BidomainProblem< DIM > Class Template Reference

#include <BidomainProblem.hpp>

Inheritance diagram for BidomainProblem< DIM >:

Collaboration diagram for BidomainProblem< DIM >:

List of all members.

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 58 of file BidomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

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 161 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem ( ) [inline]

Constructor just used for archiving

Definition at line 172 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

Member Function Documentation

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 73 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainTissue, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

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 90 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainTissue, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>

Vec BidomainProblem< DIM >::CreateInitialCondition ( ) [inline, 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 85 of file BidomainProblem.cpp.

References DistributedVector::Begin(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), DistributedVector::End(), HeartRegionCode::IsRegionBath(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and DistributedVector::Restore().

template<unsigned DIM>

void BidomainProblem< DIM >::AnalyseMeshForBath ( ) [inline, 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 39 of file BidomainProblem.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetRegion(), HeartRegionCode::GetValidBathId(), HeartRegionCode::GetValidTissueId(), HeartRegionCode::IsRegionBath(), HeartRegionCode::IsRegionTissue(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and PetscTools::ReplicateBool().

Referenced by BidomainProblem< DIM >::CreateCardiacTissue(), and BidomainProblem< DIM >::load().

template<unsigned DIM>

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

Create our bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 110 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), HeartConfig::GetUseStateVariableInterpolation(), HeartConfig::Instance(), BidomainProblem< DIM >::mpBidomainTissue, and AbstractCardiacProblem< DIM, DIM, 2 >::mpCellFactory.

template<unsigned DIM>

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

Create a suitable bidomain solver

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 118 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes, BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, BidomainProblem< DIM >::mpSolver, BidomainProblem< DIM >::mRowForAverageOfPhiZeroed, AbstractCardiacProblem< DIM, DIM, 2 >::mUseMatrixBasedRhsAssembly, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

Referenced by BidomainProblem< DIM >::OnEndOfTimestep().

template<unsigned DIM>

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

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 183 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned node ) [inline]

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:

node

the mesh node index giving the row at which to impose the constraint

Definition at line 195 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>

BidomainTissue< DIM > * BidomainProblem< DIM >::GetBidomainTissue ( ) [inline]

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

Definition at line 201 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpBidomainTissue.

template<unsigned DIM>

void BidomainProblem< DIM >::WriteInfo ( double time ) [inline, virtual]

Print out time and max/min voltage/phi_e values at current time.

Parameters:

time

current time.

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 208 of file BidomainProblem.cpp.

References PetscTools::AmMaster(), and AbstractCardiacProblem< DIM, DIM, 2 >::mSolution.

template<unsigned DIM>

void BidomainProblem< DIM >::DefineWriterColumns ( bool extending ) [inline, 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 234 of file BidomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), Hdf5DataWriter::DefineVariable(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), Hdf5DataWriter::GetVariableByName(), BidomainProblem< DIM >::mExtracelluarColumnId, and AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter.

template<unsigned DIM>

void BidomainProblem< DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)			`[inline, virtual]`

Write one timestep of output data to the primary results file. Adds the extracellular potential to the results.

Parameters:

	time	the current time
	voltageVec	the solution vector to write

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 249 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mExtracelluarColumnId, AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter, AbstractCardiacProblem< DIM, DIM, 2 >::mVoltageColumnId, Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutUnlimitedVariable(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

template<unsigned DIM>

void BidomainProblem< DIM >::PreSolveChecks ( ) [inline, 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 260 of file BidomainProblem.cpp.

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

template<unsigned DIM>

void BidomainProblem< DIM >::AtBeginningOfTimestep ( double time ) [inline, 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 297 of file BidomainProblem.cpp.

