#include <AbstractCardiacProblem.hpp>

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

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	SetUseHdf5DataWriterCache (bool useCache=true)

void	SetHdf5DataWriterTargetChunkSizeAndAlignment (hsize_t size)

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)

Public Member Functions inherited from AbstractUntemplatedCardiacProblem
virtual	~AbstractUntemplatedCardiacProblem ()

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

bool	mUseHdf5DataWriterCache

hsize_t	mHdf5DataWriterChunkSizeAndAlignment

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

template<unsigned DIM, unsigned ELEC_PROB_DIM>
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 113 of file AbstractCardiacProblem.hpp.

Member Typedef Documentation

◆ BccType

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 121 of file AbstractCardiacProblem.hpp.

Constructor & Destructor Documentation

◆ AbstractCardiacProblem() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Constructor

Parameters

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

Definition at line 52 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.

◆ AbstractCardiacProblem() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem ( )

Constructor used by archiving.

Definition at line 78 of file AbstractCardiacProblem.cpp.

◆ ~AbstractCardiacProblem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem ( )

virtual

Destructor

Definition at line 102 of file AbstractCardiacProblem.cpp.

References PetscTools::Destroy().

Member Function Documentation

◆ AddOutputModifier()

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 799 of file AbstractCardiacProblem.hpp.

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

◆ AtBeginningOfTimestep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

inlinevirtual

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 726 of file AbstractCardiacProblem.hpp.

◆ CloseFilesAndPostProcess()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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.

◆ CreateCardiacTissue()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

virtual AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateCardiacTissue ( )

protectedpure 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 >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

◆ CreateInitialCondition()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition ( )

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.

Returns: the newly created intial conditions vector

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

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

Definition at line 265 of file AbstractCardiacProblem.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), and DistributedVector::Restore().

Referenced by BidomainProblem< DIM >::CreateInitialCondition(), and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::CreateInitialCondition().

◆ CreateMeshFromHeartConfig()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateMeshFromHeartConfig ( )

protectedvirtual

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.

Reimplemented in MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

Definition at line 217 of file AbstractCardiacProblem.cpp.

References HeartConfig::Instance().

◆ CreateSolver()

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 ( )

protectedpure 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 >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

◆ DefineExtraVariablesWriterColumns()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 730 of file AbstractCardiacProblem.cpp.

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

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), ExtendedBidomainProblem< DIM >::DefineWriterColumns(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::DefineWriterColumns(), and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::DefineWriterColumns().

◆ DefineWriterColumns()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns ( bool extending )

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 >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

Definition at line 684 of file AbstractCardiacProblem.cpp.

References EXCEPTION, and HeartConfig::Instance().

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::DefineWriterColumns(), and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::DefineWriterColumns().

◆ GetCurrentTime()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Returns: the current time of the simulation

Definition at line 332 of file AbstractCardiacProblem.cpp.

◆ GetDataReader()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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

Definition at line 911 of file AbstractCardiacProblem.cpp.

References EXCEPTION, and HeartConfig::Instance().

◆ GetHasBath()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetHasBath ( )

virtual

Returns: whether there's bath defined in this problem

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

Definition at line 921 of file AbstractCardiacProblem.cpp.

◆ GetSolution()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 320 of file AbstractCardiacProblem.cpp.

◆ GetSolutionDistributedVector()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Returns: the solution vector, wrapped in a DistributedVector.

◆ GetTissue()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Returns: the cardiac tissue object used

Definition at line 345 of file AbstractCardiacProblem.cpp.

References EXCEPTION.

◆ Initialise()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 117 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), PetscTools::Destroy(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, HeartConfig::GetFibreLength(), HeartConfig::GetInterNodeSpace(), HeartConfig::GetSheetDimensions(), HeartConfig::GetSlabDimensions(), HeartConfig::Instance(), PetscTools::IsParallel(), and NEVER_REACHED.

◆ InitialiseWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 814 of file AbstractCardiacProblem.cpp.

References RelativeTo::Absolute, PetscTools::Barrier(), EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), OutputFileHandler::GetChasteTestOutputDirectory(), HeartConfig::GetOutputDirectory(), HeartConfig::GetOutputFilenamePrefix(), Hdf5DataReader::GetUnlimitedDimensionValues(), HeartConfig::Instance(), and HeartConfig::SetOutputUsingOriginalNodeOrdering().

◆ load()

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
	)

inlineprivate

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:

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

Definition at line 224 of file AbstractCardiacProblem.hpp.

◆ LoadBoundaryConditions()

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
	)

inlineprivate

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 367 of file AbstractCardiacProblem.hpp.

References ProcessSpecificArchive< Archive >::Get().

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

◆ LoadExtraArchive()

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
	)

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 813 of file AbstractCardiacProblem.hpp.

References DistributedVectorFactory::GetNumProcs(), DistributedVectorFactory::GetOriginalFactory(), BidomainProblem< DIM >::LoadExtraArchiveForBidomain(), AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpCardiacTissue, and AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh.

