AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

#include <AbstractCardiacProblem.hpp>

Inherits AbstractUntemplatedCardiacProblem.

Collaboration diagram for AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Public Member Functions
	AbstractCardiacProblem (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)
	AbstractCardiacProblem ()
virtual	~AbstractCardiacProblem ()
void	Initialise ()
void	SetNodesPerProcessorFilename (const std::string &rFilename)
void	SetBoundaryConditionsContainer (BccType pBcc)
virtual void	PreSolveChecks ()
virtual Vec	CreateInitialCondition ()
void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
void	PrintOutput (bool rPrintOutput)
void	SetWriteInfo (bool writeInfo=true)
Vec	GetSolution ()
DistributedVector	GetSolutionDistributedVector ()
double	GetCurrentTime ()
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()
AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	GetTissue ()
void	Solve ()
void	CloseFilesAndPostProcess ()
virtual void	WriteInfo (double time)=0
virtual void	DefineWriterColumns (bool extending)
void	DefineExtraVariablesWriterColumns (bool extending)
virtual void	WriteOneStep (double time, Vec voltageVec)=0
void	WriteExtraVariablesOneStep ()
bool	InitialiseWriter ()
void	SetOutputNodes (std::vector< unsigned > &rNodesToOutput)
Hdf5DataReader	GetDataReader ()
virtual void	AtBeginningOfTimestep (double time)
virtual void	OnEndOfTimestep (double time)
virtual void	SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes)
void	SetUseTimeAdaptivityController (bool useAdaptivity, AbstractTimeAdaptivityController *pController=NULL)
template<class Archive >
void	LoadExtraArchive (Archive &archive, unsigned version)
virtual bool	GetHasBath ()
virtual void	SetElectrodes ()
void	AddOutputModifier (boost::shared_ptr< AbstractOutputModifier > pOutputModifier)
Protected Member Functions
virtual AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	CreateCardiacTissue ()=0
virtual AbstractDynamicLinearPdeSolver < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	CreateSolver ()=0
virtual void	CreateMeshFromHeartConfig ()
Protected Attributes
std::string	mMeshFilename
bool	mAllocatedMemoryForMesh
bool	mWriteInfo
bool	mPrintOutput
std::vector< unsigned >	mNodesToOutput
unsigned	mVoltageColumnId
std::vector< unsigned >	mExtraVariablesId
unsigned	mTimeColumnId
unsigned	mNodeColumnId
AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	mpCardiacTissue
BccType	mpBoundaryConditionsContainer
BccType	mpDefaultBoundaryConditionsContainer
AbstractDynamicLinearPdeSolver < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpSolver
AbstractCardiacCellFactory < ELEMENT_DIM, SPACE_DIM > *	mpCellFactory
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh
Vec	mSolution
double	mCurrentTime
AbstractTimeAdaptivityController *	mpTimeAdaptivityController
Hdf5DataWriter *	mpWriter
std::vector< boost::shared_ptr < AbstractOutputModifier > >	mOutputModifiers
Private Types
typedef boost::shared_ptr < BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > >	BccType
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)
template<class Archive >
void	SaveBoundaryConditions (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BccType pBcc) const
template<class Archive >
BccType	LoadBoundaryConditions (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
Friends
class	TestBidomainWithBath
class	TestMonodomainProblem
class	TestCardiacSimulationArchiver
class	boost::serialization::access
class	CardiacElectroMechanicsProblem

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Base class for cardiac problems; contains code generic to mono-/bi-domain and bidomain-with-bath.

This class contains the tissue (PDEs and 'cells' ODEs), boundary conditions, and postprocessing/results writers.

It is called by CardiacSimulation, which is the outer wrapper class for running a cardiac simulation, used by the executable.

Many non-standard simulations will use this class directly, and this is the preferred method for non-executable users. See tutorials for usage.

Definition at line 115 of file AbstractCardiacProblem.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

typedef boost::shared_ptr<BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> > AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BccType [private]

To save typing

Definition at line 123 of file AbstractCardiacProblem.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem ( AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > * pCellFactory ) [inline]

Constructor

Parameters:

pCellFactory

User defined cell factory which shows how the pde should create cells.

Definition at line 54 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), EXCEPTION, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem ( ) [inline]

Constructor used by archiving.

Definition at line 78 of file AbstractCardiacProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem ( ) [inline, virtual]

Destructor

Definition at line 100 of file AbstractCardiacProblem.cpp.

References PetscTools::Destroy(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddOutputModifier ( boost::shared_ptr< AbstractOutputModifier > pOutputModifier ) [inline]

Add an output modifier onto a list of such objects. These will be processed in the order in which they have been given. The modifier should not be destroyed before the solve loop has completed

Parameters:

pOutputModifier

Pointer to the modifier to be added

Definition at line 754 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AtBeginningOfTimestep ( double time ) [inline, virtual]

Called at beginning of each time step in the main time-loop in Solve(). Empty implementation but can be overloaded by child classes.

