCardiacPde.hpp
/tmp/release_1.1/heart/src/pdes/AbstractCardiacPde.cpp


Public Member Functions
	AbstractCardiacPde (AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > *pCellFactory, const unsigned stride=1)
	AbstractCardiacPde (std::vector< AbstractCardiacCell * > &rCellsDistributed, const unsigned stride=1)
virtual	~AbstractCardiacPde ()
void	SetCacheReplication (bool doCacheReplication)
const c_matrix< double, SPACE_DIM, SPACE_DIM > &	rGetIntracellularConductivityTensor (unsigned elementIndex)
AbstractCardiacCell *	GetCardiacCell (unsigned globalIndex)
virtual void	SolveCellSystems (Vec existingSolution, double time, double nextTime)
ReplicatableVector &	rGetIionicCacheReplicated ()
ReplicatableVector &	rGetIntracellularStimulusCacheReplicated ()
void	UpdateCaches (unsigned globalIndex, unsigned localIndex, double nextTime)
void	ReplicateCaches ()
const std::vector < AbstractCardiacCell * > &	GetCellsDistributed () const
Protected Attributes
AbstractConductivityTensors < SPACE_DIM > *	mpIntracellularConductivityTensors
std::vector < AbstractCardiacCell * >	mCellsDistributed
ReplicatableVector	mIionicCacheReplicated
ReplicatableVector	mIntracellularStimulusCacheReplicated
const unsigned	mStride
HeartConfig *	mpConfig
bool	mDoCacheReplication
bool	mDoOneCacheReplication
DistributedVectorFactory *	mpDistributedVectorFactory
bool	mpFactoryWasUnarchived
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

AbstractCardiacPde< ELEM_DIM, SPACE_DIM > Class Template Reference

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM> class AbstractCardiacPde< ELEM_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>
class AbstractCardiacPde< ELEM_DIM, SPACE_DIM >