HeartConfig Class Reference

#include <HeartConfig.hpp>

Collaboration diagram for HeartConfig:

Collaboration graph
[legend]

List of all members.

Public Types

typedef std::map< std::string,
std::string > 
SchemaLocationsMap

Public Member Functions

void SetUseFixedSchemaLocation (bool useFixedSchemaLocation)
void SetFixedSchemaLocations (const SchemaLocationsMap &rSchemaLocations)
void SetDefaultsFile (const std::string &rFileName)
void SetParametersFile (const std::string &rFileName)
void Write (bool useArchiveLocationInfo=false, std::string subfolderName="output")
void CopySchema (const std::string &rToDirectory)
boost::shared_ptr
< cp::chaste_parameters_type > 
ReadFile (const std::string &rFileName)
 ~HeartConfig ()
unsigned GetVersionFromNamespace (const std::string &rNamespaceUri)
bool IsSimulationDefined () const
bool IsSimulationResumed () const
unsigned GetSpaceDimension () const
double GetSimulationDuration () const
cp::domain_type GetDomain () const
cp::ionic_model_selection_type GetDefaultIonicModel () const
template<unsigned DIM>
void GetIonicModelRegions (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
void SetIonicModelRegions (std::vector< ChasteCuboid< 3 > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
bool IsMeshProvided () const
bool GetCreateMesh () const
bool GetCreateSlab () const
bool GetCreateSheet () const
bool GetCreateFibre () const
bool GetLoadMesh () const
void GetSlabDimensions (c_vector< double, 3 > &slabDimensions) const
void GetSheetDimensions (c_vector< double, 2 > &sheetDimensions) const
void GetFibreLength (c_vector< double, 1 > &fibreLength) const
double GetInterNodeSpace () const
std::string GetMeshName () const
cp::media_type GetConductivityMedia () const
template<unsigned DIM>
void GetStimuli (std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuliApplied, std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rStimulatedAreas) const
template<unsigned DIM>
void GetCellHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rCellHeterogeneityRegions, std::vector< double > &rScaleFactorGks, std::vector< double > &rScaleFactorIto, std::vector< double > &rScaleFactorGkr, std::vector< std::map< std::string, double > > *pParameterSettings)
bool GetConductivityHeterogeneitiesProvided () const
bool AreCellularTransmuralHeterogeneitiesRequested ()
double GetEpiLayerFraction ()
double GetEndoLayerFraction ()
double GetMidLayerFraction ()
unsigned GetEpiLayerIndex ()
unsigned GetEndoLayerIndex ()
unsigned GetMidLayerIndex ()
template<unsigned DIM>
void GetConductivityHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &conductivitiesHeterogeneityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities) const
std::string GetOutputDirectory () const
std::string GetOutputFilenamePrefix () const
bool GetOutputVariablesProvided () const
void GetOutputVariables (std::vector< std::string > &rOutputVariables) const
bool GetOutputUsingOriginalNodeOrdering ()
bool GetCheckpointSimulation () const
double GetCheckpointTimestep () const
unsigned GetMaxCheckpointsOnDisk () const
HeartFileFinder GetArchivedSimulationDir () const
void GetIntracellularConductivities (c_vector< double, 3 > &intraConductivities) const
void GetIntracellularConductivities (c_vector< double, 2 > &intraConductivities) const
void GetIntracellularConductivities (c_vector< double, 1 > &intraConductivities) const
void GetExtracellularConductivities (c_vector< double, 3 > &extraConductivities) const
void GetExtracellularConductivities (c_vector< double, 2 > &extraConductivities) const
void GetExtracellularConductivities (c_vector< double, 1 > &extraConductivities) const
double GetBathConductivity (unsigned bathRegion=UINT_MAX) const
const std::set< unsigned > & rGetTissueIdentifiers ()
const std::set< unsigned > & rGetBathIdentifiers ()
double GetSurfaceAreaToVolumeRatio () const
double GetCapacitance () const
double GetOdeTimeStep () const
double GetPdeTimeStep () const
double GetPrintingTimeStep () const
bool GetUseAbsoluteTolerance () const
double GetAbsoluteTolerance () const
bool GetUseRelativeTolerance () const
double GetRelativeTolerance () const
const char * GetKSPSolver () const
const char * GetKSPPreconditioner () const
DistributedTetrahedralMeshPartitionType::type GetMeshPartitioning () const
bool IsAdaptivityParametersPresent () const
double GetTargetErrorForAdaptivity () const
double GetSigmaForAdaptivity () const
double GetMaxEdgeLengthForAdaptivity () const
double GetMinEdgeLengthForAdaptivity () const
double GetGradationForAdaptivity () const
unsigned GetMaxNodesForAdaptivity () const
unsigned GetNumberOfAdaptiveSweeps () const
bool IsPostProcessingSectionPresent () const
void EnsurePostProcessingSectionPresent ()
bool IsPostProcessingRequested () const
bool IsApdMapsRequested () const
void GetApdMaps (std::vector< std::pair< double, double > > &rApdMaps) const
bool IsUpstrokeTimeMapsRequested () const
void GetUpstrokeTimeMaps (std::vector< double > &rUpstrokeTimeMaps) const
bool IsMaxUpstrokeVelocityMapRequested () const
void GetMaxUpstrokeVelocityMaps (std::vector< double > &rUpstrokeVelocityMaps) const
bool IsConductionVelocityMapsRequested () const
void GetConductionVelocityMaps (std::vector< unsigned > &rConductionVelocityMaps) const
bool IsAnyNodalTimeTraceRequested () const
void GetNodalTimeTraceRequested (std::vector< unsigned > &rRequestedNodes) const
bool IsPseudoEcgCalculationRequested () const
template<unsigned SPACE_DIM>
void GetPseudoEcgElectrodePositions (std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions) const
bool GetUseStateVariableInterpolation () const
bool IsOutputVisualizerPresent () const
bool GetVisualizeWithMeshalyzer () const
bool GetVisualizeWithCmgui () const
bool GetVisualizeWithVtk () const
bool GetVisualizeWithParallelVtk () const
bool IsElectrodesPresent () const
void GetElectrodeParameters (bool &rGroundSecondElectrode, unsigned &rIndex, double &rMagnitude, double &rStartTime, double &rDuration)
bool GetUseMassLumping ()
bool GetUseMassLumpingForPrecond ()
bool GetUseReactionDiffusionOperatorSplitting ()
bool GetUseFixedNumberIterationsLinearSolver ()
unsigned GetEvaluateNumItsEveryNSolves ()
void SetSpaceDimension (unsigned spaceDimension)
void SetSimulationDuration (double simulationDuration)
void SetDomain (const cp::domain_type &rDomain)
void SetDefaultIonicModel (const cp::ionic_models_available_type &rIonicModel)
void SetSlabDimensions (double x, double y, double z, double inter_node_space)
void SetSheetDimensions (double x, double y, double inter_node_space)
void SetFibreLength (double x, double inter_node_space)
void SetMeshFileName (std::string meshPrefix, cp::media_type fibreDefinition=cp::media_type::NoFibreOrientation)
void SetConductivityHeterogeneities (std::vector< ChasteCuboid< 3 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)
void SetConductivityHeterogeneitiesEllipsoid (std::vector< ChasteEllipsoid< 3 > > &conductivityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities)
void SetOutputDirectory (const std::string &rOutputDirectory)
void SetOutputFilenamePrefix (const std::string &rOutputFilenamePrefix)
void SetOutputVariables (const std::vector< std::string > &rOutputVariables)
void SetOutputUsingOriginalNodeOrdering (bool useOriginal)
void SetCheckpointSimulation (bool checkpointSimulation, double checkpointTimestep=-1.0, unsigned maxCheckpointsOnDisk=UINT_MAX)
void SetIntracellularConductivities (const c_vector< double, 3 > &rIntraConductivities)
void SetIntracellularConductivities (const c_vector< double, 2 > &rIntraConductivities)
void SetIntracellularConductivities (const c_vector< double, 1 > &rIntraConductivities)
void SetExtracellularConductivities (const c_vector< double, 3 > &rExtraConductivities)
void SetExtracellularConductivities (const c_vector< double, 2 > &rExtraConductivities)
void SetExtracellularConductivities (const c_vector< double, 1 > &rExtraConductivities)
void SetBathConductivity (double bathConductivity)
void SetBathMultipleConductivities (std::map< unsigned, double > bathConductivities)
void SetTissueAndBathIdentifiers (const std::set< unsigned > &tissueIds, const std::set< unsigned > &bathIds)
void SetSurfaceAreaToVolumeRatio (double ratio)
void SetCapacitance (double capacitance)
void SetOdePdeAndPrintingTimeSteps (double odeTimeStep, double pdeTimeStep, double printingTimeStep)
void SetOdeTimeStep (double odeTimeStep)
void SetPdeTimeStep (double pdeTimeStep)
void SetPrintingTimeStep (double printingTimeStep)
void SetUseRelativeTolerance (double relativeTolerance)
void SetUseAbsoluteTolerance (double absoluteTolerance)
void SetKSPSolver (const char *kspSolver)
void SetKSPPreconditioner (const char *kspPreconditioner)
void SetMeshPartitioning (const char *meshPartioningMethod)
void SetAdaptivityParameters (double targetError, double sigma, double maxEdgeLength, double minEdgeLength, double gradation, unsigned maxNodes, unsigned numSweeps)
void SetTargetErrorForAdaptivity (double targetError)
void SetSigmaForAdaptivity (double sigma)
void SetMaxEdgeLengthForAdaptivity (double maxEdgeLength)
void SetMinEdgeLengthForAdaptivity (double minEdgeLength)
void SetGradationForAdaptivity (double gradation)
void SetMaxNodesForAdaptivity (unsigned maxNodes)
void SetNumberOfAdaptiveSweeps (unsigned numSweeps)
void SetApdMaps (const std::vector< std::pair< double, double > > &rApdMaps)
void SetUpstrokeTimeMaps (std::vector< double > &rUpstrokeTimeMaps)
void SetMaxUpstrokeVelocityMaps (std::vector< double > &rMaxUpstrokeVelocityMaps)
void SetConductionVelocityMaps (std::vector< unsigned > &rConductionVelocityMaps)
void SetRequestedNodalTimeTraces (std::vector< unsigned > &requestedNodes)
template<unsigned SPACE_DIM>
void SetPseudoEcgElectrodePositions (const std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions)
void EnsureOutputVisualizerExists (void)
void SetVisualizeWithMeshalyzer (bool useMeshalyzer=true)
void SetVisualizeWithCmgui (bool useCmgui=true)
void SetVisualizeWithVtk (bool useVtk=true)
void SetVisualizeWithParallelVtk (bool useParallelVtk=true)
void SetElectrodeParameters (bool groundSecondElectrode, unsigned index, double magnitude, double startTime, double duration)
void SetUseStateVariableInterpolation (bool useStateVariableInterpolation=true)
void SetUseMassLumping (bool useMassLumping=true)
void SetUseMassLumpingForPrecond (bool useMassLumping=true)
void SetUseReactionDiffusionOperatorSplitting (bool useOperatorSplitting=true)
void SetUseFixedNumberIterationsLinearSolver (bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)
bool HasDrugDose () const
double GetDrugDose () const
void SetDrugDose (double drugDose)
void SetIc50Value (const std::string &rCurrentName, double ic50, double hill=1.0)
std::map< std::string,
std::pair< double, double > > 
GetIc50Values ()

Static Public Member Functions

static HeartConfigInstance ()
static void Reset ()

Private Member Functions

void CheckTimeSteps () const
template<class Archive>
void save (Archive &archive, const unsigned int version) const
template<class Archive>
void load (Archive &archive, const unsigned int version)
void UpdateParametersFromResumeSimulation (boost::shared_ptr< cp::chaste_parameters_type > pResumeParameters)
void SetDefaultSchemaLocations ()
 HeartConfig ()
template<class TYPE>
TYPE * DecideLocation (TYPE *params_ptr, TYPE *defaults_ptr, const std::string &rNameParameter) const
void CheckSimulationIsDefined (std::string callingMethod="") const
void CheckResumeSimulationIsDefined (std::string callingMethod="") const

Private Attributes

SchemaLocationsMap mSchemaLocations
boost::shared_ptr
< cp::chaste_parameters_type > 
mpUserParameters
boost::shared_ptr
< cp::chaste_parameters_type > 
mpDefaultParameters
bool mUseFixedSchemaLocation
double mEpiFraction
double mEndoFraction
double mMidFraction
unsigned mIndexMid
unsigned mIndexEpi
unsigned mIndexEndo
bool mUserAskedForCellularTransmuralHeterogeneities
bool mUseMassLumping
bool mUseMassLumpingForPrecond
bool mUseReactionDiffusionOperatorSplitting
std::map< unsigned, double > mBathConductivities
std::set< unsigned > mTissueIdentifiers
std::set< unsigned > mBathIdentifiers
bool mUseFixedNumberIterations
unsigned mEvaluateNumItsEveryNSolves

Static Private Attributes

static std::auto_ptr< HeartConfigmpInstance

Friends

class boost::serialization::access
class TestHeartConfig


Detailed Description

A singleton class containing configuration parameters for heart simulations.

This class wraps the settings from the XML configuration file in a more friendly interface, providing methods to read and write all the settings, and round-trip them to/from XML format. It also deals with the complexities of supporting multiple versions of CodeSynthesis XSD.

chaste_parameters_type is a convenience class created by CodeSynthesis XSD

Definition at line 74 of file HeartConfig.hpp.


Member Typedef Documentation

typedef std::map<std::string, std::string> HeartConfig::SchemaLocationsMap

Our type for specifying schema location properties: a map from namespace URI to schema URI. The default namespace is specified by an empty namespace URI.

Definition at line 162 of file HeartConfig.hpp.


Constructor & Destructor Documentation

HeartConfig::~HeartConfig (  ) 

Destructor

Definition at line 206 of file HeartConfig.cpp.

HeartConfig::HeartConfig (  )  [private]


Member Function Documentation

void HeartConfig::CheckTimeSteps (  )  const [private]

Throws if the time steps don't obey constraints (within machine precision) ode_step > 0.0 pde_step = n1 * ode_step (where n1 is a positive integer) printing_step = n2 * pde_step (where n2 is a positive integer)

Definition at line 2594 of file HeartConfig.cpp.

References EXCEPTION, GetCheckpointSimulation(), GetCheckpointTimestep(), GetOdeTimeStep(), GetPdeTimeStep(), and GetPrintingTimeStep().

Referenced by SetCheckpointSimulation(), SetDefaultsFile(), SetOdePdeAndPrintingTimeSteps(), and SetParametersFile().

template<class Archive>
void HeartConfig::save ( Archive &  archive,
const unsigned int  version 
) const [inline, private]

Archive the object.

Parameters:
archive 
version 

Definition at line 94 of file HeartConfig.hpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), and mpInstance.

template<class Archive>
void HeartConfig::load ( Archive &  archive,
const unsigned int  version 
) [inline, private]

void HeartConfig::UpdateParametersFromResumeSimulation ( boost::shared_ptr< cp::chaste_parameters_type >  pResumeParameters  )  [private]

When loading a simulation from archive, some parameters can get overridden by the content of the ResumeSimulation element. This method does that.

Parameters:
pResumeParameters the parameters containing the ResumeSimulation element.

Definition at line 438 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), EXCEPTION, GetDomain(), GetSpaceDimension(), Instance(), mpUserParameters, SetCheckpointSimulation(), SetSimulationDuration(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), and SetVisualizeWithVtk().

Referenced by load().

void HeartConfig::SetDefaultSchemaLocations (  )  [private]

Set default schema locations in the Chaste source tree.

Definition at line 302 of file HeartConfig.cpp.

References ChasteBuildInfo::GetRootDir(), and mSchemaLocations.

Referenced by HeartConfig().

HeartConfig * HeartConfig::Instance (  )  [static]

Call this method to access the global parameters holder.

Returns:
a single instance of the class

Definition at line 164 of file HeartConfig.cpp.

References mpInstance.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AdaptiveTetrahedralMesh::Adapt(), AdaptiveBidomainProblem::AdaptMesh(), BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::BasicBidomainSolver(), BasicMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::BasicMonodomainSolver(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::BidomainAssembler(), BidomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::BidomainCorrectionTermAssembler(), AdaptiveTetrahedralMesh::CalculateErrorMetric(), CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), CardiacSimulation::CardiacSimulation(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), AbstractCvodeCell::Compute(), BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacSimulation::CreateAndRun(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateCardiacTissue(), BidomainProblem< DIM >::CreateCardiacTissue(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), CardiacSimulation::CreateResumeXmlFile(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateSolver(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), Electrodes< DIM >::Electrodes(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetDataReader(), AdaptiveBidomainProblem::GetGradation(), CML_noble_varghese_kohl_noble_1998_basic_with_sac::GetIIonic(), AbstractCardiacCellInterface::GetIntracellularAreaStimulus(), AdaptiveBidomainProblem::GetMaxEdgeLength(), AdaptiveBidomainProblem::GetMaxMeshNodes(), AdaptiveBidomainProblem::GetMinEdgeLength(), AdaptiveBidomainProblem::GetNumAdaptSweeps(), AdaptiveBidomainProblem::GetSigma(), AdaptiveBidomainProblem::GetTargetError(), HeartRegionCode::GetValidBathId(), HeartRegionCode::GetValidTissueId(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory(), CardiacElectroMechanicsProblem< DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), HeartRegionCode::IsRegionBath(), HeartRegionCode::IsRegionTissue(), load(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::MatrixBasedBidomainSolver(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MatrixBasedMonodomainSolver(), MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainAssembler(), MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::MonodomainCorrectionTermAssembler(), BidomainProblem< DIM >::OnEndOfTimestep(), BidomainProblem< DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), CardiacSimulation::ReadParametersFromFile(), CardiacSimulation::Run(), AbstractCardiacTissue< SPACE_DIM >::save(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::save(), HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters(), BidomainProblem< DIM >::SetElectrodes(), AdaptiveBidomainProblem::SetNeumannStimulusMagnitudeAndDuration(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), CardiacElectroMechanicsProblem< DIM >::Solve(), AdaptiveBidomainProblem::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), AbstractCvodeCell::SolveAndUpdateState(), UpdateParametersFromResumeSimulation(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFile(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

void HeartConfig::SetUseFixedSchemaLocation ( bool  useFixedSchemaLocation  ) 

Parameters:
useFixedSchemaLocation whether to read the schema location from the XML file (false) or use the schema located at heart/src/io/ChasteParameters.xsd in the Chaste source tree (or specified with SetFixedSchemaLocations()) (true).

