Chaste Release::3.1
HeartConfig Member List
This is the complete list of members for HeartConfig, including all inherited members.
AreCellularTransmuralHeterogeneitiesRequested()HeartConfig
boost::serialization::access classHeartConfig [friend]
CheckResumeSimulationIsDefined(std::string callingMethod="") const HeartConfig [private]
CheckSimulationIsDefined(std::string callingMethod="") const HeartConfig [private]
CheckTimeSteps() const HeartConfig [private]
CopySchema(const std::string &rToDirectory)HeartConfig
EnsureOutputVisualizerExists(void)HeartConfig
EnsurePostProcessingSectionPresent()HeartConfig
GetAbsoluteTolerance() const HeartConfig
GetApdMaps(std::vector< std::pair< double, double > > &rApdMaps) const HeartConfig
GetArchivedSimulationDir() const HeartConfig
GetBathConductivity(unsigned bathRegion=UINT_MAX) const HeartConfig
GetCapacitance() const 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)HeartConfig
GetCheckpointSimulation() const HeartConfig
GetCheckpointTimestep() const HeartConfig
GetConductionVelocityMaps(std::vector< unsigned > &rConductionVelocityMaps) const 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 HeartConfig
GetConductivityHeterogeneitiesProvided() const HeartConfig
GetConductivityMedia() const HeartConfig
GetCreateFibre() const HeartConfig
GetCreateMesh() const HeartConfig
GetCreateSheet() const HeartConfig
GetCreateSlab() const HeartConfig
GetDefaultIonicModel() const HeartConfig
GetDomain() const HeartConfig
GetDrugDose() const HeartConfig
GetElectrodeParameters(bool &rGroundSecondElectrode, unsigned &rIndex, double &rMagnitude, double &rStartTime, double &rDuration)HeartConfig
GetEndoLayerFraction()HeartConfig
GetEndoLayerIndex()HeartConfig
GetEpiLayerFraction()HeartConfig
GetEpiLayerIndex()HeartConfig
GetEvaluateNumItsEveryNSolves()HeartConfig
GetExtracellularConductivities(c_vector< double, 3 > &extraConductivities) const HeartConfig
GetExtracellularConductivities(c_vector< double, 2 > &extraConductivities) const HeartConfig
GetExtracellularConductivities(c_vector< double, 1 > &extraConductivities) const HeartConfig
GetFibreLength(c_vector< double, 1 > &fibreLength) const HeartConfig
GetGradationForAdaptivity() const HeartConfig
GetIc50Values()HeartConfig
GetInterNodeSpace() const HeartConfig
GetIntracellularConductivities(c_vector< double, 3 > &intraConductivities) const HeartConfig
GetIntracellularConductivities(c_vector< double, 2 > &intraConductivities) const HeartConfig
GetIntracellularConductivities(c_vector< double, 1 > &intraConductivities) const HeartConfig
GetIonicModelRegions(std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const HeartConfig
GetKSPPreconditioner() const HeartConfig
GetKSPSolver() const HeartConfig
GetLoadMesh() const HeartConfig
GetMaxCheckpointsOnDisk() const HeartConfig
GetMaxEdgeLengthForAdaptivity() const HeartConfig
GetMaxNodesForAdaptivity() const HeartConfig
GetMaxUpstrokeVelocityMaps(std::vector< double > &rUpstrokeVelocityMaps) const HeartConfig
GetMeshName() const HeartConfig
GetMeshPartitioning() const HeartConfig
GetMidLayerFraction()HeartConfig
GetMidLayerIndex()HeartConfig
GetMinEdgeLengthForAdaptivity() const HeartConfig
GetNodalTimeTraceRequested(std::vector< unsigned > &rRequestedNodes) const HeartConfig
GetNumberOfAdaptiveSweeps() const HeartConfig
GetOdeTimeStep() const HeartConfig
GetOutputDirectory() const HeartConfig
GetOutputFilenamePrefix() const HeartConfig
GetOutputUsingOriginalNodeOrdering()HeartConfig
GetOutputVariables(std::vector< std::string > &rOutputVariables) const HeartConfig
GetOutputVariablesProvided() const HeartConfig
GetParametersFilePath()HeartConfig
GetPdeTimeStep() const HeartConfig
GetPrintingTimeStep() const HeartConfig
GetPseudoEcgElectrodePositions(std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions) const HeartConfig
GetPurkinjeCapacitance()HeartConfig
GetPurkinjeConductivity()HeartConfig
GetPurkinjeSurfaceAreaToVolumeRatio()HeartConfig
GetRelativeTolerance() const HeartConfig
GetSheetDimensions(c_vector< double, 2 > &sheetDimensions) const HeartConfig
GetSigmaForAdaptivity() const HeartConfig
GetSimulationDuration() const HeartConfig
GetSlabDimensions(c_vector< double, 3 > &slabDimensions) const HeartConfig
GetSpaceDimension() const HeartConfig
GetStimuli(std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuliApplied, std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rStimulatedAreas) const HeartConfig
GetSurfaceAreaToVolumeRatio() const HeartConfig
GetTargetErrorForAdaptivity() const HeartConfig
GetUpstrokeTimeMaps(std::vector< double > &rUpstrokeTimeMaps) const HeartConfig
GetUseAbsoluteTolerance() const HeartConfig
GetUseFixedNumberIterationsLinearSolver()HeartConfig
GetUseMassLumping()HeartConfig
GetUseMassLumpingForPrecond()HeartConfig
GetUseReactionDiffusionOperatorSplitting()HeartConfig
GetUseRelativeTolerance() const HeartConfig
GetUseStateVariableInterpolation() const HeartConfig
GetVersionFromNamespace(const std::string &rNamespaceUri)HeartConfig
GetVisualizerOutputPrecision()HeartConfig
GetVisualizeWithCmgui() const HeartConfig
GetVisualizeWithMeshalyzer() const HeartConfig
GetVisualizeWithParallelVtk() const HeartConfig
GetVisualizeWithVtk() const HeartConfig
HasDrugDose() const HeartConfig
HasPurkinje()HeartConfig
HeartConfig()HeartConfig [private]
Instance()HeartConfig [static]
IsAdaptivityParametersPresent() const HeartConfig
IsAnyNodalTimeTraceRequested() const HeartConfig
IsApdMapsRequested() const HeartConfig
IsConductionVelocityMapsRequested() const HeartConfig
IsElectrodesPresent() const HeartConfig
IsMaxUpstrokeVelocityMapRequested() const HeartConfig
IsMeshProvided() const HeartConfig
IsOutputVisualizerPresent() const HeartConfig
IsPostProcessingRequested() const HeartConfig
IsPostProcessingSectionPresent() const HeartConfig
IsPseudoEcgCalculationRequested() const HeartConfig
IsSimulationDefined() const HeartConfig
IsSimulationResumed() const HeartConfig
IsUpstrokeTimeMapsRequested() const HeartConfig
load(Archive &archive, const unsigned int version)HeartConfig [inline, private]
LoadFromCheckpoint()HeartConfig [private]
mBathConductivitiesHeartConfig [private]
mBathIdentifiersHeartConfig [private]
mEndoFractionHeartConfig [private]
mEpiFractionHeartConfig [private]
mEvaluateNumItsEveryNSolvesHeartConfig [private]
mIndexEndoHeartConfig [private]
mIndexEpiHeartConfig [private]
mIndexMidHeartConfig [private]
mMidFractionHeartConfig [private]
mParametersFilePathHeartConfig [private]
mpInstanceHeartConfig [private, static]
mpParametersHeartConfig [private]
mSchemaLocationsHeartConfig [private]
mTissueIdentifiersHeartConfig [private]
mUseFixedNumberIterationsHeartConfig [private]
mUseFixedSchemaLocationHeartConfig [private]
mUseMassLumpingHeartConfig [private]
mUseMassLumpingForPrecondHeartConfig [private]
mUserAskedForCellularTransmuralHeterogeneitiesHeartConfig [private]
mUseReactionDiffusionOperatorSplittingHeartConfig [private]
ReadFile(const std::string &rFileName)HeartConfig
Reset()HeartConfig [static]
rGetBathIdentifiers()HeartConfig
rGetTissueIdentifiers()HeartConfig
save(Archive &archive, const unsigned int version) const HeartConfig [inline, private]
SchemaLocationsMap typedefHeartConfig
SetAdaptivityParameters(double targetError, double sigma, double maxEdgeLength, double minEdgeLength, double gradation, unsigned maxNodes, unsigned numSweeps)HeartConfig
SetApdMaps(const std::vector< std::pair< double, double > > &rApdMaps)HeartConfig
SetBathConductivity(double bathConductivity)HeartConfig
SetBathMultipleConductivities(std::map< unsigned, double > bathConductivities)HeartConfig
SetCapacitance(double capacitance)HeartConfig
SetCheckpointSimulation(bool checkpointSimulation, double checkpointTimestep=-1.0, unsigned maxCheckpointsOnDisk=UINT_MAX)HeartConfig
SetConductionVelocityMaps(std::vector< unsigned > &rConductionVelocityMaps)HeartConfig
SetConductivityHeterogeneities(std::vector< ChasteCuboid< 3 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)HeartConfig
SetConductivityHeterogeneitiesEllipsoid(std::vector< ChasteEllipsoid< 3 > > &conductivityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities)HeartConfig
SetDefaultIonicModel(const cp::ionic_models_available_type &rIonicModel)HeartConfig
SetDefaultSchemaLocations()HeartConfig [private]
SetDomain(const cp::domain_type &rDomain)HeartConfig
SetDrugDose(double drugDose)HeartConfig
SetElectrodeParameters(bool groundSecondElectrode, unsigned index, double magnitude, double startTime, double duration)HeartConfig
SetExtracellularConductivities(const c_vector< double, 3 > &rExtraConductivities)HeartConfig
