- s -

• Save() : TissueSimulationArchiver< DIM, SIM >
• save() : HeartConfig , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , RandomNumberGenerator
• Scale() : AbstractMesh< ELEMENT_DIM, SPACE_DIM >
• ScaleAndWrite() : InventorVoronoiWriter
• ScaleMaterialParameters() : MooneyRivlinMaterialLaw< DIM > , PoleZeroMaterialLaw< DIM > , AbstractIncompressibleMaterialLaw< DIM >
• SchmidCostaExponentialLaw2d() : SchmidCostaExponentialLaw2d
• serialize() : AbstractCardiacPde< ELEM_DIM, SPACE_DIM > , AbstractOneStepIvpOdeSolver , AbstractForce< DIM > , AbstractTwoBodyInteractionForce< DIM > , BackwardEulerIvpOdeSolver , GeneralisedLinearSpringForce< DIM > , LinearSpringWithVariableSpringConstantsForce< DIM > , BidomainPde< SPACE_DIM > , EulerIvpOdeSolver , MeshBasedTissue< DIM > , MeshBasedTissueWithGhostNodes< DIM > , MockEulerIvpOdeSolver , NodeBasedTissue< DIM > , MonodomainPde< ELEM_DIM, SPACE_DIM > , RungeKutta2IvpOdeSolver , RungeKutta4IvpOdeSolver , AbstractStimulusFunction , RungeKuttaFehlbergIvpOdeSolver , SimulationTime , MultiStimulus , TissueConfig , Cylindrical2dMesh , RegularStimulus , CryptSimulation2d , TissueSimulation< DIM > , AbstractBackwardEulerCardiacCell< SIZE > , SimpleStimulus , AbstractCellCentreBasedTissue< DIM > , AbstractTissue< DIM > , ZeroStimulus , AbstractCellCycleModel , AbstractOdeBasedCellCycleModel , AbstractCardiacCell , DistributedVectorFactory , AbstractSimpleCellCycleModel , AbstractSimpleGenerationBasedCellCycleModel , LinearSystem , AbstractWntOdeBasedCellCycleModel , FixedDurationGenerationBasedCellCycleModel , BackwardEulerFoxModel2002Modified , AbstractMesh< ELEMENT_DIM, SPACE_DIM > , IngeWntSwatCellCycleModel , SimpleWntCellCycleModel , MutableMesh< ELEMENT_DIM, SPACE_DIM > , StochasticDurationGenerationBasedCellCycleModel , StochasticWntCellCycleModel , BackwardEulerLuoRudyIModel1991 , NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , TysonNovakCellCycleModel , WntCellCycleModel , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , WntConcentration< DIM > , TissueCell , LuoRudyIModel1991OdeSystem , AbstractOdeSystem , CellwiseData< DIM > , AbstractCellKiller< SPACE_DIM > , AbstractIvpOdeSolver , RandomCellKiller< DIM > , SloughingCellKiller< DIM >
• Set() : LogFile
• SetAbsoluteTolerance() : LinearSystem
• SetActiveTensionInitialGuess() : NhsSystemWithImplicitSolver
• SetAncestor() : TissueCell
• SetApdMaps() : HeartConfig
• SetApoptosisTime() : TissueConfig
• SetApoptoticSpringCompressionStiffness() : TissueConfig
• SetApoptoticSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetApoptoticSpringTensionStiffness() : TissueConfig
• SetArchiveDirectory() : ArchiveLocationInfo , OutputFileHandler
• SetArchiveLinearSystemObject() : AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >
• SetAreaBasedDampingConstant() : MeshBasedTissue< DIM >
• SetAreaBasedDampingConstantParameter() : TissueConfig
• SetAsBoundaryNode() : Node< SPACE_DIM >
• SetAsProduct() : FourthOrderTensor< DIM >
• SetBathConductivity() : HeartConfig
• SetBetaCateninSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetBetaCatSpringScaler() : TissueConfig
• SetBirthTime() : AbstractCellCycleModel , AbstractOdeBasedCellCycleModel , TissueCell
• SetBottomCellAncestors() : MeshBasedTissue< DIM >
• SetBoundaryConditionsContainer() : AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetCacheReplication() : AbstractCardiacPde< ELEM_DIM, SPACE_DIM >
• SetCapacitance() : HeartConfig
• SetCell() : AbstractCellCycleModel
• SetCellAncestorsToNodeIndices() : AbstractTissue< DIM >
• SetCellBoundaryAdhesionEnergyParameter() : TissueConfig
• SetCellCellAdhesionEnergyParameter() : TissueConfig
• SetCellCentre() : VoronoiCell
• SetCellCycleModel() : TissueCell
• SetCellType() : TissueCell
• SetConductivityHeterogeneities() : HeartConfig
• SetConstantConductivities() : AbstractConductivityTensors< SPACE_DIM > , AxisymmetricConductivityTensors< SPACE_DIM >
• SetConstantDataForTesting() : CellwiseData< DIM >
• SetConstantWntValueForTesting() : WntConcentration< DIM >
• SetCoordinate() : ChastePoint< DIM >
• SetCriticalHypoxicDuration() : TissueConfig
• SetCryptLength() : TissueConfig
• SetCryptProjectionParameterA() : TissueConfig
• SetCryptProjectionParameterB() : TissueConfig
• SetCryptWidth() : TissueConfig
• SetDampingConstantMutant() : TissueConfig
• SetDampingConstantNormal() : TissueConfig
• SetDefaultIonicModel() : HeartConfig
• SetDefaultsFile() : HeartConfig
• SetDeformationEnergyParameter() : TissueConfig
• SetDeleted() : NodeMap
• SetDivisionRestingSpringLength() : TissueConfig
• SetDivisionSeparation() : TissueConfig
• SetDomain() : HeartConfig
• SetDt() : TissueSimulation< DIM >
• SetEdgeBasedSpringConstant() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetElectrodes() : BidomainProblem< DIM >
• SetElementOwnerships() : AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SetEndTime() : TissueSimulation< DIM >
• SetEndTimeAndNumberOfTimeSteps() : SimulationTime
• SetEpsilonForNumericalJacobian() : BackwardEulerIvpOdeSolver
• SetExtracellularConductivities() : HeartConfig
• SetFibreLength() : HeartConfig
• SetFibreOrientationFile() : AbstractConductivityTensors< SPACE_DIM >
• SetFixedExtracellularPotentialNodes() : BidomainProblem< DIM > , BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >
• SetFunctionalBodyForce() : AbstractNonlinearElasticityAssembler< DIM >
• SetFunctionalTractionBoundaryCondition() : NonlinearElasticityAssembler< DIM >
• SetG1Duration() : AbstractSimpleCellCycleModel , SimpleWntCellCycleModel , StochasticDurationGenerationBasedCellCycleModel
• SetG2Duration() : TissueConfig , StochasticWntCellCycleModel
• SetGeneration() : AbstractSimpleGenerationBasedCellCycleModel
• SetGhostNodes() : MeshBasedTissueWithGhostNodes< DIM >
• SetHepaOneCellG1Duration() : TissueConfig
• SetHepaOneCellHypoxicConcentration() : TissueConfig
• SetHepaOneCellQuiescentConcentration() : TissueConfig
• SetHepaOneParameters() : TissueConfig
• SetIndex() : AbstractElement< ELEMENT_DIM, SPACE_DIM > , Node< SPACE_DIM >
• SetInitialCondition() : AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetInitialConditions() : AbstractOdeSystem , AbstractOdeSystemInformation
• SetInitialConditionsComponent() : AbstractOdeSystem , AbstractOdeSystemInformation
• 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 >
• SetIntracellularCalciumConcentration() : NhsCellularMechanicsOdeSystem
• SetIntracellularCalciumConcentrations() : ImplicitCardiacMechanicsAssembler< DIM >
• SetIntracellularConductivities() : HeartConfig
• SetIntracellularStimulusFunction() : AbstractCardiacCell
• SetKSPPreconditioner() : HeartConfig
• SetKSPSolver() : HeartConfig
• SetKspType() : LinearSystem
• SetLambdaAndDerivative() : NhsCellularMechanicsOdeSystem
• SetLogged() : TissueCell
• SetMatrixElement() : LinearSystem
• SetMatrixIsConst() : AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >
• SetMatrixIsConstant() : LinearSystem , AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetMatrixIsNotAssembled() : AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetMatrixIsSymmetric() : LinearSystem
• SetMatrixRow() : LinearSystem
• SetMatureCellTargetArea() : TissueConfig
• SetMaxTransitGenerations() : TissueConfig
• SetMDuration() : TissueConfig
• SetMechanicsCutOffLength() : TissueConfig
• SetMembraneSurfaceEnergyParameter() : TissueConfig
• SetMesh() : AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM > , AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >
• SetMeshFileName() : HeartConfig
• SetMeshFilename() : ArchiveLocationInfo
• SetMeshPathname() : ArchiveLocationInfo
• SetMeshWidth() : AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >
• SetMinimumGapDuration() : TissueConfig
• SetMutantSprings() : LinearSpringWithVariableSpringConstantsForce< DIM >
• SetMutationState() : IngeWntSwatCellCycleOdeSystem , WntCellCycleOdeSystem , TissueCell
• SetNewIndex() : NodeMap
• SetNextBoundaryFace() : AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetNextElement() : AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetNextNode() : AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
• SetNoBirth() : TissueSimulation< DIM >
• SetNode() : MutableMesh< ELEMENT_DIM, SPACE_DIM > , Cylindrical2dMesh , AbstractTissue< DIM > , MeshBasedTissue< DIM > , NodeBasedTissue< DIM >
• SetNodeForAverageOfPhiZeroed() : BidomainProblem< DIM >
• SetNodesPerProcessorFilename() : AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >
• SetNoElectricsOutput() : CardiacElectroMechanicsProblem< DIM >
• SetNonConstantConductivities() : AbstractConductivityTensors< SPACE_DIM >
• SetNonlinearSolver() : AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >
• SetNullBasis() : LinearSystem
• SetNumberOfQuadraturePointsPerDimension() : AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >
• SetNumberOfTimeSteps() : OdeSolution
• SetNumNodesAndVars() : CellwiseData< DIM >
• SetOdePdeAndPrintingTimeSteps() : HeartConfig
• SetOdeTimeStep() : HeartConfig
• SetOutputCellAges() : TissueConfig
• SetOutputCellAncestors() : TissueConfig
• SetOutputCellAreas() : TissueConfig
• SetOutputCellCyclePhases() : TissueConfig
• SetOutputCellIdData() : TissueConfig
• SetOutputCellMutationStates() : TissueConfig
• SetOutputCellTypes() : TissueConfig
• SetOutputCellVariables() : TissueConfig
• SetOutputDirectory() : HeartConfig , TissueSimulation< DIM >
• SetOutputFilenamePrefix() : HeartConfig
• SetOutputNodes() : AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >
• SetOutputTissueAreas() : TissueConfig , MeshBasedTissue< DIM >
• SetOutputVoronoiData() : MeshBasedTissue< DIM > , TissueConfig
• SetOwnership() : AbstractElement< ELEMENT_DIM, SPACE_DIM >
• SetParameter() : AbstractOdeSystem
• SetParameters() : PoleZeroMaterialLaw< DIM >
• SetParametersFile() : HeartConfig
• SetPcType() : LinearSystem
• SetPdeTimeStep() : HeartConfig
• SetPoint() : Node< SPACE_DIM >
• SetPrecision() : LogFile
• SetPrintingTimeStep() : HeartConfig
• SetProteinConcentrationsForTestsOnly() : AbstractOdeBasedCellCycleModel
• SetRegion() : Node< SPACE_DIM > , AbstractElement< ELEMENT_DIM, SPACE_DIM >
• SetRelativeTolerance() : LinearSystem
• SetRhsVectorElement() : LinearSystem
• SetRowForAverageOfPhiZeroed() : BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >
• SetSamplingTimestepMultiple() : TissueSimulation< DIM >
• SetScaleFactorGkr() : Mahajan2008OdeSystem , TenTusscher2006OdeSystem
• SetScaleFactorGks() : Mahajan2008OdeSystem , TenTusscher2006OdeSystem
• SetScaleFactorIto() : Mahajan2008OdeSystem , TenTusscher2006OdeSystem
• SetSDuration() : TissueConfig
• SetSheetDimensions() : HeartConfig
• SetSimulationDuration() : HeartConfig
• SetSlabDimensions() : HeartConfig
• SetSlowValues() : AbstractCardiacCell
• SetSpaceDimension() : HeartConfig
• SetSpringStiffness() : TissueConfig
• SetStartTime() : SimulationTime
• SetState() : AbstractCardiacCell
• SetStateVariable() : AbstractOdeSystem
• SetStateVariables() : AbstractOdeSystem
• SetStemCellG1Duration() : TissueConfig
• SetStimulusFunction() : AbstractCardiacCell
• SetSurfaceAreaToVolumeRatio() : HeartConfig
• SetSurfaceFiles() : StreeterFibreGenerator< SPACE_DIM >
• SetSurfaceTractionBoundaryConditions() : NonlinearElasticityAssembler< DIM >
• SetSymmetricDivisionProbability() : TissueConfig
• SetTime() : PdeSimulationTime
• SetTimes() : AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• SetTissue() : CellwiseData< DIM > , WntConcentration< DIM >
• SetTolerance() : SimpleNewtonNonlinearSolver
• SetTopOfLinearWntConcentration() : TissueConfig
• SetTransitCellG1Duration() : TissueConfig
• SetType() : WntConcentration< DIM >
• setUp() : AbstractCancerTestSuite
• SetUpdateTissueRule() : TissueSimulation< DIM >
• SetupMat() : PetscTools
• SetupSolve() : TissueSimulation< DIM > , CryptSimulation2d
• SetUpstrokeTimeMaps() : HeartConfig
• SetupVectorAndMatrix() : LinearSystem
• setUpWorld() : PetscSetup
• SetupWriteBetaCatenin() : CryptSimulation2d
• SetUseAbsoluteTolerance() : HeartConfig
• SetUseAnalyticalJacobian() : AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE >
• SetUseFixedSchemaLocation() : HeartConfig
• SetUseRelativeTolerance() : HeartConfig
• SetValue() : CellwiseData< DIM >
• SetVertex() : Face< DIM > , VertexAndAngle< DIM >
• SetVoltage() : AbstractCardiacCell
• SetWatchedPosition() : CardiacElectroMechanicsProblem< DIM >
• SetWntChemotaxisStrength() : TissueConfig
• SetWntStemThreshold() : TissueConfig
• SetWntTransitThreshold() : TissueConfig
• SetWriteInfo() : AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >
• SetWriteOutput() : AbstractNonlinearElasticityAssembler< DIM >
• SetWriteStats() : SimpleNewtonNonlinearSolver
• Shuffle() : RandomNumberGenerator
• SimpleDataWriter() : SimpleDataWriter
• SimpleDg0ParabolicAssembler() : SimpleDg0ParabolicAssembler< ELEMENT_DIM, SPACE_DIM, NON_HEART, CONCRETE >
• SimpleLinearEllipticAssembler() : SimpleLinearEllipticAssembler< ELEMENT_DIM, SPACE_DIM, CONCRETE >
• SimpleNewtonNonlinearSolver() : SimpleNewtonNonlinearSolver
• SimpleNonlinearEllipticAssembler() : SimpleNonlinearEllipticAssembler< ELEMENT_DIM, SPACE_DIM >
• SimpleStimulus() : SimpleStimulus
• SimpleWntCellCycleModel() : SimpleWntCellCycleModel
• SimulationTime() : SimulationTime
• Size() : NodeMap , QuadraturePointsGroup< DIM >
• size() : ReplicatableVector
• SloughingCellKiller() : SloughingCellKiller< DIM >
• SmoothStructureTensors() : PapillaryFibreCalculator
• Solve() : SimplePetscNonlinearSolver , AbstractIvpOdeSolver , AbstractNonlinearElasticityAssembler< DIM > , AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE > , LinearSystem , CardiacNewtonSolver< SIZE > , SimpleNewtonNonlinearSolver , RungeKuttaFehlbergIvpOdeSolver , ImplicitCardiacMechanicsAssembler< DIM > , AbstractNonlinearSolver , AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractOneStepIvpOdeSolver , AbstractDynamicAssemblerMixin< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE > , TissueSimulation< DIM > , AbstractOneStepIvpOdeSolver , SimpleDg0ParabolicAssembler< ELEMENT_DIM, SPACE_DIM, NON_HEART, CONCRETE > , AbstractIvpOdeSolver , CardiacElectroMechanicsProblem< DIM >
• SolveAndUpdateStateVariable() : AbstractIvpOdeSolver
• SolveBoundaryElementMapping() : ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveCellSystems() : AbstractCardiacPde< ELEM_DIM, SPACE_DIM >
• SolveDoNotUpdate() : NhsSystemWithImplicitSolver
• SolveElementMapping() : ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveHaloNodeMapping() : ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveLinearSystem() : CardiacNewtonSolver< SIZE > , BackwardEulerIvpOdeSolver
• SolveNodeMapping() : AbstractMesh< ELEMENT_DIM, SPACE_DIM > , ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > , TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• SolveOdeToTime() : WntCellCycleModel , IngeWntSwatCellCycleModel , TysonNovakCellCycleModel , AbstractOdeBasedCellCycleModel
• SplitUpIntoBoxes() : NodeBasedTissue< DIM >
• SpringIterator() : MeshBasedTissue< DIM >::SpringIterator
• SpringsBegin() : MeshBasedTissue< DIM >
• SpringsEnd() : MeshBasedTissue< DIM >
• StandardNormalRandomDeviate() : RandomNumberGenerator
• StartApoptosis() : TissueCell
• StaticSolve() : AbstractNonlinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CONCRETE > , AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , AbstractLinearAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >
• StimulusBoundaryCondition() : StimulusBoundaryCondition< SPACE_DIM >
• StochasticDurationGenerationBasedCellCycleModel() : StochasticDurationGenerationBasedCellCycleModel
• StochasticWntCellCycleModel() : StochasticWntCellCycleModel
• StoppingEventHasOccurred() : TissueSimulation< DIM >
• StoppingEventOccurred() : AbstractIvpOdeSolver
• StreeterFibreGenerator() : StreeterFibreGenerator< SPACE_DIM >
• Stripe() : DistributedVector::Stripe
• SwitchOff() : Electrodes< DIM >