Definition at line 356 of file HeartConfig.cpp.

References mUseFixedSchemaLocation.

Referenced by CardiacSimulation::ReadParametersFromFile(), and SetFixedSchemaLocations().

void HeartConfig::SetFixedSchemaLocations ( const SchemaLocationsMap rSchemaLocations  ) 

Set the schema files to use. Also calls SetUseFixedSchemaLocation(true).

Parameters:
rSchemaLocations map from namespace URI to schema URI

Definition at line 350 of file HeartConfig.cpp.

References mSchemaLocations, and SetUseFixedSchemaLocation().

void HeartConfig::SetDefaultsFile ( const std::string &  rFileName  ) 

Allows users to override the built-in defaults.

Parameters:
rFileName The name of the defaults file

Definition at line 210 of file HeartConfig.cpp.

References CheckTimeSteps(), mpDefaultParameters, mpUserParameters, and ReadFile().

Referenced by load().

void HeartConfig::SetParametersFile ( const std::string &  rFileName  ) 

mpUserParameters is set to a new context associated with a parameters file

Parameters:
rFileName The name of the parameters file

Definition at line 430 of file HeartConfig.cpp.

References CheckTimeSteps(), mpUserParameters, and ReadFile().

Referenced by load(), and CardiacSimulation::ReadParametersFromFile().

void HeartConfig::Write ( bool  useArchiveLocationInfo = false,
std::string  subfolderName = "output" 
)

Write out the complete configuration set (ChasteParameters and ChasteDefaults) as an XML file. Note that the location of ChasteParameters.xsd (schema definition) will be hard-coded in the XML file.

Parameters:
useArchiveLocationInfo if false, then use self's GetOutputDirectory() and open in *named* subfolder if true, then use ArchiveLocationInfo
subfolderName -- where to store with respect to GetOutputDirectory()
Note:
This method is collective if useArchiveLocationInfo is false

Definition at line 223 of file HeartConfig.cpp.

References PetscTools::AmMaster(), CopySchema(), EXCEPTION, ArchiveLocationInfo::GetArchiveDirectory(), GetOutputDirectory(), OutputFileHandler::GetOutputDirectoryFullPath(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter().

void HeartConfig::CopySchema ( const std::string &  rToDirectory  ) 

Try to copy the latest version of the schema to the given directory. If we can't find the latest version of the schema, generate a warning.

Parameters:
rToDirectory directory to copy to

Definition at line 276 of file HeartConfig.cpp.

References PetscTools::AmMaster(), RelativeTo::ChasteSourceRoot, RelativeTo::CWD, FileFinder::Exists(), FileFinder::GetAbsolutePath(), MPIABORTIFNON0, and FileFinder::SetPath().

Referenced by CardiacSimulation::CreateResumeXmlFile(), and Write().

boost::shared_ptr< cp::chaste_parameters_type > HeartConfig::ReadFile ( const std::string &  rFileName  ) 

void HeartConfig::Reset (  )  [static]

Throw away the current instance by resetting auto_ptr mpInstance to NULL. "New" another mpInstance

Definition at line 547 of file HeartConfig.cpp.

References mpInstance.

Referenced by CardiacSimulation::ReadParametersFromFile(), and CardiacElectroMechanicsProblem< DIM >::Solve().

unsigned HeartConfig::GetVersionFromNamespace ( const std::string &  rNamespaceUri  ) 

Get the Chaste version of a parameters file, given its namespace URI. The version will be encoded as major*1000+minor.

Parameters:
rNamespaceUri the namespace URI of the parameters file

Definition at line 316 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by ReadFile().

bool HeartConfig::IsSimulationDefined (  )  const

Returns whether the configuration file defines a new simulation.

Returns:
is a new simulation?

Definition at line 555 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CheckResumeSimulationIsDefined(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetDomain(), GetMaxCheckpointsOnDisk(), GetSimulationDuration(), and GetSpaceDimension().

bool HeartConfig::IsSimulationResumed (  )  const

Returns whether the configuration file resumes an archived simulation.

Returns:
is a resumed simulation?

Definition at line 560 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CheckSimulationIsDefined().

unsigned HeartConfig::GetSpaceDimension (  )  const

double HeartConfig::GetSimulationDuration (  )  const

cp::domain_type HeartConfig::GetDomain (  )  const

cp::domain_type is an xsd convenience class type

Returns:
domain type of simulation: bi- or mono-domain

Definition at line 625 of file HeartConfig.cpp.

References DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile(), and UpdateParametersFromResumeSimulation().

cp::ionic_model_selection_type HeartConfig::GetDefaultIonicModel (  )  const

Default cardiac cell model to use at all mesh nodes (unless otherwise specified by GetIonicModelRegions). cp::ionic_model_selection_type is generated automatically from the XML Schema.

Returns:
type of model

Definition at line 639 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

template<unsigned DIM>
void HeartConfig::GetIonicModelRegions ( std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &  rDefinedRegions,
std::vector< cp::ionic_model_selection_type > &  rIonicModels 
) const [inline]

Regions where we need to use a different cell model (think infarction). cp::ionic_model_selection_type is generated automatically from the XML Schema.

The supplied vectors are first cleared, then filled in with the information from the parameters files. On return, both vectors will be the same length (one entry per region).

Parameters:
rDefinedRegions vector of axis-aligned box regions (one per cellular heterogeneity)
rIonicModels vector of models (one per cellular heterogeneity)

Todo:
When this is implemented, then we require an example in ChasteParametersFullFormat.xml

Definition at line 649 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mpDefaultParameters, mpUserParameters, and NEVER_REACHED.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

void HeartConfig::SetIonicModelRegions ( std::vector< ChasteCuboid< 3 > > &  rDefinedRegions,
std::vector< cp::ionic_model_selection_type > &  rIonicModels 
) const

Set the regions where we need to use a different cell model (think infarction). Unlike the get method, this is currently only supported in 3d. cp::ionic_model_selection_type is generated automatically from the XML Schema.

The input standard vectors must be of the same length (one entry per region) otherwise the method throws.

Parameters:
rDefinedRegions vector of axis-aligned box regions (one per cellular heterogeneity)
rIonicModels vector of models (one per cellular heterogeneity)

Definition at line 2265 of file HeartConfig.cpp.

References mpUserParameters.

bool HeartConfig::IsMeshProvided (  )  const

Returns:
true if a mesh file name is given. (Otherwise it's assumed that this is a cuboid simulation.)

Definition at line 756 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

bool HeartConfig::GetCreateMesh (  )  const

Returns:
true if it's a cuboid simulation (no mesh on disk)

Definition at line 773 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetInterNodeSpace().

bool HeartConfig::GetCreateSlab (  )  const

Returns:
true if it's a cuboid simulation (no mesh on disk)

Definition at line 784 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetSlabDimensions().

bool HeartConfig::GetCreateSheet (  )  const

Returns:
true if it's a cuboid simulation (no mesh on disk)

Definition at line 795 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetSheetDimensions().

bool HeartConfig::GetCreateFibre (  )  const

Returns:
true if it's a cuboid simulation (no mesh on disk)

Definition at line 806 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetFibreLength().

bool HeartConfig::GetLoadMesh (  )  const

void HeartConfig::GetSlabDimensions ( c_vector< double, 3 > &  slabDimensions  )  const

Parameters:
slabDimensions return vector for the (cuboid) mesh dimensions (cm)

Definition at line 827 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateSlab(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

void HeartConfig::GetSheetDimensions ( c_vector< double, 2 > &  sheetDimensions  )  const

Parameters:
sheetDimensions return vector for the (cuboid) mesh dimensions (cm)

Definition at line 845 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateSheet(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

void HeartConfig::GetFibreLength ( c_vector< double, 1 > &  fibreLength  )  const

Parameters:
fibreLength return vector for the (cuboid) mesh dimensions (cm)

Definition at line 862 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateFibre(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetInterNodeSpace (  )  const

std::string HeartConfig::GetMeshName (  )  const

cp::media_type HeartConfig::GetConductivityMedia (  )  const

Returns:
media (Orthotropic/Axisymmetric/NoFibreOrientation) so that we know whether to read a .ortho/.axi file

Definition at line 918 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), GetLoadMesh(), mpDefaultParameters, and mpUserParameters.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

template<unsigned DIM>
void HeartConfig::GetStimuli ( std::vector< boost::shared_ptr< AbstractStimulusFunction > > &  rStimuliApplied,
std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &  rStimulatedAreas 
) const [inline]

Return a number of stimulated regions (Axis-aligned boxes)

Todo:
  • do we assume the vectors are initially empty? The returned std::vectors are all of the same length
Parameters:
rStimuliApplied rStimuliApplied[0] is stimulus for the first region
rStimulatedAreas rStimulatedAreas[0] is the first region to be stimulated
Todo:
There is no set method

Definition at line 929 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mpDefaultParameters, mpUserParameters, and NEVER_REACHED.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

template<unsigned DIM>
void HeartConfig::GetCellHeterogeneities ( std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &  rCellHeterogeneityRegions,
std::vector< double > &  rScaleFactorGks,
std::vector< double > &  rScaleFactorIto,
std::vector< double > &  rScaleFactorGkr,
std::vector< std::map< std::string, double > > *  pParameterSettings 
) [inline]

Reads from the XML file the cellular hetrogeneities. It fugures out whether the user specified a cuboid or a transmural-type of hetrogeneities. In the latter case, it stores the percentage values of Epi and Endo layers in two member variables, accessible via get methods. It also checks if the user-supplied numbers are consistent (i.e., positive and add up to less than 1) Return a number of heterogeneous regions for special gating variable changes

Todo:
  • do we assume the vectors are initially empty? The returned std::vectors are all of the same length
Parameters:
rCellHeterogeneityRegions cellHeterogeneityAreas[0] is the first region
rScaleFactorGks scaleFactorGks[0] is a scaling factor for the first region
rScaleFactorIto scaleFactorIto[0] is a scaling factor for the first region
rScaleFactorGkr scaleFactorGkr[0] is a scaling factor for the first region
pParameterSettings specification of named parameters to set on the cell models; each entry is a map from parameter name to value.
Todo:
There is no set method

Definition at line 1072 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mEndoFraction, mEpiFraction, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpDefaultParameters, mpUserParameters, and mUserAskedForCellularTransmuralHeterogeneities.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

bool HeartConfig::GetConductivityHeterogeneitiesProvided (  )  const

Returns:
true if there are conductivity heterogeneities for GetConductivityHeterogeneities to return

Definition at line 1251 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

bool HeartConfig::AreCellularTransmuralHeterogeneitiesRequested (  ) 

Returns:
the value of the flag that tells whether the user asked for cellular transmural heterogeneities

Definition at line 1216 of file HeartConfig.cpp.

References mUserAskedForCellularTransmuralHeterogeneities.

double HeartConfig::GetEpiLayerFraction (  ) 

Returns:
the fraction of epicardial layer

Definition at line 1221 of file HeartConfig.cpp.

References mEpiFraction.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

double HeartConfig::GetEndoLayerFraction (  ) 

Returns:
the fraction of endocardial layer

Definition at line 1226 of file HeartConfig.cpp.

References mEndoFraction.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

double HeartConfig::GetMidLayerFraction (  ) 

Returns:
the fraction of endocardial layer

Definition at line 1231 of file HeartConfig.cpp.

References mMidFraction.

unsigned HeartConfig::GetEpiLayerIndex (  ) 

Returns:
the index with which the epicardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1236 of file HeartConfig.cpp.

References mIndexEpi.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned HeartConfig::GetEndoLayerIndex (  ) 

Returns:
the index with which the endocardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1241 of file HeartConfig.cpp.

References mIndexEndo.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned HeartConfig::GetMidLayerIndex (  ) 

Returns:
the index with which the midmyocardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1246 of file HeartConfig.cpp.

References mIndexMid.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

template<unsigned DIM>
void HeartConfig::GetConductivityHeterogeneities ( std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &  conductivitiesHeterogeneityAreas,
std::vector< c_vector< double, 3 > > &  intraConductivities,
std::vector< c_vector< double, 3 > > &  extraConductivities 
) const [inline]

Return a number of heterogeneous regions (Axis-aligned boxes)

Todo:
  • do we assume the vectors are initially empty? The returned std::vectors are all of the same length
Parameters:
conductivitiesHeterogeneityAreas conductivitiesHeterogeneityAreas[0] is the first region
intraConductivities intraConductivities[0] is conductivity vector for the first region
extraConductivities extraConductivities[0] is conductivity vector for the first region

Todo:
When this is implemented, then we require an example in ChasteParametersFullFormat.xml

Definition at line 1268 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetExtracellularConductivities(), GetIntracellularConductivities(), mpDefaultParameters, and mpUserParameters.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

std::string HeartConfig::GetOutputDirectory (  )  const

std::string HeartConfig::GetOutputFilenamePrefix (  )  const

Returns:
Prefix for files If set to "res" this produces [path]/res.h5 [path]/output/res_mesh.pts [path]/output/res_mesh.tri [path]/output/res_parameters.xml (a copy of this configuration at the end of the simulation) [path]/output/res_times.info [path]/output/res_V.dat

Definition at line 1352 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), AdaptiveBidomainProblem::Solve(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript().

bool HeartConfig::GetOutputVariablesProvided (  )  const

Returns:
true iff any extra output variables have been requested

Definition at line 1360 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

void HeartConfig::GetOutputVariables ( std::vector< std::string > &  rOutputVariables  )  const

Get the extra output variables from the xml file.

Parameters:
rOutputVariables reference to std::vector to contain the output variables requested. Note: will be cleared before being filled.

Definition at line 1377 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetOutputUsingOriginalNodeOrdering (  ) 

Returns:
whether to write output HDF5 file using the original mesh permutation (in situations where a parallel partition may have permuted the node). The default is to use the new, not original permutation,

Definition at line 1396 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

bool HeartConfig::GetCheckpointSimulation (  )  const

Get whether simulation should be checkpointed or not

Returns:
archive simulation

Todo:
#1160 What code covers this? Should be removed ideally.

Definition at line 1411 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

Referenced by CheckTimeSteps(), CardiacSimulation::CreateAndRun(), and HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus().

double HeartConfig::GetCheckpointTimestep (  )  const

Get checkpointing timestep

Returns:
checkpointing timestep

Todo:
#1160 What code covers this? Should be removed ideally.

Definition at line 1437 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

Referenced by CheckTimeSteps(), CardiacSimulation::CreateAndRun(), and CardiacSimulation::CreateResumeXmlFile().

unsigned HeartConfig::GetMaxCheckpointsOnDisk (  )  const

Get number of checkpoints to keep on disk

Returns:
checkpointing timestep

Todo:
#1160 What code covers this? Should be removed ideally.

Definition at line 1455 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile().

HeartFileFinder HeartConfig::GetArchivedSimulationDir (  )  const

Get directory where the archived simulation to resume is defined

Definition at line 1474 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), and mpUserParameters.

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 3 > &  intraConductivities  )  const

3D version

Parameters:
intraConductivities DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1482 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), and GetConductivityHeterogeneities().

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 2 > &  intraConductivities  )  const

2D version

Parameters:
intraConductivities DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1500 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 1 > &  intraConductivities  )  const

1D version

Parameters:
intraConductivities DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1515 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 3 > &  extraConductivities  )  const

3D version

Parameters:
extraConductivities DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1526 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and GetConductivityHeterogeneities().

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 2 > &  extraConductivities  )  const

2D version

Parameters:
extraConductivities DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1544 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 1 > &  extraConductivities  )  const

1D version

Parameters:
extraConductivities DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1559 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

double HeartConfig::GetBathConductivity ( unsigned  bathRegion = UINT_MAX  )  const

Returns bath conductivities for different regions of the bath. When called without a region identifier, it will return whatever has been defined as BathConductivity

Parameters:
bathRegion region identifier
Returns:
bath conductivity (mS/cm)

Definition at line 1570 of file HeartConfig.cpp.

References DecideLocation(), HeartRegionCode::IsRegionBath(), mBathConductivities, mpDefaultParameters, and mpUserParameters.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().

const std::set< unsigned > & HeartConfig::rGetTissueIdentifiers (  ) 

Gets region identifiers that have to be considered as cardiac tissue.

Returns:
set of identifiers

Definition at line 1607 of file HeartConfig.cpp.

References mTissueIdentifiers.

Referenced by HeartRegionCode::GetValidTissueId().

const std::set< unsigned > & HeartConfig::rGetBathIdentifiers (  ) 

Gets region identifiers that have to be considered as bath.

Returns:
set of identifiers

Definition at line 1612 of file HeartConfig.cpp.

References mBathIdentifiers.

