#include <BidomainProblem.hpp>

Inheritance diagram for BidomainProblem< DIM >:

Collaboration diagram for BidomainProblem< DIM >:

Public Member Functions
	BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false)
	BidomainProblem ()
void	SetFixedExtracellularPotentialNodes (std::vector< unsigned > nodes)
void	SetNodeForAverageOfPhiZeroed (unsigned node)
BidomainTissue< DIM > *	GetBidomainTissue ()
void	WriteInfo (double time)
virtual void	DefineWriterColumns (bool extending)
virtual void	WriteOneStep (double time, Vec voltageVec)
void	PreSolveChecks ()
void	AtBeginningOfTimestep (double time)
void	OnEndOfTimestep (double time)
void	SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes)
template<class Archive >
void	LoadExtraArchiveForBidomain (Archive &archive, unsigned version)
bool	GetHasBath ()
void	SetElectrodes ()
Protected Member Functions
Vec	CreateInitialCondition ()
void	AnalyseMeshForBath ()
virtual AbstractCardiacTissue < DIM > *	CreateCardiacTissue ()
virtual AbstractDynamicLinearPdeSolver < DIM, DIM, 2 > *	CreateSolver ()
Protected Attributes
BidomainTissue< DIM > *	mpBidomainTissue
std::vector< unsigned >	mFixedExtracellularPotentialNodes
unsigned	mExtracelluarColumnId
unsigned	mRowForAverageOfPhiZeroed
bool	mHasBath
boost::shared_ptr< Electrodes < DIM > >	mpElectrodes
AbstractBidomainSolver< DIM, DIM > *	mpSolver
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)
Friends
class	boost::serialization::access
class	TestPCTwoLevelsBlockDiagonal
class	TestBidomainWithBathProblem
class	TestCardiacSimulationArchiver

Detailed Description

template<unsigned DIM>
class BidomainProblem< DIM >

Class which specifies and solves a bidomain problem.

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 65 of file BidomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem	(	AbstractCardiacCellFactory< DIM > *	pCellFactory,
		bool	hasBath = `false`
	)

Constructor

Parameters:

pCellFactory	User defined cell factory which shows how the pde should create cells.
hasBath	Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).

Definition at line 156 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem ( )

Constructor just used for archiving

Definition at line 167 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

Member Function Documentation

template<unsigned DIM>

void BidomainProblem< DIM >::AnalyseMeshForBath ( ) [protected]

Annotate bath nodes with the correct region code, if a bath is present. Will throw if mHasBath is set but no bath is present in the mesh.

Definition at line 45 of file BidomainProblem.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetUnsignedAttribute(), HeartRegionCode::GetValidBathId(), HeartRegionCode::GetValidTissueId(), HeartRegionCode::IsRegionBath(), HeartRegionCode::IsRegionTissue(), and PetscTools::ReplicateBool().

Referenced by BidomainProblem< 3 >::load().

template<unsigned DIM>

void BidomainProblem< DIM >::AtBeginningOfTimestep ( double time ) [virtual]

Called at beginning of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch on the electrodes (if there are any).

Parameters:

time	the current time

Todo:: #1159 #1324 heart/src/problem/AbstractCardiacProblem.hpp:657 expects both pointing at the same place when unarchiving

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 292 of file BidomainProblem.cpp.

template<unsigned DIM>

AbstractCardiacTissue< DIM > * BidomainProblem< DIM >::CreateCardiacTissue ( ) [protected, virtual]

Create our bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 116 of file BidomainProblem.cpp.

References HeartConfig::GetUseStateVariableInterpolation(), and HeartConfig::Instance().

template<unsigned DIM>

Vec BidomainProblem< DIM >::CreateInitialCondition ( ) [protected, virtual]

Create normal initial condition but overwrite V to zero for bath nodes, if there are any.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 91 of file BidomainProblem.cpp.

References DistributedVector::Begin(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), DistributedVector::End(), HeartRegionCode::IsRegionBath(), and DistributedVector::Restore().

template<unsigned DIM>

AbstractDynamicLinearPdeSolver< DIM, DIM, 2 > * BidomainProblem< DIM >::CreateSolver ( ) [protected, virtual]

Create a suitable bidomain solver

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 124 of file BidomainProblem.cpp.

References AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned DIM>

void BidomainProblem< DIM >::DefineWriterColumns ( bool extending ) [virtual]

Define what variables are written to the primary results file. Adds the extracellular potential.

Parameters:

extending whether we are extending an existing results file

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 229 of file BidomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().

template<unsigned DIM>

BidomainTissue< DIM > * BidomainProblem< DIM >::GetBidomainTissue ( )

Get the pde. Can only be called after Initialise()

Definition at line 196 of file BidomainProblem.cpp.

template<unsigned DIM>

bool BidomainProblem< DIM >::GetHasBath ( ) [virtual]

Return whether this is a bidomain problem with bath or not

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 381 of file BidomainProblem.cpp.

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Load the member variables from an archive.

Parameters:

archive
version

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 97 of file BidomainProblem.hpp.

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::LoadExtraArchiveForBidomain	(	Archive &	archive,
		unsigned	version
	)

Used when loading a set of archives written by a parallel simulation onto a single process. Loads data from the given process-specific archive (written by a non-master process) and merges it into our data.

Parameters:

archive	the archive to load
version	the archive file version

Note:: The process-specific archives currently contain the following data. If the layout changes, then this method will need to be altered, since it hard-codes knowledge of the order in which things are archived.

Stuff known by AbstractCardiacProblem
mpElectrodes->mpBoundaryConditionsContainer

This gets called by AbstractCardiacProblem::LoadExtraArchive when it's done the generic stuff.

Todo:: #1159 sanity check that the contents of p_bcc and mpElectrodes->GetBoundaryConditionsContainer() match.

Definition at line 300 of file BidomainProblem.hpp.

References AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, and AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive().

template<unsigned DIM>

void BidomainProblem< DIM >::OnEndOfTimestep ( double time ) [virtual]

Called at end of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch off the electrodes (if there are any).

Parameters:

time	the current time

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 333 of file BidomainProblem.cpp.

References HeartConfig::Instance().

template<unsigned DIM>

void BidomainProblem< DIM >::PreSolveChecks ( ) [virtual]

Performs a series of checks before solving. Checks that a suitable method of resolving the singularity is being used.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 255 of file BidomainProblem.cpp.

References EXCEPTION, HeartConfig::GetUseRelativeTolerance(), HeartConfig::Instance(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().

template<unsigned DIM>

template<class Archive >

void BidomainProblem< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const `[inline, private]`

Save the member variables to an archive.

Parameters:

archive
version

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 80 of file BidomainProblem.hpp.

template<unsigned DIM>

void BidomainProblem< DIM >::SetElectrodes ( ) [virtual]

Set an electrode object (which provides boundary conditions). Only valid if there is a bath.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 275 of file BidomainProblem.cpp.

References HeartConfig::Instance().

template<unsigned DIM>

void BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned > nodes )

Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.

Parameters:

nodes the nodes to be fixed.

Note:: currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.

Definition at line 178 of file BidomainProblem.cpp.

template<unsigned DIM>

void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned node )

Set which row of the linear system should be used to enforce the condition that the average of phi_e is zero. If not called, this condition will not be used.

Parameters: