Here is a list of all documented class members with links to the class documentation for each member:

- s -

• S1S2Stimulus() : S1S2Stimulus
• save() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• Save() : CryptSimulationArchiver< DIM, SIM >
• save() : RandomNumberGenerator , BidomainProblem< DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , VertexMesh< ELEMENT_DIM, SPACE_DIM > , AbstractDynamicallyLoadableEntity , Electrodes< DIM > , AbstractOdeSystem , BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , HeartConfig
• Save() : CardiacSimulationArchiver< PROBLEM_CLASS > , CellBasedSimulationArchiver< DIM, SIM >
• SaveBoundaryConditions() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SaveCardiacCells() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• Scale() : PetscVecTools , AbstractMesh< ELEMENT_DIM, SPACE_DIM > , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• ScaleMaterialParameters() : AbstractMaterialLaw< DIM > , CompressibleMooneyRivlinMaterialLaw< DIM > , MooneyRivlinMaterialLaw< DIM > , PoleZeroMaterialLaw< DIM >
• SchemaLocationsMap : HeartConfig
• SchmidCostaExponentialLaw2d() : SchmidCostaExponentialLaw2d
• serialize() : CML_noble_varghese_kohl_noble_1998_basic_with_sac , EulerIvpOdeSolver , StochasticWntCellCycleModel , VanLeeuwen2009WntSwatCellCycleModelHypothesisOne , HeunIvpOdeSolver , VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo , WntCellCycleModel , BidomainWithBathProblem< DIM > , MockEulerIvpOdeSolver , WntConcentration< DIM > , RadialSloughingCellKiller , RungeKutta2IvpOdeSolver , SloughingCellKiller< DIM > , CryptProjectionForce , MonodomainProblem< ELEMENT_DIM, SPACE_DIM > , RungeKutta4IvpOdeSolver , LinearSpringWithVariableSpringConstantsForce< DIM > , VertexCryptBoundaryForce< DIM > , RungeKuttaFehlbergIvpOdeSolver , Mirams2010WntOdeSystem , VanLeeuwen2009WntSwatCellCycleOdeSystem , AbstractStimulusFunction , AbstractBoundaryCondition< SPACE_DIM > , WntCellCycleOdeSystem , CryptSimulation1d , ConstBoundaryCondition< SPACE_DIM > , CryptSimulation2d , VertexCryptSimulation2d , DynamicRestitutionStimulus , SimulationTime , Cylindrical2dMesh , MultiStimulus , Cylindrical2dVertexMesh , Alarcon2004OxygenBasedCellCycleOdeSystem , RegularStimulus , TysonNovak2001OdeSystem , AbstractCellPopulation< DIM > , RegularStimulusZeroNetCharge , AbstractCentreBasedCellPopulation< DIM > , AbstractCellPopulationBoundaryCondition< DIM > , S1S2Stimulus , PlaneBoundaryCondition< DIM > , Cell , SimpleStimulus , AbstractCellCycleModel , AbstractCellCycleModelOdeSolver , ZeroStimulus , AbstractOdeBasedCellCycleModel , AbstractSimpleCellCycleModel , BidomainTissue< SPACE_DIM > , AbstractSimpleGenerationBasedCellCycleModel , Alarcon2004OxygenBasedCellCycleModel , MonodomainTissue< ELEMENT_DIM, SPACE_DIM > , CellCycleModelOdeHandler , CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER > , DistributedVectorFactory , CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver > , FixedDurationGenerationBasedCellCycleModel , LinearSystem , SimpleOxygenBasedCellCycleModel , StochasticDurationGenerationBasedCellCycleModel , AbstractChasteRegion< SPACE_DIM > , StochasticOxygenBasedCellCycleModel , TysonNovakCellCycleModel , AbstractMesh< ELEMENT_DIM, SPACE_DIM > , AbstractCellMutationState , ApcOneHitCellMutationState , ChastePoint< DIM > , ApcTwoHitCellMutationState , BetaCateninOneHitCellMutationState , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , WildTypeCellMutationState , AbstractCellProperty , MutableMesh< ELEMENT_DIM, SPACE_DIM > , ApoptoticCellProperty , CellLabel , NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , CellPropertyCollection , CellPropertyRegistry , QuadraticMesh< DIM > , CellwiseData< DIM > , AbstractCellKiller< SPACE_DIM > , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , OxygenBasedCellKiller< SPACE_DIM > , PlaneBasedCellKiller< DIM > , ChasteCuboid< SPACE_DIM > , RandomCellKiller< DIM > , TargetedCellKiller< DIM > , AbstractBackwardEulerCardiacCell< SIZE > , ChasteEllipsoid< SPACE_DIM > , AbstractForce< DIM > , AbstractTwoBodyInteractionForce< DIM > , ChasteNodesList< SPACE_DIM > , ChemotacticForce< DIM > , GeneralisedLinearSpringForce< DIM > , AbstractCardiacCell , MutableVertexMesh< ELEMENT_DIM, SPACE_DIM > , NagaiHondaForce< DIM > , WelikyOsterForce< DIM > , VertexElement< ELEMENT_DIM, SPACE_DIM > , MeshBasedCellPopulation< DIM > , MeshBasedCellPopulationWithGhostNodes< DIM > , AbstractCardiacCellInterface , AbstractIvpOdeSolver , NodeBasedCellPopulation< DIM > , VertexBasedCellPopulation< DIM > , AbstractOneStepIvpOdeSolver , CellBasedSimulation< DIM > , CellBasedSimulationWithPdes< DIM > , FakeBathCell , BackwardEulerIvpOdeSolver , AbstractVanLeeuwen2009WntSwatCellCycleModel , AbstractWntOdeBasedCellCycleModel , CvodeAdaptor , SimpleWntCellCycleModel , SingleOdeWntCellCycleModel
• Set() : ProcessSpecificArchive< Archive > , LogFile
• SetAbsoluteTolerance() : LinearSystem
• SetAdaptivityParameters() : HeartConfig
• SetAdditionalFieldNames() : CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetAncestor() : Cell
• SetAnyVariable() : AbstractParameterisedSystem< VECTOR >
• SetApdMaps() : HeartConfig
• SetApexToBase() : StreeterFibreGenerator< SPACE_DIM >
• SetApoptosisTime() : Cell
• SetApoptoticSpringCompressionStiffness() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetApoptoticSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetApoptoticSpringTensionStiffness() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetApplyNeummanBoundaryConditionsToVector() : AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• SetArchiveDirectory() : ArchiveLocationInfo , OutputFileHandler
• SetAreaBasedDampingConstant() : MeshBasedCellPopulation< DIM >
• SetAreaBasedDampingConstantParameter() : MeshBasedCellPopulation< DIM >
• SetAsBoundaryNode() : Node< SPACE_DIM >
• SetAsContractionOnFirstDimension() : FourthOrderTensor< DIM1, DIM2, DIM3, DIM4 >
• SetAsContractionOnFourthDimension() : FourthOrderTensor< DIM1, DIM2, DIM3, DIM4 >
• SetAsContractionOnSecondDimension() : FourthOrderTensor< DIM1, DIM2, DIM3, DIM4 >
• SetAsContractionOnThirdDimension() : FourthOrderTensor< DIM1, DIM2, DIM3, DIM4 >
• SetBathConductivity() : HeartConfig
• SetBathMultipleConductivities() : HeartConfig
• SetBetaCateninDivisionThreshold() : SingleOdeWntCellCycleModel
• SetBetaCateninSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetBetaCatSpringScaler() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetBirthTime() : Cell , AbstractCellCycleModel , AbstractOdeBasedCellCycleModel
• SetBottomCellAncestors() : CryptSimulation2d , VertexCryptSimulation2d
• SetBoundaryConditionsContainer() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetCacheReplication() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• SetCalciumAndVoltage() : AbstractCardiacMechanicsSolver< DIM >
• SetCapacitance() : HeartConfig
• SetCell() : AbstractCellCycleModel
• SetCellAncestorsToLocationIndices() : AbstractCellPopulation< DIM >
• SetCellCycleModel() : Cell
• SetCellIntracellularStimulus() : HeartConfigRelatedCellFactory< SPACE_DIM >
• SetCellParameters() : HeartConfigRelatedCellFactory< SPACE_DIM >
• SetCellPopulation() : CellwiseData< DIM > , WntConcentration< DIM >
• SetCellProliferativeType() : AbstractCellCycleModel
• SetCellPropertyRegistry() : CellPropertyCollection
• SetCellRearrangementRatio() : MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >
• SetCellRearrangementThreshold() : MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >
• SetChangeOfBasisMatrix() : AbstractIsotropicCompressibleMaterialLaw< DIM > , AbstractIsotropicIncompressibleMaterialLaw< DIM > , AbstractMaterialLaw< DIM > , PoleZeroMaterialLaw< DIM > , SchmidCostaExponentialLaw2d
• SetCheckNumberOfProcessesOnLoad() : DistributedVectorFactory
• SetCheckpointSimulation() : HeartConfig
• SetCommentForInfoFile() : ColumnDataWriter
• SetConductionVelocityMaps() : HeartConfig
• SetConductivityHeterogeneities() : HeartConfig
• SetConductivityHeterogeneitiesEllipsoid() : HeartConfig
• SetConductivityModifier() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• SetConstantConductivities() : AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM > , AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >
• SetConstantDataForTesting() : CellwiseData< DIM >
• SetConstantFibreSheetDirections() : AbstractCardiacMechanicsSolver< DIM >
• SetConstantWntValueForTesting() : WntConcentration< DIM >
• SetCoordinate() : ChastePoint< DIM >
• SetCriticalHypoxicDuration() : SimpleOxygenBasedCellCycleModel
• SetCryptLength() : WntConcentration< DIM >
• SetCryptProjectionParameterA() : WntConcentration< DIM >
• SetCryptProjectionParameterB() : WntConcentration< DIM >
• SetCurrentHypoxiaOnsetTime() : SimpleOxygenBasedCellCycleModel
• SetCurrentSolution() : AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• SetCurrentTime() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetCutOffLength() : AbstractTwoBodyInteractionForce< DIM >
• SetDampingConstantMutant() : AbstractCellPopulation< DIM >
• SetDampingConstantNormal() : AbstractCellPopulation< DIM >
• SetDefaultInitialCondition() : AbstractOdeSystem , AbstractOdeSystemInformation
• SetDefaultInitialConditions() : AbstractOdeSystem , AbstractOdeSystemInformation
• SetDefaultIonicModel() : HeartConfig
• SetDefaultMutationStateOrdering() : AbstractCellPopulation< DIM >
• SetDefaultSchemaLocations() : HeartConfig
• SetDefaultsFile() : HeartConfig
• SetDeleted() : NodeMap , VertexElementMap
• SetDiffusionCoefficient() : PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetDimension() : AbstractCellCycleModel
• SetDistributedVectorFactory() : AbstractMesh< ELEMENT_DIM, SPACE_DIM > , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SetDivideTime() : AbstractOdeBasedCellCycleModel
• SetDomain() : HeartConfig
• SetDt() : CellCycleModelOdeHandler , CellBasedSimulation< DIM >
• SetEdgeBasedSpringConstant() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetElectrodeParameters() : HeartConfig
• SetElectrodes() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , BidomainProblem< DIM >
• SetElement() : PetscMatTools , PetscVecTools
• SetElementOwnerships() : AbstractMesh< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SetEndTime() : CellBasedSimulation< DIM >
• SetEndTimeAndNumberOfTimeSteps() : SimulationTime
• SetEpsilonForNumericalJacobian() : BackwardEulerIvpOdeSolver
• SetExtracellularConductivities() : HeartConfig
• SetFibreLength() : HeartConfig
• SetFibreOrientationFile() : AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >
• SetFinishedRunningOdes() : AbstractOdeBasedCellCycleModel
• SetFixedChunkSize() : Hdf5DataWriter
• SetFixedExtracellularPotentialNodes() : BidomainProblem< DIM > , AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
• SetFixedSchemaLocations() : HeartConfig
• SetFromFactory() : DistributedVectorFactory
• SetFunctionalBodyForce() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetFunctionalTractionBoundaryCondition() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetG1Duration() : AbstractSimpleCellCycleModel , StochasticDurationGenerationBasedCellCycleModel , SimpleWntCellCycleModel
• SetG2Duration() : AbstractCellCycleModel
• SetG2PhaseStartTime() : AbstractOdeBasedCellCycleModel
• SetGeneration() : AbstractSimpleGenerationBasedCellCycleModel
• SetGhostNodes() : MeshBasedCellPopulationWithGhostNodes< DIM >
• SetGradationForAdaptivity() : HeartConfig
• SetHeartGeometryInformation() : AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >
• SetHypoxicConcentration() : SimpleOxygenBasedCellCycleModel
• SetIndex() : AbstractElement< ELEMENT_DIM, SPACE_DIM > , Node< SPACE_DIM >
• SetInitialCondition() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetInitialConvergenceParameters() : AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , OdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , OdePdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , PdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , SpaceConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >
• SetInputParameters() : AbstractContractionModel , Kerchoffs2003ContractionModel , Nash2004ContractionModel , NhsContractionModel , NonPhysiologicalContractionModel
• SetIntracellularCalciumConcentration() : NhsContractionModel
• SetIntracellularConductivities() : HeartConfig
• SetIntracellularStimulusFunction() : AbstractCardiacCellInterface
• SetIonicModelRegions() : HeartConfig
• SetIsLabelled() : Alarcon2004OxygenBasedCellCycleOdeSystem
• SetKspAbsoluteTolerance() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetKSPPreconditioner() : HeartConfig
• SetKSPSolver() : HeartConfig
• SetKspType() : LinearSystem
• SetLastTime() : CellCycleModelOdeHandler
• SetLoader() : AbstractDynamicallyLoadableEntity
• SetLogged() : Cell
• SetMatrixElement() : LinearSystem
• SetMatrixIsConstant() : LinearSystem
• SetMatrixIsNotAssembled() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetMatrixIsSymmetric() : LinearSystem
• SetMatrixRow() : LinearSystem
• SetMatrixToAssemble() : AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• SetMatureCellTargetArea() : NagaiHondaForce< DIM >
• SetMaxEdgeLengthForAdaptivity() : HeartConfig
• SetMaxNodesForAdaptivity() : HeartConfig
• SetMaxSteps() : AbstractCvodeCell , CvodeAdaptor , AbstractCellCycleModelOdeSolver
• SetMaxTransitGenerations() : AbstractSimpleGenerationBasedCellCycleModel
• SetMaxUpstrokeVelocityMaps() : HeartConfig
• SetMDuration() : AbstractCellCycleModel
• SetMechanicsCutOffLength() : NodeBasedCellPopulation< DIM >
• SetMeinekeDivisionRestingSpringLength() : GeneralisedLinearSpringForce< DIM >
• SetMeinekeDivisionSeparation() : AbstractCentreBasedCellPopulation< DIM >
• SetMeinekeSpringGrowthDuration() : GeneralisedLinearSpringForce< DIM >
• SetMeinekeSpringStiffness() : GeneralisedLinearSpringForce< DIM >
• SetMesh() : AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > , AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetMeshFileName() : HeartConfig
• SetMeshFilename() : ArchiveLocationInfo
• SetMeshHasChangedSinceLoading() : AbstractMesh< ELEMENT_DIM, SPACE_DIM >
• SetMeshPartitioning() : HeartConfig
• SetMeshPathname() : ArchiveLocationInfo
• SetMeshWidth() : AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >
• SetMinEdgeLengthForAdaptivity() : HeartConfig
• SetMinimumGapDuration() : AbstractCellCycleModel
• SetModifier() : AbstractCardiacCellWithModifiers< CARDIAC_CELL >
• SetMutantSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetMutationState() : Cell , Mirams2010WntOdeSystem , VanLeeuwen2009WntSwatCellCycleOdeSystem , WntCellCycleOdeSystem
• SetNagaiHondaCellBoundaryAdhesionEnergyParameter() : NagaiHondaForce< DIM >
• SetNagaiHondaCellCellAdhesionEnergyParameter() : NagaiHondaForce< DIM >
• SetNagaiHondaDeformationEnergyParameter() : NagaiHondaForce< DIM >
• SetNagaiHondaMembraneSurfaceEnergyParameter() : NagaiHondaForce< DIM >
• SetNamespace() : XmlTools
• SetNewIndex() : NodeMap , VertexElementMap
• SetNextBoundaryFace() : AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetNoBirth() : CellBasedSimulation< DIM >
• SetNode() : MutableMesh< ELEMENT_DIM, SPACE_DIM > , MutableVertexMesh< ELEMENT_DIM, SPACE_DIM > , Cylindrical2dMesh , Cylindrical2dVertexMesh , AbstractCellPopulation< DIM > , MeshBasedCellPopulation< DIM > , NodeBasedCellPopulation< DIM > , VertexBasedCellPopulation< DIM >
• SetNodeForAverageOfPhiZeroed() : BidomainProblem< DIM >
• SetNodePermutation() : TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >
• SetNodesPerProcessorFilename() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetNoElectricsOutput() : CardiacElectroMechanicsProblem< DIM >
• SetNonConstantConductivities() : AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >
• SetNonlinearSolver() : AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetNullBasis() : LinearSystem
• SetNumberOfAdaptiveSweeps() : HeartConfig
• SetNumberOfTimeSteps() : OdeSolution
• SetNumCellsAndVars() : CellwiseData< DIM >
• SetOdePdeAndPrintingTimeSteps() : HeartConfig
• SetOdeSystem() : CellCycleModelOdeHandler
• SetOdeSystemInformation() : OdeSolution
• SetOdeTimeStep() : HeartConfig
• SetOption() : PetscMatTools
• SetOriginalFactory() : DistributedVectorFactory
• SetOutputCellAges() : AbstractCellPopulation< DIM >
• SetOutputCellAncestors() : AbstractCellPopulation< DIM >
• SetOutputCellCyclePhases() : AbstractCellPopulation< DIM >
• SetOutputCellIdData() : AbstractCellPopulation< DIM >
• SetOutputCellMutationStates() : AbstractCellPopulation< DIM >
• SetOutputCellPopulationVolumes() : MeshBasedCellPopulation< DIM >
• SetOutputCellProliferativeTypes() : AbstractCellPopulation< DIM >
• SetOutputCellVariables() : AbstractCellPopulation< DIM >
• SetOutputCellVolumes() : AbstractCellPopulation< DIM > , NodeBasedCellPopulation< DIM >
• SetOutputDirectory() : HeartConfig , ExecutableSupport , CellBasedSimulation< DIM >
• SetOutputFilenamePrefix() : HeartConfig
• SetOutputNodes() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetOutputNodeVelocities() : CellBasedSimulation< DIM >
• SetOutputUsingOriginalNodeOrdering() : HeartConfig
• SetOutputVariables() : HeartConfig
• SetOutputVoronoiData() : MeshBasedCellPopulation< DIM >
• SetOwnership() : AbstractElement< ELEMENT_DIM, SPACE_DIM >
• SetParallelFiles() : VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetParameter() : AbstractParameterisedSystem< VECTOR >
• SetParameters() : PoleZeroMaterialLaw< DIM >
• SetParametersFile() : HeartConfig
• SetPath() : FileFinder
• SetPcType() : LinearSystem
• SetPdeAndBcCollection() : CellBasedSimulationWithPdes< DIM >
• SetPdeTimeStep() : HeartConfig , PdeSimulationTime
• SetPeriod() : RegularStimulus
• SetPoint() : Node< SPACE_DIM >
• SetPrecision() : LogFile
• SetPrecondMatrixIsDifferentFromLhs() : LinearSystem
• SetPrintingTimeStep() : HeartConfig
• SetProteinConcentrationsForTestsOnly() : AbstractOdeBasedCellCycleModel
• SetPseudoEcgElectrodePositions() : HeartConfig
• SetQuiescentConcentration() : SimpleOxygenBasedCellCycleModel
• SetReadBufferSize() : TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >
• SetRegion() : AbstractElement< ELEMENT_DIM, SPACE_DIM > , Node< SPACE_DIM >
• SetRegionNames() : CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetRelativeTolerance() : LinearSystem
• SetRequestedNodalTimeTraces() : HeartConfig
• SetRhsVectorElement() : LinearSystem
• SetRow() : PetscMatTools
• SetRowForAverageOfPhiZeroed() : AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
• SetS2ExperimentPeriodIndex() : S1S2Stimulus
• SetSamplingTimestepMultiple() : CellBasedSimulation< DIM >
• SetSDuration() : AbstractCellCycleModel
• SetSheetDimensions() : HeartConfig
• SetSigmaForAdaptivity() : HeartConfig
• SetSimulationDuration() : HeartConfig
• SetSizeOfOdeSystem() : AbstractCellCycleModelOdeSolver
• SetSlabDimensions() : HeartConfig
• SetSlowValues() : AbstractCardiacCell
• SetSolution() : PdeAndBoundaryConditions< DIM >
• SetSolverName() : OdeSolution
• SetSpaceDimension() : HeartConfig
• SetStartTime() : RegularStimulus , SimulationTime
• SetState() : AbstractCardiacCell
• SetStateVariable() : AbstractParameterisedSystem< VECTOR >
• SetStateVariables() : CellCycleModelOdeHandler , AbstractCvodeCell , AbstractOdeSystem
• SetStateVariablesUsingACopyOfThisVector() : AbstractCvodeCell
• SetStemCellG1Duration() : AbstractCellCycleModel
• SetStimulusFunction() : AbstractCardiacCellInterface
• SetStopTime() : RegularStimulus
• SetStretch() : AbstractCardiacCell , CML_noble_varghese_kohl_noble_1998_basic_with_sac , AbstractContractionModel
• SetStretchAndStretchRate() : NonPhysiologicalContractionModel , AbstractContractionModel , Kerchoffs2003ContractionModel , NhsContractionModel , Nash2004ContractionModel
• SetSurfaceAreaToVolumeRatio() : HeartConfig
• SetSurfaceFiles() : StreeterFibreGenerator< SPACE_DIM >
• SetSurfaceTractionBoundaryConditions() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetT2Threshold() : MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >
• SetTableProperties() : AbstractLookupTableCollection
• SetTargetErrorForAdaptivity() : HeartConfig
• SetTime() : PdeSimulationTime
• SetTimeAdaptivityController() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetTimes() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetTimeStep() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetTimestep() : AbstractCardiacCell , AbstractLookupTableCollection , AbstractCardiacCellInterface , AbstractCvodeCell
• SetTissueAndBathIdentifiers() : HeartConfig
• SetTolerance() : SimpleNewtonNonlinearSolver
• SetTolerances() : CvodeAdaptor , AbstractCvodeCell , AbstractCellCycleModelOdeSolver
• SetTransitCellG1Duration() : AbstractCellCycleModel
• SetType() : WntConcentration< DIM >
• setUp() : AbstractCellBasedTestSuite
• SetUpAdditionalStoppingTimes() : BidomainProblem< DIM > , AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetupAllLocalBoxes() : BoxCollection< DIM >
• SetUpBoxes() : FineCoarseMeshPair< DIM >
• SetUpBoxesOnCoarseMesh() : FineCoarseMeshPair< DIM >
• SetUpBoxesOnFineMesh() : FineCoarseMeshPair< DIM >
• SetupCvode() : CvodeAdaptor , AbstractCvodeCell
• SetUpdateCellPopulationRule() : CellBasedSimulation< DIM >
• SetupGivenLinearSystem() : AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >
• SetupGradients() : CellwiseDataGradient< DIM >
• SetUpHaloCells() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• SetupInterleavedVectorScatterGather() : PetscVecTools
• SetupLinearSystem() : SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM > , AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM > , MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM > , OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM > , BasicMonodomainSolver< ELEMENT_DIM, SPACE_DIM > , MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM > , SimpleLinearParabolicSolver< ELEMENT_DIM, SPACE_DIM >
• SetupLocalBoxesHalfOnly() : BoxCollection< DIM >
• SetupMat() : PetscTools
• SetupSolve() : VertexCryptSimulation2d , CryptSimulation2d , CellBasedSimulation< DIM > , CellBasedSimulationWithPdes< DIM >
• SetupSourceTerms() : AveragedSourcePde< DIM >
• SetUpSourceTermsForAveragedSourcePde() : PdeAndBoundaryConditions< DIM >
• SetUpstrokeTimeMaps() : HeartConfig
• setUpWorld() : PetscSetup
• SetupWriteBetaCatenin() : CryptSimulation2d , VertexCryptSimulation2d
• SetupWritePdeSolution() : CellBasedSimulationWithPdes< DIM >
• SetUseAbsoluteTolerance() : HeartConfig
• SetUseCellProliferativeTypeDependentG1Duration() : SimpleWntCellCycleModel
• SetUsedInTissueSimulation() : AbstractCardiacCellInterface
• SetUseFixedNumberIterations() : LinearSystem
• SetUseFixedNumberIterationsLinearSolver() : HeartConfig
• SetUseFixedSchemaLocation() : HeartConfig
• SetUseMassLumping() : HeartConfig
• SetUseMassLumpingForPrecond() : HeartConfig
• SetUseReactionDiffusionOperatorSplitting() : HeartConfig
• SetUseRelativeTolerance() : HeartConfig
• SetUseStateVariableInterpolation() : HeartConfig
• SetUseTimeAdaptivityController() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetValue() : CellwiseData< DIM >
• SetVariableFibreSheetDirections() : AbstractCardiacMechanicsSolver< DIM >
• SetVariableFibreSheetDirectionsFile() : CardiacElectroMechanicsProblem< DIM >
• SetVectorToAssemble() : AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• SetVisualizeWithCmgui() : HeartConfig
• SetVisualizeWithMeshalyzer() : HeartConfig
• SetVisualizeWithParallelVtk() : HeartConfig
• SetVisualizeWithVtk() : HeartConfig
• SetVoltage() : AbstractCardiacCell , AbstractCardiacCellInterface , AbstractCvodeCell
• SetVoltageDerivativeToZero() : AbstractCvodeCell
• SetWatchedPosition() : CardiacElectroMechanicsProblem< DIM >
• SetWelikyOsterAreaParameter() : WelikyOsterForce< DIM >
• SetWelikyOsterPerimeterParameter() : WelikyOsterForce< DIM >
• SetWntChemotaxis() : CryptProjectionForce
• SetWntChemotaxisStrength() : CryptProjectionForce
• SetWntConcentrationParameter() : WntConcentration< DIM >
• SetWntLabelledThreshold() : SimpleWntCellCycleModel
• SetWntStemThreshold() : SimpleWntCellCycleModel
• SetWntTransitThreshold() : SimpleWntCellCycleModel
• SetWriteAverageRadialPdeSolution() : CellBasedSimulationWithPdes< DIM >
• SetWriteFilesAsBinary() : TrianglesMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetWriteInfo() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetWriteOutput() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetWriteOutputEachNewtonIteration() : AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM >
• SetWriteStats() : SimpleNewtonNonlinearSolver
• SetWriteVtkAsPoints() : MeshBasedCellPopulation< DIM >
• ShowCopyright() : ExecutableSupport
• ShowParallelLaunching() : ExecutableSupport
• Shuffle() : RandomNumberGenerator
• SimpleDataWriter() : SimpleDataWriter
• SimpleLinearEllipticSolver() : SimpleLinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >
• SimpleLinearParabolicSolver() : SimpleLinearParabolicSolver< ELEMENT_DIM, SPACE_DIM >
• SimpleNewtonNonlinearSolver() : SimpleNewtonNonlinearSolver
• SimpleNonlinearEllipticSolver() : SimpleNonlinearEllipticSolver< ELEMENT_DIM, SPACE_DIM >
• SimpleOxygenBasedCellCycleModel() : SimpleOxygenBasedCellCycleModel
• SimpleStimulus() : SimpleStimulus
• SimpleUniformSourcePde() : SimpleUniformSourcePde< DIM >
• SimpleWntCellCycleModel() : SimpleWntCellCycleModel
• SimulateFullActionPotential : AbstractUntemplatedConvergenceTester
• SimulationTime() : SimulationTime
• SingleDistance() : DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >
• SingleOdeWntCellCycleModel() : SingleOdeWntCellCycleModel
• Size() : QuadraturePointsGroup< DIM > , VertexElementMap , NodeMap
• SloughingCellKiller() : SloughingCellKiller< DIM >
• SmoothStructureTensors() : PapillaryFibreCalculator
• Solve() : AbstractNonlinearSolver , SimpleNewtonNonlinearSolver , CardiacNewtonSolver< SIZE, CELLTYPE > , AbstractCvodeCell , RungeKuttaFehlbergIvpOdeSolver , AbstractOneStepIvpOdeSolver , AbstractCardiacMechanicsSolver< DIM > , CardiacElectroMechanicsProblem< DIM > , ImplicitCardiacMechanicsSolver< DIM > , AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , LinearSystem , SimplePetscNonlinearSolver , AbstractIvpOdeSolver , AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , CvodeAdaptor , AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , CellBasedSimulation< DIM > , AbstractStaticLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractNonlinearElasticitySolver< COMPRESSIBILITY_TYPE, DIM > , AbstractIvpOdeSolver , RungeKuttaFehlbergIvpOdeSolver , ExplicitCardiacMechanicsSolver< DIM > , AbstractOneStepIvpOdeSolver , AbstractCvodeCell , CvodeAdaptor
• SolveAndUpdateState() : AbstractCardiacCell , AbstractCvodeCell , AbstractCardiacCellInterface , AbstractBackwardEulerCardiacCell< SIZE >
• SolveAndUpdateStateVariable() : AbstractIvpOdeSolver , AbstractCellCycleModelOdeSolver
• SolveBoundaryElementMapping() : TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , VertexMesh< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveCellSystems() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• SolveElementMapping() : DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , VertexMesh< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveLinearSystem() : CardiacNewtonSolver< SIZE, CELLTYPE > , BackwardEulerIvpOdeSolver
• SolveNodeMapping() : TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , VertexMesh< ELEMENT_DIM, SPACE_DIM > , AbstractMesh< ELEMENT_DIM, SPACE_DIM >
• SolveOdeToTime() : CellCycleModelOdeHandler
• SolvePde() : CellBasedSimulationWithPdes< DIM >
• SolvePdeUsingCoarseMesh() : CellBasedSimulationWithPdes< DIM >
• SPACING : ColumnDataWriter , ColumnDataReader
• SpecifyOrdering() : CellPropertyRegistry
• SplitUpIntoBoxes() : NodeBasedCellPopulation< DIM >
• SpringIterator() : MeshBasedCellPopulation< DIM >::SpringIterator
• SpringsBegin() : MeshBasedCellPopulation< DIM >
• SpringsEnd() : MeshBasedCellPopulation< DIM >
• StandardNormalRandomDeviate() : RandomNumberGenerator
• StandardStartup() : ExecutableSupport
• StartApoptosis() : Cell
• StartTime : Timer
• STENCIL_SIZE : CompressibleNonlinearElasticitySolver< DIM > , NonlinearElasticitySolver< DIM > , AbstractCardiacMechanicsSolver< DIM >
• Stimulus : AbstractUntemplatedConvergenceTester
• StimulusBoundaryCondition() : StimulusBoundaryCondition< SPACE_DIM >
• StochasticDurationGenerationBasedCellCycleModel() : StochasticDurationGenerationBasedCellCycleModel
• StochasticOxygenBasedCellCycleModel() : StochasticOxygenBasedCellCycleModel
• StochasticWntCellCycleModel() : StochasticWntCellCycleModel
• StopFaking() : FileFinder
• StoppingEventHasOccurred() : CellBasedSimulation< DIM >
• StoppingEventOccurred() : AbstractIvpOdeSolver , AbstractCellCycleModelOdeSolver
• StreeterFibreGenerator() : StreeterFibreGenerator< SPACE_DIM >
• Stripe() : DistributedVector::Stripe
• subsystemInformation : CombinedOdeSystemInformation::InstancePointers
• SurfaceBasisFunction : AbstractFeObjectAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• SwitchOff() : Electrodes< DIM >
• SwitchOn() : Electrodes< DIM >