Referenced by HeartRegionCode::GetValidBathId().

double HeartConfig::GetSurfaceAreaToVolumeRatio (  )  const

double HeartConfig::GetCapacitance (  )  const

double HeartConfig::GetOdeTimeStep (  )  const

Returns:
ODE time-step (ms)

Definition at line 1633 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by CheckTimeSteps(), SetPdeTimeStep(), and SetPrintingTimeStep().

double HeartConfig::GetPdeTimeStep (  )  const

double HeartConfig::GetPrintingTimeStep (  )  const

bool HeartConfig::GetUseAbsoluteTolerance (  )  const

Returns:
true if we are using KSP absolute tolerance

Definition at line 1654 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), and GetAbsoluteTolerance().

double HeartConfig::GetAbsoluteTolerance (  )  const

bool HeartConfig::GetUseRelativeTolerance (  )  const

Returns:
true if we are using KSP relative tolerance

Definition at line 1672 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetRelativeTolerance (  )  const

const char * HeartConfig::GetKSPSolver (  )  const

Returns:
name of -ksp_type from {"gmres", "cg", "symmlq"}

Definition at line 1690 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

const char * HeartConfig::GetKSPPreconditioner (  )  const

Returns:
name of -pc_type from {"jacobi", "bjacobi", "hypre", "ml", "spai", "blockdiagonal", "ldufactorisation", "none"}

Definition at line 1710 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

DistributedTetrahedralMeshPartitionType::type HeartConfig::GetMeshPartitioning (  )  const

Returns:
the mesh partitioning method to use

Definition at line 1741 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::IsAdaptivityParametersPresent (  )  const

double HeartConfig::GetTargetErrorForAdaptivity (  )  const

double HeartConfig::GetSigmaForAdaptivity (  )  const

double HeartConfig::GetMaxEdgeLengthForAdaptivity (  )  const

double HeartConfig::GetMinEdgeLengthForAdaptivity (  )  const

double HeartConfig::GetGradationForAdaptivity (  )  const

unsigned HeartConfig::GetMaxNodesForAdaptivity (  )  const

unsigned HeartConfig::GetNumberOfAdaptiveSweeps (  )  const

bool HeartConfig::IsPostProcessingSectionPresent (  )  const

void HeartConfig::EnsurePostProcessingSectionPresent (  ) 

Create a PostProcessing section in the user parameters if one doesn't exist.

Definition at line 1897 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by SetApdMaps(), SetConductionVelocityMaps(), SetMaxUpstrokeVelocityMaps(), SetPseudoEcgElectrodePositions(), SetRequestedNodalTimeTraces(), SetUpstrokeTimeMaps(), and UpdateParametersFromResumeSimulation().

bool HeartConfig::IsPostProcessingRequested (  )  const

bool HeartConfig::IsApdMapsRequested (  )  const

Returns:
true if APD maps have been requested

Definition at line 1918 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetApdMaps(), and IsPostProcessingRequested().

void HeartConfig::GetApdMaps ( std::vector< std::pair< double, double > > &  rApdMaps  )  const

Parameters:
rApdMaps each entry is a request for a map with
  • a percentage in the range [1, 100)
  • a threshold (in mV)

Definition at line 1929 of file HeartConfig.cpp.

References DecideLocation(), IsApdMapsRequested(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::IsUpstrokeTimeMapsRequested (  )  const

Returns:
true if upstroke time maps have been requested

Definition at line 1949 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetUpstrokeTimeMaps(), and IsPostProcessingRequested().

void HeartConfig::GetUpstrokeTimeMaps ( std::vector< double > &  rUpstrokeTimeMaps  )  const

Parameters:
rUpstrokeTimeMaps each entry is a request for a map with
  • a threshold (in mV)

Definition at line 1959 of file HeartConfig.cpp.

References DecideLocation(), IsUpstrokeTimeMapsRequested(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::IsMaxUpstrokeVelocityMapRequested (  )  const

Returns:
true maximum upstroke velocity maps have been requested

Definition at line 1977 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetMaxUpstrokeVelocityMaps(), and IsPostProcessingRequested().

void HeartConfig::GetMaxUpstrokeVelocityMaps ( std::vector< double > &  rUpstrokeVelocityMaps  )  const

Parameters:
rUpstrokeVelocityMaps each entry is a request for a map with
  • a threshold (in mV, defaulted to -30 mV)

Definition at line 1989 of file HeartConfig.cpp.

References DecideLocation(), IsMaxUpstrokeVelocityMapRequested(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::IsConductionVelocityMapsRequested (  )  const

Returns:
true if conduction velocity maps have been requested

Definition at line 2007 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetConductionVelocityMaps(), and IsPostProcessingRequested().

void HeartConfig::GetConductionVelocityMaps ( std::vector< unsigned > &  rConductionVelocityMaps  )  const

Parameters:
rConductionVelocityMaps each entry is a request for a map with
  • an index to treat as the source for wave propagation

Definition at line 2018 of file HeartConfig.cpp.

References DecideLocation(), IsConductionVelocityMapsRequested(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::IsAnyNodalTimeTraceRequested (  )  const

Returns:
true if any nodal time trace is requested

Definition at line 2036 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetNodalTimeTraceRequested(), and IsPostProcessingRequested().

void HeartConfig::GetNodalTimeTraceRequested ( std::vector< unsigned > &  rRequestedNodes  )  const

Parameters:
rRequestedNodes vector of indices of requested nodes that will be filled in by this function

Definition at line 2047 of file HeartConfig.cpp.

References DecideLocation(), IsAnyNodalTimeTraceRequested(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::IsPseudoEcgCalculationRequested (  )  const

Returns:
true iff pseudo-ECG calculation has been requested

Definition at line 2066 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by IsPostProcessingRequested().

template<unsigned SPACE_DIM>
void HeartConfig::GetPseudoEcgElectrodePositions ( std::vector< ChastePoint< SPACE_DIM > > &  rPseudoEcgElectrodePositions  )  const [inline]

Parameters:
rPseudoEcgElectrodePositions will be filled in with the positions of electrodes to use in calculating pseudo-ECGs (if any)

Definition at line 2078 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::GetUseStateVariableInterpolation (  )  const

bool HeartConfig::IsOutputVisualizerPresent (  )  const

Whether there is an OutputVisualizer element present.

Definition at line 2098 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), and GetVisualizeWithVtk().

bool HeartConfig::GetVisualizeWithMeshalyzer (  )  const

Whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 2117 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetVisualizeWithCmgui (  )  const

Whether to convert the output from HDF5 to Cmgui readable format

Definition at line 2131 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::GetVisualizeWithVtk (  )  const

Whether to convert the output from HDF5 to Vtk readable format

Definition at line 2159 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::GetVisualizeWithParallelVtk (  )  const

Whether to convert the output from HDF5 to parallel Vtk readable format

Definition at line 2145 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::IsElectrodesPresent (  )  const

void HeartConfig::GetElectrodeParameters ( bool &  rGroundSecondElectrode,
unsigned &  rIndex,
double &  rMagnitude,
double &  rStartTime,
double &  rDuration 
)

Get electrode parameters.

Parameters:
rGroundSecondElectrode Whether to ground the second electrode (see class documentation)
rIndex The value i when applying the electrodes to x_i=a and x_i=b (a<b)
rMagnitude Magnitude of the stimulus
rStartTime Switch on time
rDuration Duration of the stimulus.

Definition at line 3061 of file HeartConfig.cpp.

References EXCEPTION, IsElectrodesPresent(), and mpUserParameters.

Referenced by Electrodes< DIM >::Electrodes().

bool HeartConfig::GetUseMassLumping (  ) 

Get whether to use mass lumping in the FE solver or not.

Definition at line 3220 of file HeartConfig.cpp.

References mUseMassLumping.

bool HeartConfig::GetUseMassLumpingForPrecond (  ) 

Get whether to use mass lumping in the construction of the preconditioner of the FE solver or not.

Definition at line 3230 of file HeartConfig.cpp.

References mUseMassLumpingForPrecond.

bool HeartConfig::GetUseReactionDiffusionOperatorSplitting (  ) 

Get whether to use Strang operator splitting of the reaction and diffusion terms (see Set method documentation).

Definition at line 3240 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

Referenced by MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateSolver().

bool HeartConfig::GetUseFixedNumberIterationsLinearSolver (  ) 

Get whether to use a fixed number of iterations in the linear solver

Definition at line 3251 of file HeartConfig.cpp.

References mUseFixedNumberIterations.

unsigned HeartConfig::GetEvaluateNumItsEveryNSolves (  ) 

Get how often perform a solve with residual-based stop criteria in order to decide how many iterations to perform in following linear solves.

Definition at line 3256 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves.

void HeartConfig::SetSpaceDimension ( unsigned  spaceDimension  ) 

Set the configuration dimension

Parameters:
spaceDimension 1, 2 or 3.

Definition at line 2193 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSimulationDuration ( double  simulationDuration  ) 

Set the configuration simulation end time.

Parameters:
simulationDuration end time for the next call to Solve() (in ms).

Definition at line 2198 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacSimulation::CreateAndRun(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetDomain ( const cp::domain_type &  rDomain  ) 

Set the configuration to run mono or bidomain cp::domain_type is an xsd convenience class type

Parameters:
rDomain type of simulation bi- mono-domain

Definition at line 2204 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetDefaultIonicModel ( const cp::ionic_models_available_type &  rIonicModel  ) 

Set the configuration to place the given cardiac cell models at all mesh nodes (unless otherwise specified by SetIonicModelRegions). cp::ionic_models_available_type is generated automatically from the XML Schema.

Parameters:
rIonicModel type of model

Definition at line 2209 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSlabDimensions ( double  x,
double  y,
double  z,
double  inter_node_space 
)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 3-D.

Parameters:
x length in 1st dimension (cm)
y length in 2nd dimension (cm)
z length in 3rd dimension (cm)
inter_node_space Spacing in cartesian direction (cm). Diagonals will be longer.

