, including all inherited members.
| AreCellularTransmuralHeterogeneitiesRequested() | HeartConfig | |
| boost::serialization::access class | 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 | |
| DecideLocation(TYPE *params_ptr, TYPE *defaults_ptr, const std::string &rNameParameter) const | HeartConfig | [inline, private] |
| 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 | [inline] |
| 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 | [inline] |
| 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 | [inline] |
| 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 | [inline] |
| 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 | [inline] |
| 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 | |
| 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] |
| 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] |
| mpDefaultParameters | HeartConfig | [private] |
| mpInstance | HeartConfig | [private, static] |
| mpUserParameters | 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 | [inline, private] |
| SchemaLocationsMap typedef | HeartConfig | |
| 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] |
| SetDefaultsFile(const std::string &rFileName) | HeartConfig | |
| 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 | [inline] |
| 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 | |