SetExtracellularConductivities(const c_vector< double, 2 > &rExtraConductivities)HeartConfig
SetExtracellularConductivities(const c_vector< double, 1 > &rExtraConductivities)HeartConfig
SetFibreLength(double x, double inter_node_space)HeartConfig
SetFixedSchemaLocations(const SchemaLocationsMap &rSchemaLocations)HeartConfig
SetGradationForAdaptivity(double gradation)HeartConfig
SetIc50Value(const std::string &rCurrentName, double ic50, double hill=1.0)HeartConfig
SetIntracellularConductivities(const c_vector< double, 3 > &rIntraConductivities)HeartConfig
SetIntracellularConductivities(const c_vector< double, 2 > &rIntraConductivities)HeartConfig
SetIntracellularConductivities(const c_vector< double, 1 > &rIntraConductivities)HeartConfig
SetIonicModelRegions(std::vector< ChasteCuboid< 3 > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const HeartConfig
SetKSPPreconditioner(const char *kspPreconditioner)HeartConfig
SetKSPSolver(const char *kspSolver)HeartConfig
SetMaxEdgeLengthForAdaptivity(double maxEdgeLength)HeartConfig
SetMaxNodesForAdaptivity(unsigned maxNodes)HeartConfig
SetMaxUpstrokeVelocityMaps(std::vector< double > &rMaxUpstrokeVelocityMaps)HeartConfig
SetMeshFileName(std::string meshPrefix, cp::media_type fibreDefinition=cp::media_type::NoFibreOrientation)HeartConfig
SetMeshPartitioning(const char *meshPartioningMethod)HeartConfig
SetMinEdgeLengthForAdaptivity(double minEdgeLength)HeartConfig
SetNumberOfAdaptiveSweeps(unsigned numSweeps)HeartConfig
SetOdePdeAndPrintingTimeSteps(double odeTimeStep, double pdeTimeStep, double printingTimeStep)HeartConfig
SetOdeTimeStep(double odeTimeStep)HeartConfig
SetOutputDirectory(const std::string &rOutputDirectory)HeartConfig
SetOutputFilenamePrefix(const std::string &rOutputFilenamePrefix)HeartConfig
SetOutputUsingOriginalNodeOrdering(bool useOriginal)HeartConfig
SetOutputVariables(const std::vector< std::string > &rOutputVariables)HeartConfig
SetParametersFile(const std::string &rFileName)HeartConfig
SetPdeTimeStep(double pdeTimeStep)HeartConfig
SetPrintingTimeStep(double printingTimeStep)HeartConfig
SetPseudoEcgElectrodePositions(const std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions)HeartConfig
SetPurkinjeCapacitance(double capacitance)HeartConfig
SetPurkinjeConductivity(double conductivity)HeartConfig
SetPurkinjeSurfaceAreaToVolumeRatio(double ratio)HeartConfig
SetRequestedNodalTimeTraces(std::vector< unsigned > &requestedNodes)HeartConfig
SetSheetDimensions(double x, double y, double inter_node_space)HeartConfig
SetSigmaForAdaptivity(double sigma)HeartConfig
SetSimulationDuration(double simulationDuration)HeartConfig
SetSlabDimensions(double x, double y, double z, double inter_node_space)HeartConfig
SetSpaceDimension(unsigned spaceDimension)HeartConfig
SetSurfaceAreaToVolumeRatio(double ratio)HeartConfig
SetTargetErrorForAdaptivity(double targetError)HeartConfig
SetTissueAndBathIdentifiers(const std::set< unsigned > &tissueIds, const std::set< unsigned > &bathIds)HeartConfig
SetUpstrokeTimeMaps(std::vector< double > &rUpstrokeTimeMaps)HeartConfig
SetUseAbsoluteTolerance(double absoluteTolerance)HeartConfig
SetUseFixedNumberIterationsLinearSolver(bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)HeartConfig
SetUseFixedSchemaLocation(bool useFixedSchemaLocation)HeartConfig
SetUseMassLumping(bool useMassLumping=true)HeartConfig
SetUseMassLumpingForPrecond(bool useMassLumping=true)HeartConfig
SetUseReactionDiffusionOperatorSplitting(bool useOperatorSplitting=true)HeartConfig
SetUseRelativeTolerance(double relativeTolerance)HeartConfig
SetUseStateVariableInterpolation(bool useStateVariableInterpolation=true)HeartConfig
SetVisualizerOutputPrecision(unsigned numberOfDigits)HeartConfig
SetVisualizeWithCmgui(bool useCmgui=true)HeartConfig
SetVisualizeWithMeshalyzer(bool useMeshalyzer=true)HeartConfig
SetVisualizeWithParallelVtk(bool useParallelVtk=true)HeartConfig
SetVisualizeWithVtk(bool useVtk=true)HeartConfig
TestHeartConfig (defined in HeartConfig)HeartConfig [friend]
UpdateParametersFromResumeSimulation(boost::shared_ptr< cp::chaste_parameters_type > pResumeParameters)HeartConfig [private]
Write(bool useArchiveLocationInfo=false, std::string subfolderName="output")HeartConfig
~HeartConfig()HeartConfig