Definition at line 2217 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSheetDimensions ( double  x,
double  y,
double  inter_node_space 
)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 2-D.

Parameters:
x length in 1st dimension (cm)
y length in 2nd dimension (cm)
inter_node_space Spacing in cartesian direction (cm). Diagonals will be longer.

Definition at line 2229 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetFibreLength ( double  x,
double  inter_node_space 
)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 1-D.

Parameters:
x length in 1st dimension (cm)
inter_node_space Spacing in cartesian direction (cm).

Definition at line 2241 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetMeshFileName ( std::string  meshPrefix,
cp::media_type  fibreDefinition = cp::media_type::NoFibreOrientation 
)

Sets the name of a mesh to be read from disk for this simulation

Parameters:
meshPrefix path and basename of a set of mesh files (.nodes .ele etc) in triangle/tetget format
fibreDefinition if set (Orthotropic/Axisymmetric) then a (.ortho/.axi) file should also be read
Todo:
There is no Get method

Definition at line 2253 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetConductivityHeterogeneities ( std::vector< ChasteCuboid< 3 > > &  rConductivityAreas,
std::vector< c_vector< double, 3 > > &  rIntraConductivities,
std::vector< c_vector< double, 3 > > &  rExtraConductivities 
)

Set a number of heterogeneous regions (Axis-aligned boxes) It is assumed that the std::vectors are all of the same length

Parameters:
rConductivityAreas conductivityAreas[0] is the first region
rIntraConductivities intraConductivities[0] is conductivity vector for the first region
rExtraConductivities extraConductivities[0] is conductivity vector for the first region

Definition at line 2292 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetConductivityHeterogeneitiesEllipsoid ( std::vector< ChasteEllipsoid< 3 > > &  conductivityAreas,
std::vector< c_vector< double, 3 > > &  intraConductivities,
std::vector< c_vector< double, 3 > > &  extraConductivities 
)

Set a number of heterogeneous regions (Axis-aligned ellipsoids) It is assumed that the std::vectors are all of the same length

Parameters:
conductivityAreas conductivityAreas[0] is the first region
intraConductivities intraConductivities[0] is conductivity vector for the first region
extraConductivities extraConductivities[0] is conductivity vector for the first region

Definition at line 2340 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetOutputDirectory ( const std::string &  rOutputDirectory  ) 

void HeartConfig::SetOutputFilenamePrefix ( const std::string &  rOutputFilenamePrefix  ) 

Parameters:
rOutputFilenamePrefix Prefix for files If set to "res" this will produce [path]/res.h5 [path]/output/res_mesh.pts [path]/output/res_mesh.tri [path]/output/res_parameters.xml (a copy of this configuration at the end of the simulation) [path]/output/res_times.info [path]/output/res_V.dat

Definition at line 2393 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), and AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge().

void HeartConfig::SetOutputVariables ( const std::vector< std::string > &  rOutputVariables  ) 

Parameters:
rOutputVariables a vector of std::strings of the names of each variable that should be outputted at each time step.
USING THIS METHOD WILL OVERRIDE THE ANY OUTPUT VARIABLES SET IN THE XML FILE

Warning: when specifying output variables, you cannot convert the HDF5 output to Meshalyzer, Cmgui or VTK formats, since the converter will get confused by the presence of extra data. This method thus also turns off visualizer output if the provided vector is non-empty.

Definition at line 2398 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetOutputUsingOriginalNodeOrdering ( bool  useOriginal  ) 

This method may set the output HDF5 file to be written using the original mesh permutation (in situations where a parallel partition may have permuted the node). The default is to use the new, not original permutation, i.e. useOriginal=false

Parameters:
useOriginal whether to use the original permutation

Definition at line 2428 of file HeartConfig.cpp.

References mpUserParameters.

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

void HeartConfig::SetCheckpointSimulation ( bool  checkpointSimulation,
double  checkpointTimestep = -1.0,
unsigned  maxCheckpointsOnDisk = UINT_MAX 
)

Set whether the simulation should be checkpointed or not.

Parameters:
checkpointSimulation whether to do checkpointing
checkpointTimestep checkpointing timestep
maxCheckpointsOnDisk maximum number of checkpoint archives to keep on disk

Definition at line 2434 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

Referenced by load(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 3 > &  rIntraConductivities  ) 

3D version

Parameters:
rIntraConductivities DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2458 of file HeartConfig.cpp.

References mpUserParameters.

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

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 2 > &  rIntraConductivities  ) 

2D version

Parameters:
rIntraConductivities DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2469 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 1 > &  rIntraConductivities  ) 

1D version

Parameters:
rIntraConductivities DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2479 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 3 > &  rExtraConductivities  ) 

3D version

Parameters:
rExtraConductivities DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2488 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 2 > &  rExtraConductivities  ) 

2D version

Parameters:
rExtraConductivities DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2499 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 1 > &  rExtraConductivities  ) 

1D version

Parameters:
rExtraConductivities DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2509 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetBathConductivity ( double  bathConductivity  ) 

Set bath default conductivity

Parameters:
bathConductivity default conductivity for perfusing bath (mS/cm)
Todo:
Is this used anywhere?

Definition at line 2518 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetBathMultipleConductivities ( std::map< unsigned, double >  bathConductivities  ) 

Set multiple bath conductivities based on element region label (mS/cm)

Parameters:
bathConductivities map between different bath region identifier and their conductivity (if different from default)

Todo:
: This implementation is temporary until we incorporate the bath heterogeneities to the XML schema

Definition at line 2524 of file HeartConfig.cpp.

References mBathConductivities.

void HeartConfig::SetTissueAndBathIdentifiers ( const std::set< unsigned > &  tissueIds,
const std::set< unsigned > &  bathIds 
)

Sets which region identifiers have to be considered cardiac tissue and bath.

Parameters:
tissueIds set of identifiers
bathIds set of identifiers

Definition at line 2536 of file HeartConfig.cpp.

References EXCEPTION, mBathIdentifiers, and mTissueIdentifiers.

void HeartConfig::SetSurfaceAreaToVolumeRatio ( double  ratio  ) 

Sets which region identifiers have to be considered cardiac tissue.

param tissueIds set of identifiers

Todo:
#1703 Think about adding this convenience method either copying the existing BathIds, resetting them out of the way, or making them empty...
Set surface area to volume ratio Am (for PDE)
Parameters:
ratio (1/cm)

Definition at line 2557 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetCapacitance ( double  capacitance  ) 

Set surface capacitance Cm (for PDE)

Parameters:
capacitance (uF/cm^2)

Definition at line 2563 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetOdePdeAndPrintingTimeSteps ( double  odeTimeStep,
double  pdeTimeStep,
double  printingTimeStep 
)

Set the configuration to use ode, pde and printing times of given values Calls CheckTimeSteps to ensure compatibility

Parameters:
odeTimeStep ode value to use
pdeTimeStep pde value to use
printingTimeStep printing value to use

Definition at line 2571 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), SetOdeTimeStep(), SetPdeTimeStep(), and SetPrintingTimeStep().

void HeartConfig::SetOdeTimeStep ( double  odeTimeStep  ) 

Set the configuration to use ode time of given value Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:
odeTimeStep the value to use

Definition at line 2579 of file HeartConfig.cpp.

References GetPdeTimeStep(), GetPrintingTimeStep(), and SetOdePdeAndPrintingTimeSteps().

void HeartConfig::SetPdeTimeStep ( double  pdeTimeStep  ) 

Set the configuration to use pde time of given value Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:
pdeTimeStep the value to use

Definition at line 2584 of file HeartConfig.cpp.

References GetOdeTimeStep(), GetPrintingTimeStep(), and SetOdePdeAndPrintingTimeSteps().

void HeartConfig::SetPrintingTimeStep ( double  printingTimeStep  ) 

Set the configuration to use printing time of given value Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:
printingTimeStep the value to use

Definition at line 2589 of file HeartConfig.cpp.

References GetOdeTimeStep(), GetPdeTimeStep(), and SetOdePdeAndPrintingTimeSteps().

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

void HeartConfig::SetUseRelativeTolerance ( double  relativeTolerance  ) 

Set the configuration to use KSP relative tolerance of given value

Parameters:
relativeTolerance the value to use

Definition at line 2639 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetUseAbsoluteTolerance ( double  absoluteTolerance  ) 

Set the configuration to use KSP absolute tolerance of given value

Parameters:
absoluteTolerance the value to use

Definition at line 2647 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetKSPSolver ( const char *  kspSolver  ) 

Set the type of KSP solver as with the flag "-ksp_type"

Parameters:
kspSolver a string from {"gmres", "cg", "symmlq"}

Definition at line 2655 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void HeartConfig::SetKSPPreconditioner ( const char *  kspPreconditioner  ) 

Set the type of preconditioner as with the flag "-pc_type"

Parameters:
kspPreconditioner a string from {"jacobi", "bjacobi", "hypre", "ml", "spai", "blockdiagonal", "ldufactorisation", "none"}

Definition at line 2682 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

void HeartConfig::SetMeshPartitioning ( const char *  meshPartioningMethod  ) 

Set the type of mesh partitioning method

Parameters:
meshPartioningMethod a string from {"dumb", "metis", "parmetis", "petsc"}

Definition at line 2734 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

void HeartConfig::SetAdaptivityParameters ( double  targetError,
double  sigma,
double  maxEdgeLength,
double  minEdgeLength,
double  gradation,
unsigned  maxNodes,
unsigned  numSweeps 
)

Set the parameters to be used during mesh adaptation.

Parameters:
targetError is the target error passed to the adaptivity library
sigma is the value of sigma passed to the adaptivity library
maxEdgeLength is the maximum edge length permitted in the adapted mesh
minEdgeLength is the minimum edge length permitted in the adapted mesh
gradation is the value of gradation passed to the adaptivity library
maxNodes is the maximum number of nodes permitted in the adapted mesh
numSweeps is the number of adaptive sweeps through the mesh performed by the adaptivity library

Definition at line 2761 of file HeartConfig.cpp.

References EXCEPTION, IsAdaptivityParametersPresent(), and mpUserParameters.

Referenced by SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

void HeartConfig::SetTargetErrorForAdaptivity ( double  targetError  ) 

Set the target error to be used during mesh adaptation.

Parameters:
targetError is the target error passed to the adaptivity library

Definition at line 2795 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetSigmaForAdaptivity ( double  sigma  ) 

Set the value of sigma to be used during mesh adaptation.

Parameters:
sigma is the value of sigma passed to the adaptivity library

Definition at line 2806 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetMaxEdgeLengthForAdaptivity ( double  maxEdgeLength  ) 

Set the maximum edge length to be used during mesh adaptation.

Parameters:
maxEdgeLength is the maximum edge length permitted in the adapted mesh

Definition at line 2817 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetMinEdgeLengthForAdaptivity ( double  minEdgeLength  ) 

Set the minimum edge length to be used during mesh adaptation.

Parameters:
minEdgeLength is the minimum edge length permitted in the adapted mesh

Definition at line 2828 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetGradationForAdaptivity ( double  gradation  ) 

Set the gradation to be used during mesh adaptation.

Parameters:
gradation is the gradation passed to the adaptivity library

Definition at line 2839 of file HeartConfig.cpp.

References GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetMaxNodesForAdaptivity ( unsigned  maxNodes  ) 

Set the maximum number of nodes to be used during mesh adaptation.

Parameters:
maxNodes is the maximum number of nodes permitted in the adapted mesh

Definition at line 2850 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetNumberOfAdaptiveSweeps ( unsigned  numSweeps  ) 

Set the number of adaptive sweeps to be used during mesh adaptation.

Parameters:
numSweeps is the number of adaptive sweeps through the mesh performed by the adaptivity library

Definition at line 2861 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetApdMaps ( const std::vector< std::pair< double, double > > &  rApdMaps  ) 

Set the parameters of the apd map requested

Parameters:
rApdMaps each entry is a request for a map with
  • a percentage in the range [1, 100) (ranges are not checked by this method, but during the calculation)
  • a threshold (in mV)

Definition at line 2872 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::SetUpstrokeTimeMaps ( std::vector< double > &  rUpstrokeTimeMaps  ) 

Set the parameters of the upstroke time map requested

Parameters:
rUpstrokeTimeMaps is the list of thresholds (mV) with respect to which the upstroke time maps are calculated. The threshold is used for determining when an action potential occurs.

Definition at line 2890 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::SetMaxUpstrokeVelocityMaps ( std::vector< double > &  rMaxUpstrokeVelocityMaps  ) 

Set the parameters of the maximal upstroke velocity map requested

Parameters:
rMaxUpstrokeVelocityMaps is the list of thresholds (mV) with respect to which the upstroke velocity maps are calculated. The threshold is used for determining when an action potential occurs.

Definition at line 2908 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::SetConductionVelocityMaps ( std::vector< unsigned > &  rConductionVelocityMaps  ) 

Set the parameters of the conduction velocity map requested

Parameters:
rConductionVelocityMaps is a list of origin node indices. One map is created for each origin node.

Definition at line 2929 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::SetRequestedNodalTimeTraces ( std::vector< unsigned > &  requestedNodes  ) 

Sets the requested nodes for extrapolation of the time trace. The node numbering is referred to the original numbering (unpermuted).

Parameters:
requestedNodes the node indices (in the unpermuted mesh) where we want the plot over time

Definition at line 2945 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

template<unsigned SPACE_DIM>
void HeartConfig::SetPseudoEcgElectrodePositions ( const std::vector< ChastePoint< SPACE_DIM > > &  rPseudoEcgElectrodePositions  )  [inline]

Set the parameters for pseudo-ECG calculation.

Parameters:
rPseudoEcgElectrodePositions should contan the positions of electrodes to use in calculating pseudo-ECGs (if any)

Definition at line 2962 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::EnsureOutputVisualizerExists ( void   ) 

Create the OutputVisualizer element if it doesn't exist

Definition at line 2985 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), and SetVisualizeWithVtk().

void HeartConfig::SetVisualizeWithMeshalyzer ( bool  useMeshalyzer = true  ) 

Set whether to convert the output from HDF5 to meshalyzer readable format

Parameters:
useMeshalyzer 

Definition at line 2990 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithCmgui ( bool  useCmgui = true  ) 

Set whether to convert the output from HDF5 to Cmgui readable format

Parameters:
useCmgui 

Definition at line 2998 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithVtk ( bool  useVtk = true  ) 

Set whether to convert the output from HDF5 to Vtk readable format

Parameters:
useVtk 

Definition at line 3006 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithParallelVtk ( bool  useParallelVtk = true  ) 

Set whether to convert the output from HDF5 to parallel Vtk readable format

Parameters:
useParallelVtk 

Definition at line 3014 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetElectrodeParameters ( bool  groundSecondElectrode,
unsigned  index,
double  magnitude,
double  startTime,
double  duration 
)

Setup electrode parameters.

Parameters:
groundSecondElectrode Whether to ground the second electrode (see class documentation)
index The value i when applying the electrodes to x_i=a and x_i=b (a<b)
magnitude Magnitude of the stimulus
startTime Switch on time
duration Duration of the stimulus.

Definition at line 3022 of file HeartConfig.cpp.

References IsElectrodesPresent(), and mpUserParameters.

void HeartConfig::SetUseStateVariableInterpolation ( bool  useStateVariableInterpolation = true  ) 

Set the use of State Variable Interpolation in the computation of ionic currents. See documentation page ChasteGuides/StateVariableInterpolation.

Parameters:
useStateVariableInterpolation Whether to use it.

Definition at line 3109 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetUseMassLumping ( bool  useMassLumping = true  ) 

Set the use of mass lumping in the FE solver.

Parameters:
useMassLumping Whether to use it

Definition at line 3215 of file HeartConfig.cpp.

References mUseMassLumping.

Referenced by MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void HeartConfig::SetUseMassLumpingForPrecond ( bool  useMassLumping = true  ) 

Set the use of mass lumping in the construction of the preconditioner in the FE solver.

Parameters:
useMassLumping Whether to use it

Definition at line 3225 of file HeartConfig.cpp.

References mUseMassLumpingForPrecond.

void HeartConfig::SetUseReactionDiffusionOperatorSplitting ( bool  useOperatorSplitting = true  ) 

Use Strang operator splitting of the diffusion (conductivity) term and the reaction (ionic current) term, instead of solving the full reaction-diffusion PDE. This does NOT refer to operator splitting of the two PDEs in the bidomain equations. For details see for example Sundnes et al "Computing the Electrical Activity of the Heart".

Parameters:
useOperatorSplitting Whether to use operator splitting (defaults to true).

Definition at line 3235 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

void HeartConfig::SetUseFixedNumberIterationsLinearSolver ( bool  useFixedNumberIterations = true,
unsigned  evaluateNumItsEveryNSolves = UINT_MAX 
)

Set the use of fixed number of iterations in the linear solver

Parameters:
useFixedNumberIterations Whether to use a fixed number of iterations for the linear solver
evaluateNumItsEveryNSolves Perform a solve with convergence-based stop criteria every n solves to decide how many iterations perform for the next n-1 solves. Default is perfoming a single evaluation at the beginning of the simulation.

Definition at line 3245 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves, and mUseFixedNumberIterations.

bool HeartConfig::HasDrugDose (  )  const

Returns:
whether HeartConfig has a drug concentration and any IC50s set up

Definition at line 3123 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

double HeartConfig::GetDrugDose (  )  const

Returns:
the dose of the drug (in the same units as the IC50s)

Definition at line 3140 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

void HeartConfig::SetDrugDose ( double  drugDose  ) 

Parameters:
drugDose The dose of the drug to use (should be in units consistent with the IC50s).

Definition at line 3147 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by SetIc50Value().

void HeartConfig::SetIc50Value ( const std::string &  rCurrentName,
double  ic50,
double  hill = 1.0 
)

Add a new conductance block model for a particular channel.