◆ OnEndOfTimestep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

inlinevirtual

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 736 of file AbstractCardiacProblem.hpp.

◆ PreSolveChecks()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks ( )

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 229 of file AbstractCardiacProblem.cpp.

References EXCEPTION, HeartConfig::GetPdeTimeStep(), HeartConfig::GetSimulationDuration(), and HeartConfig::Instance().

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

◆ PrintOutput()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Set whether the simulation will generate results files.

Parameters

rPrintOutput

Definition at line 308 of file AbstractCardiacProblem.cpp.

◆ rGetMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Returns: the mesh used

Definition at line 338 of file AbstractCardiacProblem.cpp.

◆ save()

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

inlineprivate

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.

Definition at line 134 of file AbstractCardiacProblem.hpp.

◆ SaveBoundaryConditions()

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

inlineprivate

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 352 of file AbstractCardiacProblem.hpp.

References ProcessSpecificArchive< Archive >::Get().

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

◆ SetBoundaryConditionsContainer()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Set the boundary conditions container.

Parameters

pBcc	is a pointer to a boundary conditions container

Definition at line 223 of file AbstractCardiacProblem.cpp.

◆ SetElectrodes()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetElectrodes ( )

virtual

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

Reimplemented in BidomainProblem< DIM >.

Definition at line 927 of file AbstractCardiacProblem.cpp.

◆ SetHdf5DataWriterTargetChunkSizeAndAlignment()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetHdf5DataWriterTargetChunkSizeAndAlignment ( hsize_t size )

Set Hdf5DataWriter target chunk size and alignment parameters.

The most likely use case for this is setting it to the stripe size on a striped filesystem. This results in the writer choosing chunk dimensions that should efficiently fit within a stripe, AND padding the chunks so each chunk fits in one stripe.

For example, if your filesystem uses 1 M stripes, call this method with argument 1048576 (or 0x100000 if you like round numbers).

NOTE: The alignment parameter is only used for NEW HDF5 files. The chunk size is only used for NEW datasets (e.g. results or postprocessing) and NOT when EXTENDING a dataset. In other words, when adding a dataset to a file the alignment parameter will be ignored. When adding to a dataset, both will be ignored. etc.

Parameters

size	size in bytes to use for target chunk size and alignment

Definition at line 899 of file AbstractCardiacProblem.cpp.

◆ SetMesh()

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 )

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

Parameters

pMesh the mesh object to use

Definition at line 295 of file AbstractCardiacProblem.cpp.

◆ SetNodesPerProcessorFilename()

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

◆ SetOutputNodes()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 905 of file AbstractCardiacProblem.cpp.

◆ SetUpAdditionalStoppingTimes()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

inlinevirtual

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 746 of file AbstractCardiacProblem.hpp.

◆ SetUseHdf5DataWriterCache()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetUseHdf5DataWriterCache ( bool useCache = true )

Set whether to use caching in the Hdf5DataWriter. This tells the Hdf5DataWriter to write only whole chunks to disk, rather than every print timestep, which is much faster when running with many processes.

Parameters

useCache Whether to use the cache

Definition at line 893 of file AbstractCardiacProblem.cpp.

◆ SetUseTimeAdaptivityController()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 355 of file AbstractCardiacProblem.cpp.

◆ SetWriteInfo()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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

Parameters

writeInfo

Definition at line 314 of file AbstractCardiacProblem.cpp.

◆ Solve()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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 371 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), PetscTools::Destroy(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), HeartConfig::GetOutputDirectory(), TimeStepper::GetTime(), and HeartConfig::Instance().

◆ WriteExtraVariablesOneStep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

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

Definition at line 768 of file AbstractCardiacProblem.cpp.

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

Referenced by BidomainProblem< DIM >::WriteOneStep(), ExtendedBidomainProblem< DIM >::WriteOneStep(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteOneStep(), and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >::WriteOneStep().

◆ WriteInfo()

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 >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

◆ WriteOneStep()

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 >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainPurkinjeProblem< ELEMENT_DIM, SPACE_DIM >.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 125 of file AbstractCardiacProblem.hpp.

◆ CardiacElectroMechanicsProblem

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<unsigned DIM, unsigned ELEC_PROB_DIM>

friend class CardiacElectroMechanicsProblem

friend

CardiacElectroMechanicsProblem needs access to mpWriter.

Definition at line 467 of file AbstractCardiacProblem.hpp.

◆ TestBidomainWithBath

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class TestBidomainWithBath

friend

Definition at line 115 of file AbstractCardiacProblem.hpp.

◆ TestCardiacSimulationArchiver

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class TestCardiacSimulationArchiver

friend

Definition at line 117 of file AbstractCardiacProblem.hpp.

◆ TestMonodomainProblem

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class TestMonodomainProblem

friend

Definition at line 116 of file AbstractCardiacProblem.hpp.

Member Data Documentation

◆ mAllocatedMemoryForMesh

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 390 of file AbstractCardiacProblem.hpp.

◆ mCurrentTime

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 433 of file AbstractCardiacProblem.hpp.

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