#include <AbstractCardiacProblem.hpp>
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 () |
AbstractCardiacPde < ELEMENT_DIM, SPACE_DIM > * | GetPde () |
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 () |
void | InitialiseWriter () |
void | SetOutputNodes (std::vector< unsigned > &rNodesToOutput) |
Hdf5DataReader | GetDataReader () |
void | UseMatrixBasedRhsAssembly (bool usematrix=true) |
virtual void | AtBeginningOfTimestep (double time) |
virtual void | OnEndOfTimestep (double time) |
virtual void | SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes) |
template<class Archive > | |
void | LoadExtraArchive (Archive &archive, unsigned version) |
Protected Member Functions | |
virtual AbstractCardiacPde < ELEMENT_DIM, SPACE_DIM > * | CreateCardiacPde ()=0 |
virtual AbstractDynamicAssemblerMixin < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > * | CreateAssembler ()=0 |
Protected Attributes | |
std::string | mMeshFilename |
bool | mUseMatrixBasedRhsAssembly |
bool | mAllocatedMemoryForMesh |
bool | mWriteInfo |
bool | mPrintOutput |
std::vector< unsigned > | mNodesToOutput |
unsigned | mVoltageColumnId |
std::vector< unsigned > | mExtraVariablesId |
unsigned | mTimeColumnId |
unsigned | mNodeColumnId |
AbstractCardiacPde < ELEMENT_DIM, SPACE_DIM > * | mpCardiacPde |
BccType | mpBoundaryConditionsContainer |
BccType | mpDefaultBoundaryConditionsContainer |
AbstractDynamicAssemblerMixin < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > * | mpAssembler |
AbstractCardiacCellFactory < ELEMENT_DIM, SPACE_DIM > * | mpCellFactory |
AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > * | mpMesh |
Vec | mSolution |
double | mCurrentTime |
Hdf5DataWriter * | mpWriter |
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 | TestBidomainWithBathAssembler |
class | TestCardiacSimulationArchiver |
class | boost::serialization::access |
class | CardiacElectroMechanicsProblem |
Base class for cardiac problems; contains code generic to both mono- and bidomain.
See tutorials for usage.
Definition at line 84 of file AbstractCardiacProblem.hpp.
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 91 of file AbstractCardiacProblem.hpp.
AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem | ( | AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > * | pCellFactory | ) | [inline] |
Constructor
pCellFactory | User defined cell factory which shows how the pde should create cells. |
Definition at line 46 of file AbstractCardiacProblem.cpp.
References GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput.
AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem | ( | ) | [inline] |
Constructor used by archiving.
Definition at line 68 of file AbstractCardiacProblem.cpp.
AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem | ( | ) | [inline, virtual] |
Destructor
Definition at line 91 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.
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.
time | the current time |
Reimplemented in BidomainProblem< DIM >.
Definition at line 570 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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.
Definition at line 488 of file AbstractCardiacProblem.cpp.
References GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), 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, and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
virtual AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEMENT_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< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
virtual AbstractCardiacPde<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_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< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise().
Vec AbstractCardiacProblem< ELEMENT_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 242 of file AbstractCardiacProblem.cpp.
References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and DistributedVector::Restore().
Referenced by CardiacElectroMechanicsProblem< DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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
extending | whether we are extending an existing results file |
Definition at line 559 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.
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns | ( | bool | extending | ) | [inline, virtual] |
Define what variables are written to the primary results file.
extending | whether we are extending an existing results file |
Reimplemented in BidomainProblem< DIM >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Definition at line 533 of file AbstractCardiacProblem.cpp.
References Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::DefineVariable(), Hdf5DataWriter::GetVariableByName(), 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().
double AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetCurrentTime | ( | ) | [inline] |
Definition at line 307 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime.
Hdf5DataReader AbstractCardiacProblem< ELEMENT_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 662 of file AbstractCardiacProblem.cpp.
References HeartConfig::Instance().
AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM > * AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetPde | ( | ) | [inline] |
Definition at line 320 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde.
Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().
Vec AbstractCardiacProblem< ELEMENT_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 295 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.
DistributedVector AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector | ( | ) | [inline] |
Get the solution vector, wrapped in a DistributedVector.
See also GetSolution.
Definition at line 301 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.
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 106 of file AbstractCardiacProblem.cpp.
References GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateCardiacPde(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), HeartConfig::GetFibreLength(), HeartConfig::GetInterNodeSpace(), HeartConfig::GetSheetDimensions(), Exception::GetShortMessage(), HeartConfig::GetSlabDimensions(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAllocatedMemoryForMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCellFactory, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.
Referenced by CardiacElectroMechanicsProblem< DIM >::Initialise().
void 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.
Definition at line 619 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), Hdf5DataWriter::EndDefineMode(), HeartConfig::GetOutputDirectory(), HeartConfig::GetOutputFilenamePrefix(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution.
Referenced by CardiacElectroMechanicsProblem< DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::load | ( | Archive & | archive, | |
const unsigned int | version | |||
) | [inline, private] |
Load the member variables.
archive | ||
version |
Reimplemented in BidomainProblem< DIM >.
Definition at line 165 of file AbstractCardiacProblem.hpp.
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.
archive | the archive to load from | |
pMesh | the mesh boundary conditions are to be defined on |
Definition at line 272 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load().
