HeartConfig Member List

This is the complete list of members for HeartConfig, including all inherited members.

AreCellularTransmuralHeterogeneitiesRequested()	HeartConfig
boost::serialization::access	HeartConfig	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 > &rExtraConductivities) const	HeartConfig
GetExtracellularConductivities(c_vector< double, 2 > &rExtraConductivities) const	HeartConfig
GetExtracellularConductivities(c_vector< double, 1 > &rExtraConductivities) const	HeartConfig
GetFibreLength(c_vector< double, 1 > &fibreLength) const	HeartConfig
GetIc50Values()	HeartConfig
GetInterNodeSpace() const	HeartConfig
GetIntracellularConductivities(c_vector< double, 3 > &rIntraConductivities) const	HeartConfig
GetIntracellularConductivities(c_vector< double, 2 > &rIntraConductivities) const	HeartConfig
GetIntracellularConductivities(c_vector< double, 1 > &rIntraConductivities) 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
GetMaxUpstrokeVelocityMaps(std::vector< double > &rUpstrokeVelocityMaps) const	HeartConfig
GetMeshName() const	HeartConfig
GetMeshPartitioning() const	HeartConfig
GetMidLayerFraction()	HeartConfig
GetMidLayerIndex()	HeartConfig
GetNodalTimeTraceRequested(std::vector< unsigned > &rRequestedNodes) 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
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
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	inlineprivate
LoadFromCheckpoint()	HeartConfig	private
mBathConductivities	HeartConfig	private
mBathIdentifiers	HeartConfig	private
mEndoFraction	HeartConfig	private
mEpiFraction	HeartConfig	private
mEvaluateNumItsEveryNSolves	HeartConfig	private
mIndexEndo	HeartConfig	private
mIndexEpi	HeartConfig	private
mIndexMid	HeartConfig	private
mMidFraction	HeartConfig	private
mParametersFilePath	HeartConfig	private
mpInstance	HeartConfig	privatestatic
mpParameters	HeartConfig	private
mSchemaLocations	HeartConfig	private
mTissueIdentifiers	HeartConfig	private
mUseFixedNumberIterations	HeartConfig	private
mUseFixedSchemaLocation	HeartConfig	private
mUseMassLumping	HeartConfig	private
mUseMassLumpingForPrecond	HeartConfig	private
mUserAskedForCellularTransmuralHeterogeneities	HeartConfig	private
mUseReactionDiffusionOperatorSplitting	HeartConfig	private
ReadFile(const std::string &rFileName)	HeartConfig
Reset()	HeartConfig	static
rGetBathIdentifiers()	HeartConfig
rGetTissueIdentifiers()	HeartConfig
save(Archive &archive, const unsigned int version) const	HeartConfig	inlineprivate
SchemaLocationsMap typedef	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 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)	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
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, bool warnOfChange=false)	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
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
SetSimulationDuration(double simulationDuration)	HeartConfig
SetSlabDimensions(double x, double y, double z, double inter_node_space)	HeartConfig
SetSpaceDimension(unsigned spaceDimension)	HeartConfig
SetSurfaceAreaToVolumeRatio(double ratio)	HeartConfig
SetTissueAndBathIdentifiers(const std::set< unsigned > &rTissueIds, const std::set< unsigned > &rBathIds)	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