Parameters:

time

the current time

Reimplemented in BidomainProblem< DIM >.

Definition at line 679 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess ( ) [inline]

Closes the files where the solution is stored and, if specified so (as it is by default), converts the output to Meshalyzer format by calling the WriteFilesUsingMesh method in the MeshalyzerWriter class.

Note:: This method is collective, and hence must be called by all processes.

Definition at line 587 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), RelativeTo::ChasteTestOutput, GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetHasBath(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GetSubdirectory(), HeartConfig::GetVisualizeWithMeshalyzer(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, HeartConfig::Write(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateCardiacTissue ( ) [protected, pure virtual]

Subclasses must override this method to create a PDE object of the appropriate type.

This class will take responsibility for freeing the object when it is finished with.

Returns:: a pointer to the newly created tissue

Implemented in BidomainProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition ( ) [inline, virtual]

This method sets the initial condition for the PDE by getting the voltages (V) from the cell models at the nodes.

If the problem dimension is two (Bidomain) the second variable (phi_e) is set to zero.

This is virtual so BidomainProblem can overwrite V to zero for bath nodes, if there are any.

Todo:: Perhaps this should be a method of AbstractCardiacTissue??

Returns:: the newly created intial conditions vector

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 263 of file AbstractCardiacProblem.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and DistributedVector::Restore().

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateMeshFromHeartConfig ( ) [inline, protected, virtual]

Subclasses must override this method to create a suitable mesh object.

Only needed if the subclass needs something other than a DistributedTetrahedralMesh.

This class will take responsibility for freeing the object when it is finished with.

Definition at line 215 of file AbstractCardiacProblem.cpp.

References HeartConfig::GetMeshPartitioning(), HeartConfig::Instance(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateSolver ( ) [protected, pure virtual]

Subclasses must override this method to create a suitable solver object.

This class will take responsibility for freeing the object when it is finished with.

Returns:: pointer to newly created PDE solver

Implemented in BidomainProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns ( bool extending ) [inline]

Define the user specified variables to be written to the primary results file

Parameters:

extending

whether we are extending an existing results file

Definition at line 710 of file AbstractCardiacProblem.cpp.

References Hdf5DataWriter::DefineVariable(), HeartConfig::GetOutputVariables(), Hdf5DataWriter::GetVariableByName(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mExtraVariablesId, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns ( bool extending ) [inline, virtual]

Define what variables are written to the primary results file.

Parameters:

extending

whether we are extending an existing results file

Reimplemented in BidomainProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

Definition at line 679 of file AbstractCardiacProblem.cpp.

References Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::DefineVariable(), TimeStepper::EstimateTimeSteps(), Hdf5DataWriter::GetVariableByName(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVoltageColumnId.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetCurrentTime ( ) [inline]

Returns:: the current time of the simulation

Definition at line 330 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Hdf5DataReader AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetDataReader ( ) [inline]

Returns:: a newly created data reader configured to read the results we've been outputting.

Definition at line 868 of file AbstractCardiacProblem.cpp.

References EXCEPTION, and HeartConfig::Instance().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetHasBath ( ) [inline, virtual]

Returns:: whether there's bath defined in this problem

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 878 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolution ( ) [inline]

Returns:: the final solution vector. This vector is distributed over all processes.

In case of Bidomain, this is of length 2*numNodes, and 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.

Use with caution since we don't want to alter the state of the PETSc vector.

Definition at line 318 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

DistributedVector AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector ( ) [inline]

Returns:: the solution vector, wrapped in a DistributedVector.

See also GetSolution.

Definition at line 324 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetTissue ( ) [inline]

Returns:: the cardiac tissue object used

Definition at line 343 of file AbstractCardiacProblem.cpp.

References EXCEPTION, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise ( ) [inline]

Initialise the system, once parameters have been set up.

Must be called before first calling Solve(). If loading from a checkpoint, do NOT call this method, as it can also be used to reset the problem to perform another simulation from time 0.

Definition at line 115 of file AbstractCardiacProblem.cpp.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter ( ) [inline]

It creates and initialises the hdf writer from the Hdf5DataWriter class. It passes the output directory and file name to it. It is called by Solve(), if the output needs to be generated.

This method will try to open an existing .h5 file for extension if we are loading from an archive and one is present.

Returns:: whether the writer is outputting to an existing file.

Definition at line 795 of file AbstractCardiacProblem.cpp.

References RelativeTo::Absolute, Hdf5DataWriter::ApplyPermutation(), PetscTools::Barrier(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), Hdf5DataWriter::EndDefineMode(), EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), OutputFileHandler::GetChasteTestOutputDirectory(), HeartConfig::GetOutputDirectory(), HeartConfig::GetOutputFilenamePrefix(), Hdf5DataReader::GetUnlimitedDimensionValues(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution, and HeartConfig::SetOutputUsingOriginalNodeOrdering().

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive >

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Load the member variables.

Parameters:

	archive
	version

Todo:: #1317 code for saving/loading mSolution is PROBLEM_DIM specific, move it into the save/load methods for Mono and BidomainProblem. (ExtendedBidomain has its own already.)

Todo:: #1317 is there a reason we can't use PETSc's load/save vector functionality?

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 220 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive >

BccType AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadBoundaryConditions	(	Archive &	archive,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh
	)			`[inline, private]`

Serialization helper method to load a boundary conditions container.

Parameters:

	archive	the archive to load from
	pMesh	the mesh boundary conditions are to be defined on

Returns:: the loaded container

Definition at line 357 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::load().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive >

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive	(	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.

(via mpMesh) DistributedVectorFactory*
(via mpCardiacTissue LoadCardiacCells) DistributedVectorFactory*
(via mpCardiacTissue LoadCardiacCells) number_of_cells and sequence of AbstractCardiacCell*, possibly with Purkinje interleaved
(via mpCardiacTissue) DistributedVectorFactory*
mpBoundaryConditionsContainer
mpDefaultBoundaryConditionsContainer
(if we're a BidomainProblem) stuff in BidomainProblem::LoadExtraArchiveForBidomain

Definition at line 768 of file AbstractCardiacProblem.hpp.

References DistributedVectorFactory::GetNumProcs(), DistributedVectorFactory::GetOriginalFactory(), and BidomainProblem< DIM >::LoadExtraArchiveForBidomain().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::OnEndOfTimestep ( double time ) [inline, virtual]

Called at end of each time step in the main time-loop in Solve(). Empty implementation but can be overloaded by child classes.

Parameters:

time

the current time

Reimplemented in BidomainProblem< DIM >.

Definition at line 689 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks ( ) [inline, virtual]

Performs a series of checks before solving. It checks whether the cardiac pde has been defined, whether the simulation time is greater than zero and whether the output directory is specified (or the output is set not to be produced). It throws exceptions if any of the above checks fails.

Todo:: remove magic number? (#1884)

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 227 of file AbstractCardiacProblem.cpp.

References EXCEPTION, HeartConfig::GetPdeTimeStep(), HeartConfig::GetSimulationDuration(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrintOutput ( bool rPrintOutput ) [inline]

Set whether the simulation will generate results files.

Parameters:

rPrintOutput

Definition at line 306 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::rGetMesh ( ) [inline]

Returns:: the mesh used

Definition at line 336 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive >

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)			const `[inline, private]`

Save the member variables.

Parameters:

	archive
	version

Todo:: #1317 code for saving/loading mSolution is PROBLEM_DIM specific, move it into the save/load methods for Mono and BidomainProblem. Note that extended_bidomain has its own version of this code.

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 136 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive >

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SaveBoundaryConditions	(	Archive &	archive,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		BccType	pBcc
	)			const `[inline, private]`

Serialization helper method to save a boundary conditions container.

Parameters:

	archive	the archive to save to
	pMesh	the mesh boundary conditions are defined on
	pBcc	the container to save

Definition at line 342 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::save().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer ( BccType pBcc ) [inline]

Set the boundary conditions container.

Parameters:

pBcc

is a pointer to a boundary conditions container

Definition at line 221 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetElectrodes ( ) [inline, virtual]

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

Reimplemented in BidomainProblem< DIM >.

Definition at line 884 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * pMesh ) [inline]

This only needs to be called if a mesh filename has not been set.

Parameters:

pMesh

the mesh object to use

Definition at line 293 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetNodesPerProcessorFilename ( const std::string & rFilename )

Set a file from which the nodes for each processor are read

Parameters:

rFilename

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputNodes ( std::vector< unsigned > & rNodesToOutput ) [inline]

Specifies which nodes in the mesh to output. This method must be called before InitialiseWriter, otherwise all nodes will still be output. If this method is called when extending an existing HDF5 file, it will be ignored.

Parameters:

rNodesToOutput

is a reference to a vector with the indexes of the nodes where the output is desired. If empty, the output will be for all the nodes in the mesh.

Definition at line 862 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetUpAdditionalStoppingTimes ( std::vector< double > & rAdditionalStoppingTimes ) [inline, virtual]

Allow subclasses to define additional 'stopping times' for the printing time step loop. This allows bidomain simulations to specify exactly when the Electrodes should be turned on or off.

Parameters:

rAdditionalStoppingTimes

to be filled in with the additional stopping times

Reimplemented in BidomainProblem< DIM >.