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.
archive | the archive to load | |
version | the archive file version |
Definition at line 625 of file AbstractCardiacProblem.hpp.
References BidomainProblem< DIM >::LoadExtraArchiveForBidomain(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh.
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.
time | the current time |
Reimplemented in BidomainProblem< DIM >.
Definition at line 580 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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.
Reimplemented in BidomainProblem< DIM >.
Definition at line 210 of file AbstractCardiacProblem.cpp.
References HeartConfig::GetPdeTimeStep(), HeartConfig::GetSimulationDuration(), HeartConfig::Instance(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrintOutput | ( | bool | rPrintOutput | ) | [inline] |
Set whether the simulation will generate results files.
rPrintOutput |
Definition at line 283 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput.
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::rGetMesh | ( | ) | [inline] |
Definition at line 313 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh.
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::save | ( | Archive & | archive, | |
const unsigned int | version | |||
) | const [inline, private] |
Save the member variables.
archive | ||
version |
Reimplemented in BidomainProblem< DIM >.
Definition at line 104 of file AbstractCardiacProblem.hpp.
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.
archive | the archive to save to | |
pMesh | the mesh boundary conditions are defined on | |
pBcc | the container to save |
Definition at line 257 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save().
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer | ( | BccType | pBcc | ) | [inline] |
Set the boundary conditions container.
pBcc | is a pointer to a boundary conditions container |
Definition at line 204 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer.
Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().
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.
pMesh | the mesh object to use |
Definition at line 272 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 >::Initialise().
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
rFilename |
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputNodes | ( | std::vector< unsigned > & | rNodesToOutput | ) | [inline] |
Specifies which nodes in the mesh to output.
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 656 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodesToOutput.
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.
rAdditionalStoppingTimes | to be filled in with the additional stopping times |
Reimplemented in BidomainProblem< DIM >.
Definition at line 590 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetWriteInfo | ( | bool | writeInfo = true |
) | [inline] |
Set whether extra info will be written to stdout during computation.
writeInfo |
Definition at line 289 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo.
void AbstractCardiacProblem< ELEMENT_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.
Definition at line 326 of file AbstractCardiacProblem.cpp.
References Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), TimeStepper::AdvanceOneTimeStep(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AtBeginningOfTimestep(), GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateAssembler(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), TimeStepper::GetNextTime(), HeartConfig::GetOutputDirectory(), HeartConfig::GetPdeTimeStep(), TimeStepper::GetTime(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), HeartConfig::Instance(), TimeStepper::IsTimeAtEnd(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCurrentTime, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpAssembler, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDefaultBoundaryConditionsContainer, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSolution, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mWriteInfo, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::OnEndOfTimestep(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), ProgressReporter::PrintFinalising(), PetscTools::ReplicateException(), GenericEventHandler< 13, HeartEventHandler >::Reset(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetUpAdditionalStoppingTimes(), ProgressReporter::Update(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteInfo(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().
void AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::UseMatrixBasedRhsAssembly | ( | bool | usematrix = true |
) | [inline] |
Whether to use matrix-based RHS assembly or not.
usematrix |
Definition at line 672 of file AbstractCardiacProblem.cpp.
References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mUseMatrixBasedRhsAssembly.
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 592 of file AbstractCardiacProblem.cpp.
References DistributedVector::Begin(), DistributedVector::End(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mExtraVariablesId, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, Hdf5DataWriter::PutVector(), and DistributedVector::Restore().
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.
time | the current time |
Implemented in BidomainProblem< DIM >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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.
time | the current time | |
voltageVec | the solution vector to write |
Implemented in BidomainProblem< DIM >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented in BidomainProblem< DIM >, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >, and MonodomainProblem< DIM >.
Definition at line 95 of file AbstractCardiacProblem.hpp.
friend class CardiacElectroMechanicsProblem [friend] |
CardiacElectroMechanicsProblem needs access to mpWriter.
Definition at line 364 of file AbstractCardiacProblem.hpp.
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 300 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().
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 343 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetCurrentTime(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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 312 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().
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 292 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), and AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save().
unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNodeColumnId [protected] |
Used by the writer
Definition at line 316 of file AbstractCardiacProblem.hpp.
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 307 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< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputNodes().
AbstractDynamicAssemblerMixin<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpAssembler [protected] |
The PDE solver
Reimplemented in BidomainProblem< DIM >.
Definition at line 326 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
BccType AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpBoundaryConditionsContainer [protected] |
Boundary conditions container used in the simulation
Definition at line 322 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
AbstractCardiacPde<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpCardiacPde [protected] |
The monodomain or bidomain pde
Definition at line 319 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetPde(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().
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 328 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise().
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 324 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
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 330 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::rGetMesh(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().
bool AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintOutput [protected] |
Whether to write any output at all
Definition at line 304 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrintOutput(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().
Hdf5DataWriter* AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter [protected] |
The object to use to write results to disk.
Definition at line 368 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 >::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().
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 334 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolution(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~AbstractCardiacProblem().
unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTimeColumnId [protected] |
Used by the writer
Definition at line 314 of file AbstractCardiacProblem.hpp.
bool AbstractCardiacProblem< ELEMENT_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 298 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::UseMatrixBasedRhsAssembly().
unsigned AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVoltageColumnId [protected] |
Used by the writer
Definition at line 310 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().
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 302 of file AbstractCardiacProblem.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetWriteInfo(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().