Parameters:
rCurrentName The Oxford metadata name of the current (e.g. membrane_fast_sodium_current)
ic50 The IC50 value for this channel (should be in consistent units with drug dose)
hill The hill coefficient to use (usually default to 1)

Definition at line 3181 of file HeartConfig.cpp.

References mpUserParameters, and SetDrugDose().

std::map< std::string, std::pair< double, double > > HeartConfig::GetIc50Values (  ) 

Get the parameters for the model of "conductance-block" drug action on a set of ion channels.

Returns:
A map between the current/channel name, and a pair giving IC50 value and hill coefficient.

Definition at line 3160 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

template<class TYPE>
TYPE * HeartConfig::DecideLocation ( TYPE *  params_ptr,
TYPE *  defaults_ptr,
const std::string &  rNameParameter 
) const [inline, private]

DecideLocation is a convenience method used to get the correct parameter value from the defaults/parameters files. It checks if the first value is present and (if not) moves onto the second

Parameters:
params_ptr Pointer to quantity within the parameters file (checked first, since it will override a default)
defaults_ptr Pointer to quantity within the defaults file (used if there was no override)
rNameParameter Name of quatity within params_ptr/defaults_ptr (so we can throw a meaningful exception if it's not found)

Definition at line 567 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by GetAbsoluteTolerance(), GetApdMaps(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), and IsUpstrokeTimeMapsRequested().

void HeartConfig::CheckSimulationIsDefined ( std::string  callingMethod = ""  )  const [private]

CheckSimulationIsDefined is a convience method for checking if the "<"Simulation">" element has been defined and therefore is safe to use the Simulation().get() pointer to access other data.

Throws an exception if not.

Parameters:
callingMethod string describing the get method performing the check.

Definition at line 581 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationResumed().

Referenced by GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetFibreLength(), GetInterNodeSpace(), GetIonicModelRegions(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMeshName(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputVariables(), GetOutputVariablesProvided(), GetSheetDimensions(), GetSlabDimensions(), GetStimuli(), IsMeshProvided(), and IsOutputVisualizerPresent().

void HeartConfig::CheckResumeSimulationIsDefined ( std::string  callingMethod = ""  )  const [private]

CheckSimulationIsDefined is a convience method for checking if the "<"ResumeSimulation">" element has been defined and therefore is safe to use the ResumeSimulation().get() pointer to access other data.

Throws an exception if not.

Parameters:
callingMethod string describing the get method performing the check.

Definition at line 589 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationDefined().

Referenced by GetArchivedSimulationDir(), GetCheckpointSimulation(), GetCheckpointTimestep(), and GetMaxCheckpointsOnDisk().


Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 86 of file HeartConfig.hpp.


Member Data Documentation

Fixed location of schema files for the different Chaste parameters namespaces.

Definition at line 168 of file HeartConfig.hpp.

Referenced by ReadFile(), SetDefaultSchemaLocations(), and SetFixedSchemaLocations().

boost::shared_ptr<cp::chaste_parameters_type> HeartConfig::mpUserParameters [private]

Pointer to parameters read from the user's input XML file (override those given by mpDefaultParameters).

Definition at line 1256 of file HeartConfig.hpp.

Referenced by EnsureOutputVisualizerExists(), EnsurePostProcessingSectionPresent(), GetAbsoluteTolerance(), GetApdMaps(), GetArchivedSimulationDir(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetElectrodeParameters(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), HeartConfig(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), IsSimulationDefined(), IsSimulationResumed(), IsUpstrokeTimeMapsRequested(), load(), ReadFile(), SetAdaptivityParameters(), SetApdMaps(), SetBathConductivity(), SetCapacitance(), SetCheckpointSimulation(), SetConductionVelocityMaps(), SetConductivityHeterogeneities(), SetConductivityHeterogeneitiesEllipsoid(), SetDefaultIonicModel(), SetDefaultsFile(), SetDomain(), SetDrugDose(), SetElectrodeParameters(), SetExtracellularConductivities(), SetFibreLength(), SetIc50Value(), SetIntracellularConductivities(), SetIonicModelRegions(), SetKSPPreconditioner(), SetKSPSolver(), SetMaxUpstrokeVelocityMaps(), SetMeshFileName(), SetMeshPartitioning(), SetOdePdeAndPrintingTimeSteps(), SetOutputDirectory(), SetOutputFilenamePrefix(), SetOutputUsingOriginalNodeOrdering(), SetOutputVariables(), SetParametersFile(), SetPseudoEcgElectrodePositions(), SetRequestedNodalTimeTraces(), SetSheetDimensions(), SetSimulationDuration(), SetSlabDimensions(), SetSpaceDimension(), SetSurfaceAreaToVolumeRatio(), SetUpstrokeTimeMaps(), SetUseAbsoluteTolerance(), SetUseRelativeTolerance(), SetUseStateVariableInterpolation(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), SetVisualizeWithVtk(), UpdateParametersFromResumeSimulation(), and Write().

boost::shared_ptr<cp::chaste_parameters_type> HeartConfig::mpDefaultParameters [private]

Pointer to parameters read from the default input XML file (to be read before mpUserParameters, but may be subsequently overridden).

Definition at line 1261 of file HeartConfig.hpp.

Referenced by GetAbsoluteTolerance(), GetApdMaps(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), HeartConfig(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), IsUpstrokeTimeMapsRequested(), ReadFile(), SetDefaultsFile(), and Write().

std::auto_ptr< HeartConfig > HeartConfig::mpInstance [static, private]

The single instance of the class

Definition at line 1264 of file HeartConfig.hpp.

Referenced by HeartConfig(), Instance(), Reset(), and save().

Whether to read the schema location from the XML file (false) or use the schema located at heart/src/io/ChasteParameters.xsd in the Chaste source tree (true).

Definition at line 1270 of file HeartConfig.hpp.

Referenced by HeartConfig(), ReadFile(), and SetUseFixedSchemaLocation().

double HeartConfig::mEpiFraction [private]

Fraction of epicardial layer

Definition at line 1275 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEpiLayerFraction(), and HeartConfig().

double HeartConfig::mEndoFraction [private]

Fraction of endocardial layer

Definition at line 1280 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEndoLayerFraction(), and HeartConfig().

double HeartConfig::mMidFraction [private]

Fraction of midmyocardial layer

Definition at line 1285 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetMidLayerFraction(), and HeartConfig().

unsigned HeartConfig::mIndexMid [private]

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1290 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetMidLayerIndex(), and HeartConfig().

unsigned HeartConfig::mIndexEpi [private]

Order index in which the epicardial heterogeneities are supplied

Definition at line 1295 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEpiLayerIndex(), and HeartConfig().

unsigned HeartConfig::mIndexEndo [private]

Order index in which the endocardial heterogeneities are supplied

Definition at line 1300 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEndoLayerIndex(), and HeartConfig().

Flag to check whether the user asked for cellular transmural heterogeneities

Definition at line 1305 of file HeartConfig.hpp.

Referenced by AreCellularTransmuralHeterogeneitiesRequested(), GetCellHeterogeneities(), and HeartConfig().

Flag telling whether to use mass lumping or not.

Definition at line 1310 of file HeartConfig.hpp.

Referenced by GetUseMassLumping(), and SetUseMassLumping().

Flag telling whether to use mass lumping in the preconditioner or not.

Definition at line 1315 of file HeartConfig.hpp.

Referenced by GetUseMassLumpingForPrecond(), and SetUseMassLumpingForPrecond().

Whether to use Strang operator splitting of the diffusion and reaction terms (see Set method documentation).

Definition at line 1321 of file HeartConfig.hpp.

Referenced by GetUseReactionDiffusionOperatorSplitting(), HeartConfig(), and SetUseReactionDiffusionOperatorSplitting().

std::map<unsigned, double> HeartConfig::mBathConductivities [private]

Map defining bath conductivity for multiple bath regions

Definition at line 1326 of file HeartConfig.hpp.

Referenced by GetBathConductivity(), and SetBathMultipleConductivities().

std::set<unsigned> HeartConfig::mTissueIdentifiers [private]

Mesh region identifiers to be considered as cardiac tissue

Definition at line 1331 of file HeartConfig.hpp.

Referenced by HeartConfig(), rGetTissueIdentifiers(), and SetTissueAndBathIdentifiers().

std::set<unsigned> HeartConfig::mBathIdentifiers [private]

Mesh region identifiers to be considered as Bath

Definition at line 1336 of file HeartConfig.hpp.

Referenced by HeartConfig(), rGetBathIdentifiers(), and SetTissueAndBathIdentifiers().

Whether to use a fixed number of iterations for the linear solver

Definition at line 1341 of file HeartConfig.hpp.

Referenced by GetUseFixedNumberIterationsLinearSolver(), and SetUseFixedNumberIterationsLinearSolver().

Perform a solve with convergence-based stop criteria every n solves to decide how many iterations perform for the next n-1 solves. Default is perfoming a single evaluation at the beginning of the simulation.

Definition at line 1348 of file HeartConfig.hpp.

Referenced by GetEvaluateNumItsEveryNSolves(), and SetUseFixedNumberIterationsLinearSolver().


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

Generated on Tue May 31 14:33:30 2011 for Chaste by  doxygen 1.5.5