References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetLinearSystem(), AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, BidomainProblem< DIM >::mpSolver, LinearSystem::RemoveNullSpace(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::ResetBoundaryConditionsContainer().

template<unsigned DIM>

void BidomainProblem< DIM >::OnEndOfTimestep ( double time ) [inline, 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 338 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::CreateSolver(), HeartConfig::Instance(), AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, BidomainProblem< DIM >::mpSolver, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::ResetBoundaryConditionsContainer(), and AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep().

template<unsigned DIM>

void BidomainProblem< DIM >::SetUpAdditionalStoppingTimes ( std::vector< double > & rAdditionalStoppingTimes ) [inline, virtual]

Method to fill in a vector of additional stopping times consisting of the times when the electrodes are to be turned on and off

Parameters:

rAdditionalStoppingTimes

reference to vector that will contain the on and off times for the electrodes

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 376 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpElectrodes.

template<unsigned DIM>

template<class Archive>

void BidomainProblem< DIM >::LoadExtraArchiveForBidomain	(	Archive &	archive,
		unsigned	version
	)			`[inline]`

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 293 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>

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

Return whether this is a bidomain problem with bath or not

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 386 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mHasBath.

template<unsigned DIM>

void BidomainProblem< DIM >::SetElectrodes ( ) [inline, 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 280 of file BidomainProblem.cpp.

References HeartConfig::Instance(), BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpElectrodes, and AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Reimplemented in BidomainWithBathProblem< DIM >.

Definition at line 61 of file BidomainProblem.hpp.

Member Data Documentation

template<unsigned DIM>

BidomainTissue<DIM>* BidomainProblem< DIM >::mpBidomainTissue [protected]

The bidomain PDE

Definition at line 112 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateCardiacTissue(), BidomainProblem< DIM >::CreateSolver(), BidomainProblem< DIM >::GetBidomainTissue(), BidomainProblem< DIM >::load(), and BidomainProblem< DIM >::save().

template<unsigned DIM>

std::vector<unsigned> BidomainProblem< DIM >::mFixedExtracellularPotentialNodes [protected]

Nodes at which the extracellular voltage is fixed to zero (replicated)

Definition at line 115 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::BidomainProblem(), BidomainProblem< DIM >::CreateSolver(), BidomainProblem< DIM >::PreSolveChecks(), and BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned DIM>

unsigned BidomainProblem< DIM >::mExtracelluarColumnId [protected]

Used by the writer

Definition at line 117 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), and BidomainProblem< DIM >::WriteOneStep().

template<unsigned DIM>

unsigned BidomainProblem< DIM >::mRowForAverageOfPhiZeroed [protected]

Another method of resolving the singularity in the bidomain equations. Specifies a row of the matrix at which to impose an extra condition.

Definition at line 122 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateSolver(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::PreSolveChecks(), BidomainProblem< DIM >::save(), and BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed().

template<unsigned DIM>

bool BidomainProblem< DIM >::mHasBath [protected]

Whether the mesh has a bath, ie whether this is a bath simulation

Definition at line 125 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::CreateInitialCondition(), BidomainProblem< DIM >::CreateSolver(), BidomainProblem< DIM >::GetHasBath(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::save(), and BidomainProblem< DIM >::SetElectrodes().

template<unsigned DIM>

boost::shared_ptr<Electrodes<DIM> > BidomainProblem< DIM >::mpElectrodes [protected]

Electrodes used to provide a shock

Definition at line 128 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::OnEndOfTimestep(), BidomainProblem< DIM >::save(), BidomainProblem< DIM >::SetElectrodes(), and BidomainProblem< DIM >::SetUpAdditionalStoppingTimes().

template<unsigned DIM>

AbstractBidomainSolver<DIM,DIM>* BidomainProblem< DIM >::mpSolver [protected]

We need to save the solver that is being used to be able to switch off the electrodes (by adding default boundary conditions to the solver)

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 147 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep(), BidomainProblem< DIM >::CreateSolver(), and BidomainProblem< DIM >::OnEndOfTimestep().

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

heart/src/problem/BidomainProblem.hpp
heart/src/problem/BidomainProblem.cpp


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

BidomainProblem< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class BidomainProblem< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class BidomainProblem< DIM >