Definition at line 699 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetUseTimeAdaptivityController	(	bool	useAdaptivity,
		AbstractTimeAdaptivityController *	pController = `NULL`
	)			`[inline]`

Todo:: #1704 add default adaptivity controller and allow the user just to call with true

Set whether (or not) to use a time adaptivity controller

Parameters:

	useAdaptivity	whether to use adaptivity
	pController	The controller (only relevant if useAdaptivity==true)

Definition at line 353 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpTimeAdaptivityController.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetWriteInfo ( bool writeInfo = true ) [inline]

Set whether extra info will be written to stdout during computation.

Parameters:

writeInfo

Definition at line 312 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve ( ) [inline]

First performs some checks by calling the PreSolveChecks method. It creates an solver to which it passes the boundary conditions specified by the user (otherwise it passes the defauls bcc). It then calls the Solve method on the solver class. It also handles the output, if necessary.

Note:: This method is collective, and hence must be called by all processes.

Definition at line 370 of file AbstractCardiacProblem.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep ( ) [inline]

Write one timestep of output data for the extra variables to the primary results file.

Definition at line 748 of file AbstractCardiacProblem.cpp.

References DistributedVector::Begin(), PetscTools::Destroy(), DistributedVector::End(), HeartConfig::GetOutputVariables(), HeartConfig::Instance(), HeartRegionCode::IsRegionBath(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mExtraVariablesId, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, Hdf5DataWriter::PutVector(), and DistributedVector::Restore().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteInfo ( double time ) [pure virtual]

Write informative details about the progress of the simulation to standard output.

Implemented only in subclasses.

Parameters:

time

the current time

Implemented in BidomainProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)			`[pure virtual]`

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

Parameters:

	time	the current time
	voltageVec	the solution vector to write

Implemented in BidomainProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Needed for serialization.

Reimplemented in BidomainProblem< DIM >, BidomainWithBathProblem< DIM >, ExtendedBidomainProblem< DIM >, and MonodomainProblem< ELEMENT_DIM, SPACE_DIM >.

Definition at line 127 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class CardiacElectroMechanicsProblem [friend]

CardiacElectroMechanicsProblem needs access to mpWriter.

Definition at line 459 of file AbstractCardiacProblem.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh [protected]

Whether this problem class has created the mesh itself, as opposed to being given it

Definition at line 380 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime [protected]

The current simulation time.

This is used to be able to restart simulations at a point other than time zero, either because of repeated calls to Solve (with increased simulation duration) or because of restarting from a checkpoint.

Definition at line 423 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::vector<unsigned> AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mExtraVariablesId [protected]

List of extra variables to be written to HDF5 file

Definition at line 392 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::string AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mMeshFilename [protected]

Meshes can be read from file or instantiated and passed directly to this class, this is for the former

Definition at line 377 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::load(), and AbstractCardiacProblem< DIM, DIM, 1 >::save().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodeColumnId [protected]

Used by the writer

Definition at line 396 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::vector<unsigned> AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput [protected]

If only outputing voltage for selected nodes, which nodes to output at

Definition at line 387 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::vector<boost::shared_ptr<AbstractOutputModifier> > AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOutputModifiers [protected]

A vector of user-defined output modifiers which may be used to produce lightweight on the fly output

Definition at line 469 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::AddOutputModifier(), AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BccType AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer [protected]

Boundary conditions container used in the simulation

Definition at line 402 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacTissue [protected]

The monodomain or bidomain pde

Definition at line 399 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetTissue(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory [protected]

The cell factory creates the cells for each node

Definition at line 408 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BccType AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDefaultBoundaryConditionsContainer [protected]

It is convenient to also have a separate variable for default (zero-Neumann) boundary conditions

Definition at line 404 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh [protected]

The mesh. Can either by passed in, or the mesh filename can be set

Definition at line 410 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput [protected]

Whether to write any output at all

Definition at line 384 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrintOutput(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpSolver [protected]

The PDE solver

Reimplemented in BidomainProblem< DIM >, and ExtendedBidomainProblem< DIM >.

Definition at line 406 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTimeAdaptivityController* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpTimeAdaptivityController [protected]

Adaptivity controller (defaults to NULL).

Definition at line 426 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetUseTimeAdaptivityController(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Hdf5DataWriter* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter [protected]

The object to use to write results to disk.

Definition at line 464 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution [protected]

The current solution vector, of the form [V_0 .. V_N ] for monodomain and [V_0 phi_0 .. V_N phi_N] for bidomain

Definition at line 414 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTimeColumnId [protected]

Used by the writer

Definition at line 394 of file AbstractCardiacProblem.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVoltageColumnId [protected]

Used by the writer

Definition at line 390 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo [protected]

Whether to print some statistics (max/min voltage) to screen during the simulation

Definition at line 382 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< DIM, DIM, 1 >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetWriteInfo(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

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

heart/src/problem/AbstractCardiacProblem.hpp
heart/src/problem/AbstractCardiacProblem.cpp

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM> class AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >