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• Abscissa() : AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , OdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , PdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , SpaceConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM > , OdePdeConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >
• AbstractAlgebraicContractionModel() : AbstractAlgebraicContractionModel
• AbstractAssemblerSolverHybrid() : AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >
• AbstractBackwardEulerCardiacCell() : AbstractBackwardEulerCardiacCell< SIZE >
• AbstractBidomainSolver() : AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
• AbstractBoundaryCondition() : AbstractBoundaryCondition< SPACE_DIM >
• AbstractBoundaryConditionsContainer() : AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractCachedMeshReader() : AbstractCachedMeshReader< ELEMENT_DIM, SPACE_DIM >
• AbstractCardiacCell() : AbstractCardiacCell
• AbstractCardiacCellFactory() : AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >
• AbstractCardiacCellInterface() : AbstractCardiacCellInterface
• AbstractCardiacCellWithModifiers() : AbstractCardiacCellWithModifiers< CARDIAC_CELL >
• AbstractCardiacFeVolumeIntegralAssembler() : AbstractCardiacFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• AbstractCardiacMechanicsSolver() : AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >
• AbstractCardiacMechanicsSolverInterface() : AbstractCardiacMechanicsSolverInterface< DIM >
• AbstractCardiacProblem() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractCardiacTissue() : AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >
• AbstractCaUpdateRule() : AbstractCaUpdateRule< DIM >
• AbstractCellBasedSimulation() : AbstractCellBasedSimulation< DIM >
• AbstractCellCycleModel() : AbstractCellCycleModel
• AbstractCellCycleModelOdeSolver() : AbstractCellCycleModelOdeSolver
• AbstractCellKiller() : AbstractCellKiller< SPACE_DIM >
• AbstractCellMutationState() : AbstractCellMutationState
• AbstractCellPopulation() : AbstractCellPopulation< DIM >
• AbstractCellPopulationBoundaryCondition() : AbstractCellPopulationBoundaryCondition< DIM >
• AbstractCellProperty() : AbstractCellProperty
• AbstractCentreBasedCellPopulation() : AbstractCentreBasedCellPopulation< DIM >
• AbstractChasteRegion() : AbstractChasteRegion< SPACE_DIM >
• AbstractCompressibleMaterialLaw() : AbstractCompressibleMaterialLaw< DIM >
• AbstractConductivityModifier() : AbstractConductivityModifier< ELEMENT_DIM, SPACE_DIM >
• AbstractContinuumMechanicsAssembler() : AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
• AbstractContractionModel() : AbstractContractionModel
• AbstractCorrectionTermAssembler() : AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractCryptStatistics() : AbstractCryptStatistics
• AbstractCvodeCell() : AbstractCvodeCell
• AbstractCvodeSystem() : AbstractCvodeSystem
• AbstractDynamicLinearPdeSolver() : AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractElement() : AbstractElement< ELEMENT_DIM, SPACE_DIM >
• AbstractExtendedBidomainSolver() : AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >
• AbstractFeAssemblerCommon() : AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• AbstractFeAssemblerInterface() : AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
• AbstractFeCableIntegralAssembler() : AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• AbstractFeSurfaceIntegralAssembler() : AbstractFeSurfaceIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractFeVolumeIntegralAssembler() : AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• AbstractForce() : AbstractForce< DIM >
• AbstractHdf5Converter() : AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
• AbstractIncompressibleMaterialLaw() : AbstractIncompressibleMaterialLaw< DIM >
• AbstractIvpOdeSolver() : AbstractIvpOdeSolver
• AbstractLinearEllipticPde() : AbstractLinearEllipticPde< ELEMENT_DIM, SPACE_DIM >
• AbstractLinearPdeSolver() : AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractLookupTableCollection() : AbstractLookupTableCollection
• AbstractMaterialLaw() : AbstractMaterialLaw< DIM >
• AbstractMesh() : AbstractMesh< ELEMENT_DIM, SPACE_DIM >
• AbstractMeshWriter() : AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
• AbstractModifier() : AbstractModifier
• AbstractNonlinearAssemblerSolverHybrid() : AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractNonlinearElasticitySolver() : AbstractNonlinearElasticitySolver< DIM >
• AbstractOdeBasedCellCycleModel() : AbstractOdeBasedCellCycleModel
• AbstractOdeBasedContractionModel() : AbstractOdeBasedContractionModel
• AbstractOdeSystem() : AbstractOdeSystem
• AbstractOdeSystemForCoupledPdeSystem() : AbstractOdeSystemForCoupledPdeSystem
• AbstractOdeSystemInformation() : AbstractOdeSystemInformation
• AbstractOdeSystemWithAnalyticJacobian() : AbstractOdeSystemWithAnalyticJacobian
• AbstractOffLatticeCellPopulation() : AbstractOffLatticeCellPopulation< DIM >
• AbstractOnLatticeCellPopulation() : AbstractOnLatticeCellPopulation< DIM >
• AbstractParameterisedSystem() : AbstractParameterisedSystem< VECTOR >
• AbstractPottsUpdateRule() : AbstractPottsUpdateRule< DIM >
• AbstractRushLarsenCardiacCell() : AbstractRushLarsenCardiacCell
• AbstractSimpleCellCycleModel() : AbstractSimpleCellCycleModel
• AbstractSimpleGenerationBasedCellCycleModel() : AbstractSimpleGenerationBasedCellCycleModel
• AbstractStaticLinearPdeSolver() : AbstractStaticLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AbstractStimulusFactory() : AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >
• AbstractTetrahedralElement() : AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralElement< 0, SPACE_DIM >
• AbstractTetrahedralMesh() : AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
• AbstractTetrahedralMeshWriter() : AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
• AbstractTimeAdaptivityController() : AbstractTimeAdaptivityController
• AbstractTwoBodyInteractionForce() : AbstractTwoBodyInteractionForce< DIM >
• AbstractUntemplatedParameterisedSystem() : AbstractUntemplatedParameterisedSystem
• AbstractVanLeeuwen2009WntSwatCellCycleModel() : AbstractVanLeeuwen2009WntSwatCellCycleModel
• AbstractWntOdeBasedCellCycleModel() : AbstractWntOdeBasedCellCycleModel
• Adapt() : AdaptiveTetrahedralMesh
• AdaptiveBidomainProblem() : AdaptiveBidomainProblem
• AdaptiveTetrahedralMesh() : AdaptiveTetrahedralMesh
• AdaptMesh() : AdaptiveBidomainProblem , AdaptiveTetrahedralMesh
• AddBoundaryElement() : Node< SPACE_DIM >
• AddCaUpdateRule() : OnLatticeSimulation< DIM >
• AddCell() : AbstractCellPopulation< DIM > , AbstractCentreBasedCellPopulation< DIM > , CaBasedCellPopulation< DIM > , MeshBasedCellPopulation< DIM > , MeshBasedCellPopulationWithGhostNodes< DIM > , NodeBasedCellPopulation< DIM > , PottsBasedCellPopulation< DIM > , VertexBasedCellPopulation< DIM >
• AddCellData() : VertexMeshWriter< ELEMENT_DIM, SPACE_DIM > , VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >
• AddCellKiller() : AbstractCellBasedSimulation< DIM >
• AddCellPopulationBoundaryCondition() : OffLatticeSimulation< DIM >
• AddCellProperty() : Cell
• AddCurrentSolutionToAdaptiveMesh() : AdaptiveBidomainProblem
• AddDirichletBoundaryCondition() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AddElement() : Node< SPACE_DIM > , Box< DIM > , MutableVertexMesh< ELEMENT_DIM, SPACE_DIM > , PottsMesh< DIM >
• AddExtraBoundaryNodes() : QuadraticMesh< DIM >
• AddFace() : VertexElement< ELEMENT_DIM, SPACE_DIM >
• AddForce() : OffLatticeSimulation< DIM >
• AddForceContribution() : AbstractTwoBodyInteractionForce< DIM > , BuskeCompressionForce< DIM > , ChemotacticForce< DIM > , NagaiHondaForce< DIM > , RepulsionForce< DIM > , WelikyOsterForce< DIM > , CryptProjectionForce , VertexCryptBoundaryForce< DIM > , LinearSpringWithVariableSpringConstantsForce< DIM > , AbstractForce< DIM >
• AddLhsMultipleValues() : LinearSystem
• AddModifier() : AbstractCardiacCellWithModifiers< CARDIAC_CELL >
• AddMultipleValues() : PetscVecTools , PetscMatTools
• AddNeumannBoundaryCondition() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AddNode() : AbstractElement< ELEMENT_DIM, SPACE_DIM > , Box< DIM > , MutableVertexMesh< ELEMENT_DIM, SPACE_DIM > , VertexElement< ELEMENT_DIM, SPACE_DIM > , VertexElement< 1, SPACE_DIM > , Cylindrical2dMesh , Cylindrical2dVertexMesh , NodesOnlyMesh< SPACE_DIM > , AbstractOffLatticeCellPopulation< DIM > , MeshBasedCellPopulation< DIM > , NodeBasedCellPopulation< DIM > , VertexBasedCellPopulation< DIM > , PottsElement< DIM > , MutableMesh< ELEMENT_DIM, SPACE_DIM >
• AddNodeAttribute() : Node< SPACE_DIM >
• AddNodesToBoundaryElements() : QuadraticMesh< DIM >
• AddNodeToBoundaryElement() : QuadraticMesh< DIM >
• AddPdeAndBc() : CellBasedPdeHandler< DIM >
• AddPointData() : AdaptiveTetrahedralMesh , VertexMeshWriter< ELEMENT_DIM, SPACE_DIM > , VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >
• AddPottsUpdateRule() : OnLatticeSimulation< DIM >
• AddProperty() : CellPropertyCollection
• AddProvenance() : VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >
• AddRhsMultipleValues() : LinearSystem
• AddScaledVector() : PetscVecTools
• AddStimulus() : MultiStimulus
• AddToElement() : PetscMatTools , PetscVecTools
• AddToMatrixElement() : LinearSystem
• AddToRhsVectorElement() : LinearSystem
• AddTrailingSlash() : OutputFileHandler
• AddUpdateRule() : PottsBasedCellPopulation< DIM > , CaBasedCellPopulation< DIM >
• AddWarning() : Warnings
• AdhesionPottsUpdateRule() : AdhesionPottsUpdateRule< DIM >
• AdjustOdeParameters() : SingleOdeWntCellCycleModel , Alarcon2004OxygenBasedCellCycleModel , WntCellCycleModel , AbstractVanLeeuwen2009WntSwatCellCycleModel , CellCycleModelOdeHandler
• AdjustOutOfRangeSlowValues() : AbstractCardiacCell
• AdjustStepSize() : RungeKuttaFehlbergIvpOdeSolver
• AdvanceAlongUnlimitedDimension() : ColumnDataWriter , ParallelColumnDataWriter , Hdf5DataWriter , AbstractDataWriter
• AdvanceOneTimeStep() : TimeStepper
• AdvectionCaUpdateRule() : AdvectionCaUpdateRule< DIM >
• AfterSolve() : AbstractCellBasedSimulation< DIM > , OnLatticeSimulation< DIM > , CryptSimulation2d , OffLatticeSimulation< DIM >
• Alarcon2004OxygenBasedCellCycleModel() : Alarcon2004OxygenBasedCellCycleModel
• Alarcon2004OxygenBasedCellCycleOdeSystem() : Alarcon2004OxygenBasedCellCycleOdeSystem
• AllocateMatrixMemory() : AbstractNonlinearElasticitySolver< DIM >
• AmMaster() : PetscTools
• AmTopMost() : PetscTools
• AnalyseMeshForBath() : ExtendedBidomainProblem< DIM > , BidomainProblem< DIM >
• AnalyticJacobian() : AbstractOdeSystemWithAnalyticJacobian , TysonNovak2001OdeSystem
• AnyNonZeroNeumannConditions() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• ApcOneHitCellMutationState() : ApcOneHitCellMutationState
• ApcTwoHitCellMutationState() : ApcTwoHitCellMutationState
• ApoptoticCellProperty() : ApoptoticCellProperty
• AppendLocalDataToFiles() : CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM > , MeshalyzerMeshWriter< ELEMENT_DIM, SPACE_DIM > , AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
• ApplyDirichletBoundaryConditions() : AbstractNonlinearElasticitySolver< DIM >
• ApplyDirichletConditions() : AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• ApplyDirichletToLinearProblem() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• ApplyDirichletToNonlinearJacobian() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• ApplyDirichletToNonlinearResidual() : BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• ApplyPermutation() : Hdf5DataWriter
• ApplyUndeformedElementAndDisplacement() : DeformedBoundaryElement< ELEM_DIM, SPACE_DIM >
• ArchiveOpener() : ArchiveOpener< Archive, Stream >
• AreCellularTransmuralHeterogeneitiesRequested() : HeartConfig
• AreCryptSectionCellsLabelled() : AbstractCryptStatistics
• Assemble() : AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
• AssembleFinalLinearSystem() : LinearSystem
• AssembleIntermediateLinearSystem() : LinearSystem
• AssembleMatrix() : AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
• AssembleOnBoundaryElement() : IncompressibleNonlinearElasticitySolver< DIM > , CompressibleNonlinearElasticitySolver< DIM >
• AssembleOnCableElement() : AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
• AssembleOnElement() : CompressibleNonlinearElasticitySolver< DIM > , AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX > , AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL > , IncompressibleNonlinearElasticitySolver< DIM >
• AssembleOnSurfaceElement() : AbstractFeSurfaceIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
• AssembleSystem() : CompressibleNonlinearElasticitySolver< DIM > , IncompressibleNonlinearElasticitySolver< DIM > , AbstractNonlinearElasticitySolver< DIM >
• AssembleVector() : AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
• AtBeginningOfTimestep() : AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > , BidomainProblem< DIM >
• AveragedSourcePde() : AveragedSourcePde< DIM >
• AxisymmetricConductivityTensors() : AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >