AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

#include <AbstractCardiacProblem.hpp>

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

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

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List of all members.

Public Member Functions

 AbstractCardiacProblem (AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > *pCellFactory)
virtual ~AbstractCardiacProblem ()
void Initialise ()
void SetNodesPerProcessorFilename (const std::string &rFilename)
void SetBoundaryConditionsContainer (BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > *pbcc)
virtual void PreSolveChecks ()
virtual Vec CreateInitialCondition ()
void ConvertOutputToMeshalyzerFormat (bool call=true)
void SetMesh (AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > *pMesh)
void PrintOutput (bool rPrintOutput)
void SetWriteInfo (bool writeInfo=true)
Vec GetSolution ()
DistributedVector GetSolutionDistributedVector ()
AbstractTetrahedralMesh
< ELEM_DIM, SPACE_DIM > & 		rGetMesh ()
AbstractCardiacPde< ELEM_DIM,
SPACE_DIM > * 		GetPde ()
void Solve ()
void CloseFilesAndPostProcess ()
virtual void WriteInfo (double time)=0
virtual void DefineWriterColumns ()
virtual void WriteOneStep (double time, Vec voltageVec)
void InitialiseWriter ()
void SetOutputNodes (std::vector< unsigned > &rNodesToOutput)
Hdf5DataReader GetDataReader ()
void UseMatrixBasedRhsAssembly (bool usematrix=true)
virtual void OnEndOfTimestep (double time)
void SetArchiveLinearSystemObject (bool archive=true)

Public Attributes

Hdf5DataWriter * mpWriter

Protected Member Functions

virtual AbstractCardiacPde
< ELEM_DIM, SPACE_DIM > * 		CreateCardiacPde ()=0
virtual
AbstractDynamicAssemblerMixin
< ELEM_DIM, SPACE_DIM,
PROBLEM_DIM > * 		CreateAssembler ()=0

Protected Attributes

std::string mMeshFilename
std::string mNodesPerProcessorFilename
bool mUseMatrixBasedRhsAssembly
bool mAllocatedMemoryForMesh
bool mWriteInfo
bool mPrintOutput
bool mCallChaste2Meshalyzer
std::vector< unsigned > mNodesToOutput
unsigned mVoltageColumnId
unsigned mTimeColumnId
unsigned mNodeColumnId
AbstractCardiacPde< ELEM_DIM,
SPACE_DIM > * 		mpCardiacPde
BoundaryConditionsContainer
< ELEM_DIM, SPACE_DIM,
PROBLEM_DIM > * 		mpBoundaryConditionsContainer
BoundaryConditionsContainer
< ELEM_DIM, SPACE_DIM,
PROBLEM_DIM > * 		mpDefaultBoundaryConditionsContainer
AbstractDynamicAssemblerMixin
< ELEM_DIM, SPACE_DIM,
PROBLEM_DIM > * 		mpAssembler
AbstractCardiacCellFactory
< ELEM_DIM, SPACE_DIM > * 		mpCellFactory
AbstractTetrahedralMesh
< ELEM_DIM, SPACE_DIM > * 		mpMesh
Vec mSolution
bool mArchiveKSP

Friends

class TestBidomainWithBathAssembler

Detailed Description

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

Base class for cardiac problems; contains code generic to both mono- and bidomain.

See tutorials for usage.

Definition at line 51 of file AbstractCardiacProblem.hpp.

Constructor & Destructor Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem ( AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > *  pCellFactory  )  [inline]

Constructor

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

Definition at line 49 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 11, HeartEventHandler >::BeginEvent(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mCallChaste2Meshalyzer, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpAssembler, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem (  )  [inline, virtual]

Destructor

Definition at line 74 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpDefaultBoundaryConditionsContainer, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.

Member Function Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
virtual AbstractCardiacPde<ELEM_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateCardiacPde (  )  [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.

Implemented in BidomainProblem< DIM >, MonodomainProblem< ELEM_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
virtual AbstractDynamicAssemblerMixin<ELEM_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateAssembler (  )  [protected, pure virtual]

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

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

Implemented in BidomainProblem< DIM >, MonodomainProblem< ELEM_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise (  )  [inline]

Initialise the system. Must be called before Solve()

Todo:
: Only considering <LoadMesh/> definition. Consider <Slab/> too

Todo:
We can't currently instantiate the parallel mesh in 1D

Todo:
Should this method be rolled into the Solve() method or the PreSolveChecks()?

Definition at line 94 of file AbstractCardiacProblem.cpp.

References GenericEventHandler< 11, HeartEventHandler >::BeginEvent(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateCardiacPde(), GenericEventHandler< 11, HeartEventHandler >::EndEvent(), HeartConfig::GetFibreLength(), HeartConfig::GetInterNodeSpace(), Exception::GetMessage(), HeartConfig::GetSheetDimensions(), HeartConfig::GetSlabDimensions(), HeartConfig::Instance(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesPerProcessorFilename, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile().

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetNodesPerProcessorFilename ( const std::string &  rFilename  )  [inline]

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

Parameters:
rFilename 

Definition at line 225 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesPerProcessorFilename.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer ( BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > *  pbcc  )  [inline]

Set the boundary conditions container.

Parameters:
pbcc is a pointer to a boundary conditions container

Definition at line 231 of file AbstractCardiacProblem.cpp.

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

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_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.

Reimplemented in BidomainProblem< DIM >.

Definition at line 237 of file AbstractCardiacProblem.cpp.

References HeartConfig::GetPdeTimeStep(), HeartConfig::GetSimulationDuration(), HeartConfig::Instance(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput.

Referenced by BidomainProblem< DIM >::PreSolveChecks(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition (  )  [inline, virtual]

Perhaps this should be a method of AbstractCardiacPde?? This is virtual so BidomainProblem can overwrite V to zero for bath nodes, if there are any.

Reimplemented in BidomainProblem< DIM >.

Definition at line 269 of file AbstractCardiacProblem.cpp.

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

Referenced by BidomainProblem< DIM >::CreateInitialCondition(), CardiacElectroMechanicsProblem< DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::ConvertOutputToMeshalyzerFormat ( bool  call = true  )  [inline]

Set whether to call the Chaste2Meshalyzer script. This script gets everything ready to visualize the results with meshalyser and is useful in testing. By default the script is called. In performance testing for example it desirable to disable the script.

Parameters:
call whether to call the script

Definition at line 303 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mCallChaste2Meshalyzer.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh ( AbstractTetrahedralMesh< ELEM_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 309 of file AbstractCardiacProblem.cpp.

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

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

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

Set whether the simulation will generate results files.

Parameters:
rPrintOutput 

Definition at line 320 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_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 326 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolution (  )  [inline]

Get 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 332 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
DistributedVector AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector (  )  [inline]

Get the solution vector, wrapped in a DistributedVector.

See also GetSolution.

Definition at line 338 of file AbstractCardiacProblem.cpp.

References DistributedVectorFactory::CreateDistributedVector(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > & AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::rGetMesh (  )  [inline]

Returns:
the mesh used

Definition at line 344 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacPde< ELEM_DIM, SPACE_DIM > * AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetPde (  )  [inline]

Returns:
the cardiac PDE used

Definition at line 351 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve (  )  [inline]

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

Todo:
This should go in a location set in ArchiveLocationInfo (see LinearSystem::load_construct_data(...))

Definition at line 357 of file AbstractCardiacProblem.cpp.

References Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), TimeStepper::AdvanceOneTimeStep(), GenericEventHandler< 11, HeartEventHandler >::BeginEvent(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateAssembler(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), GenericEventHandler< 11, HeartEventHandler >::EndEvent(), AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetLinearSystem(), TimeStepper::GetNextTime(), HeartConfig::GetOutputDirectory(), OutputFileHandler::GetOutputDirectoryFullPath(), HeartConfig::GetOutputFilenamePrefix(), HeartConfig::GetPdeTimeStep(), TimeStepper::GetTime(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), HeartConfig::Instance(), TimeStepper::IsTimeAtEnd(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mArchiveKSP, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpAssembler, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpDefaultBoundaryConditionsContainer, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::OnEndOfTimestep(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), ProgressReporter::PrintFinalising(), PetscTools::ReplicateException(), GenericEventHandler< 11, HeartEventHandler >::Reset(), OutputFileHandler::SetArchiveDirectory(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetInitialCondition(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimes(), AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), ProgressReporter::Update(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteInfo(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_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.

Todo:
WriteFilesUsingMesh cannot handle ParallelTetrahedralMesh objects. Abort if so.

Definition at line 496 of file AbstractCardiacProblem.cpp.

References PetscTools::AmMaster(), GenericEventHandler< 11, HeartEventHandler >::BeginEvent(), Hdf5DataWriter::Close(), GenericEventHandler< 11, HeartEventHandler >::EndEvent(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), HeartConfig::GetOutputDirectory(), HeartConfig::Instance(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mCallChaste2Meshalyzer, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation(), HeartConfig::Write(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReader().

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
virtual void AbstractCardiacProblem< ELEM_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 >, MonodomainProblem< ELEM_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns (  )  [inline, virtual]

Define what variables are written to the primary results file.

Reimplemented in BidomainProblem< DIM >.

Definition at line 542 of file AbstractCardiacProblem.cpp.

References Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::DefineVariable(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mVoltageColumnId.

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep ( double  time,
Vec  voltageVec 
) [inline, virtual]

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

Parameters:
time the current time
voltageVec the solution vector to write

Reimplemented in BidomainProblem< DIM >.

Definition at line 562 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mVoltageColumnId, Hdf5DataWriter::PutUnlimitedVariable(), and Hdf5DataWriter::PutVector().

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_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.

Definition at line 571 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), Hdf5DataWriter::EndDefineMode(), HeartConfig::GetOutputDirectory(), HeartConfig::GetOutputFilenamePrefix(), HeartConfig::Instance(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter.

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

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

Specifies which nodes in the mesh to output.

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 579 of file AbstractCardiacProblem.cpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Hdf5DataReader AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetDataReader (  )  [inline]

Create and return a data reader configured to read the results we've been outputting.

Definition at line 585 of file AbstractCardiacProblem.cpp.

References HeartConfig::Instance().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::UseMatrixBasedRhsAssembly ( bool  usematrix = true  )  [inline]

Whether to use matrix-based RHS assembly or not.

Parameters:
usematrix 

Definition at line 595 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mUseMatrixBasedRhsAssembly.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
virtual void AbstractCardiacProblem< ELEM_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 314 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetArchiveLinearSystemObject ( bool  archive = true  )  [inline]

Tells the problem class to archive the linear system after every call to Solve()

Parameters:
archive set true to archive the LinearSystem object at the end

Definition at line 601 of file AbstractCardiacProblem.cpp.

References AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mArchiveKSP.

Member Data Documentation

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
std::string AbstractCardiacProblem< ELEM_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 58 of file AbstractCardiacProblem.hpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
std::string AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesPerProcessorFilename [protected]

If this is set, the nodes for each processor are read

Definition at line 61 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mUseMatrixBasedRhsAssembly [protected]

Whether to use matrix-based assembly of the RHS vector (much more efficient). True by default

Definition at line 67 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::UseMatrixBasedRhsAssembly().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_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 69 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo [protected]

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

Definition at line 71 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetWriteInfo(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput [protected]

Whether to write any output at all

Definition at line 73 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::PrintOutput(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mCallChaste2Meshalyzer [protected]

Whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 75 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::ConvertOutputToMeshalyzerFormat().

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

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

Definition at line 78 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputNodes().

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

Used by the writer

Definition at line 81 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().

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

Used by the writer

Definition at line 83 of file AbstractCardiacProblem.hpp.

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

Used by the writer

Definition at line 85 of file AbstractCardiacProblem.hpp.

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacPde<ELEM_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde [protected]

The monodomain or bidomain pde

Definition at line 88 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetPde(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
BoundaryConditionsContainer<ELEM_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer [protected]

Boundary conditions container used in the simulation

Definition at line 91 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
BoundaryConditionsContainer<ELEM_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEM_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 93 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractDynamicAssemblerMixin<ELEM_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpAssembler [protected]

The PDE solver

Reimplemented in BidomainProblem< DIM >.

Definition at line 95 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacCellFactory<ELEM_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory [protected]

The cell factory creates the cells for each node

Definition at line 97 of file AbstractCardiacProblem.hpp.

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

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractTetrahedralMesh<ELEM_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh [protected]

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

Definition at line 99 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::rGetMesh(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractCardiacProblem< ELEM_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 103 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolution(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mArchiveKSP [protected]

Tells the destructor to archive the linear system

Definition at line 106 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::SetArchiveLinearSystemObject(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

template<unsigned ELEM_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Hdf5DataWriter* AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter

The object to use to write results to disk.

This (and things in MonodomainProblem) being public are hacks for CardiacElectroMechanicsProblem to work.

Todo:
CardiacElectroMechanicsProblem should be a friend, but not sure how to get friends to work when both friends are templated and abstract.

Definition at line 132 of file AbstractCardiacProblem.hpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), CardiacElectroMechanicsProblem< DIM >::Solve(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().

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