Index

A

AbstractBoundaryCondition2 (class in chaste.pde) AbstractBoundaryCondition3 (class in chaste.pde) AbstractCaUpdateRule2 (class in chaste.cell_based) AbstractCaUpdateRule3 (class in chaste.cell_based) AbstractCellBasedSimulation2_2 (class in chaste.cell_based) AbstractCellBasedSimulation3_3 (class in chaste.cell_based) AbstractCellBasedSimulationModifier2_2 (class in chaste.cell_based) AbstractCellBasedSimulationModifier3_3 (class in chaste.cell_based) AbstractCellCycleModel (class in chaste.cell_based) AbstractCellKiller2 (class in chaste.cell_based) AbstractCellKiller3 (class in chaste.cell_based) AbstractCellMutationState (class in chaste.cell_based) AbstractCellPopulationBoundaryCondition2_2 (class in chaste.cell_based) AbstractCellPopulationBoundaryCondition3_3 (class in chaste.cell_based) AbstractCellProliferativeType (class in chaste.cell_based) AbstractCellProperty (class in chaste.cell_based) AbstractForce2_2 (class in chaste.cell_based) AbstractForce3_3 (class in chaste.cell_based) AbstractGrowingDomainPdeModifier2 (class in chaste.cell_based) AbstractGrowingDomainPdeModifier3 (class in chaste.cell_based) AbstractLinearEllipticPde2_2 (class in chaste.cell_based) (class in chaste.pde) AbstractLinearEllipticPde3_3 (class in chaste.cell_based) (class in chaste.pde) AbstractLinearPde2_2 (class in chaste.cell_based) (class in chaste.pde) AbstractLinearPde3_3 (class in chaste.cell_based) (class in chaste.pde) AbstractMesh2_2 (class in chaste.mesh) AbstractMesh3_3 (class in chaste.mesh) AbstractOdeSystem (class in chaste.ode) AbstractOdeSystemInformation (class in chaste.ode) AbstractPdeModifier2 (class in chaste.cell_based) AbstractPdeModifier3 (class in chaste.cell_based) AbstractPhaseBasedCellCycleModel (class in chaste.cell_based) AbstractPottsUpdateRule2 (class in chaste.cell_based) AbstractPottsUpdateRule3 (class in chaste.cell_based) AbstractPyChasteActorGenerator2 (class in chaste.visualization) AbstractPyChasteActorGenerator3 (class in chaste.visualization) AbstractPythonOdeSystemInformation (class in chaste.ode) AbstractSimpleCellCycleModel (class in chaste.cell_based) AbstractSimpleGenerationalCellCycleModel (class in chaste.cell_based) AbstractSimplePhaseBasedCellCycleModel (class in chaste.cell_based) AbstractTargetAreaModifier2 (class in chaste.cell_based) AbstractTargetAreaModifier3 (class in chaste.cell_based) AbstractTetrahedralMesh2_2 (class in chaste.mesh) AbstractTetrahedralMesh3_3 (class in chaste.mesh) AbstractTwoBodyInteractionForce2_2 (class in chaste.cell_based) AbstractTwoBodyInteractionForce3_3 (class in chaste.cell_based) AbstractUpdateRule2 (class in chaste.cell_based) AbstractUpdateRule3 (class in chaste.cell_based) AddActor() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) AddAppliedForceContribution() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) AddAttribute() (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) AddBoundaryElement() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) AddCaBasedCellPopulationActor() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) AddCellKiller() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method)

AddCellPopulationBoundaryCondition() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) AddCellProperty() (chaste.cell_based.Cell method) AddElement() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) AddForce() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) AddForceContribution() (chaste.cell_based.AbstractForce2_2 method) (chaste.cell_based.AbstractForce3_3 method) (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) AddHaloNode() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) AddHaloNodesToBoxes() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) AddMeshBasedCellPopulationActor() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) AddMovedNode() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) AddNeighbour() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) AddNode() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) AddNodeAttribute() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) AddNodesToBoxes() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) AddPottsBasedCellPopulationActor() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) AddProperty() (chaste.cell_based.CellPropertyCollection method) AddSimulationModifier() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) AddUpdateRule() (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) AddVariableName() (chaste.ode.AbstractPythonOdeSystemInformation method) AddVariableUnit() (chaste.ode.AbstractPythonOdeSystemInformation method) AddVertexBasedCellPopulationActor() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) AdhesionPottsUpdateRule2 (class in chaste.cell_based) AdhesionPottsUpdateRule3 (class in chaste.cell_based) AmMaster() (chaste.core.PetscTools static method) AmTopMost() (chaste.core.PetscTools static method) ApcOneHitCellMutationState (class in chaste.cell_based) ApcTwoHitCellMutationState (class in chaste.cell_based) ApoptoticCellKiller2 (class in chaste.cell_based) ApoptoticCellKiller3 (class in chaste.cell_based) ApplyBoundaries() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) AssignCellId() (chaste.cell_based.CellId method) AttractingPlaneBoundaryCondition2_2 (class in chaste.cell_based) AttractingPlaneBoundaryCondition3_3 (class in chaste.cell_based)

B

Barrier() (chaste.core.PetscTools static method) Begin() (chaste.cell_based.CellPropertyCollection method)

BeginRoundRobin() (chaste.core.PetscTools static method) BetaCateninOneHitCellMutationState (class in chaste.cell_based)

C

CalculateAreaOfFace() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) CalculateBoundaryNodePairs() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) CalculateBoundingBox() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) CalculateDesignatedOwnershipOfBoundaryElement() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) CalculateDesignatedOwnershipOfElement() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) CalculateForceBetweenNodes() (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) CalculateInteriorNodePairs() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) CalculateMaximumContainingElementsPerProcess() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) CalculateMaximumNodeConnectivityPerProcess() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) CalculateMinMaxEdgeLengths() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) CalculateMomentsOfElement() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) CalculateNodeExchange() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) CalculateNodesOutsideLocalDomain() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) CalculateRootFunction() (chaste.ode.AbstractOdeSystem method) CalculateStoppingEvent() (chaste.ode.AbstractOdeSystem method) CalculateUnitNormalToFaceWithArea() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) CanCellTerminallyDifferentiate() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) Cell (class in chaste.cell_based) CellAncestor (class in chaste.cell_based) CellData (class in chaste.cell_based) CellId (class in chaste.cell_based) CellLabel (class in chaste.cell_based) CellPopulationPyChasteActorGenerator2 (class in chaste.visualization) CellPopulationPyChasteActorGenerator3 (class in chaste.visualization) CellPropertyCollection (class in chaste.cell_based) CellPropertyRegistry (class in chaste.cell_based) CellwiseSourceEllipticPde2 (class in chaste.cell_based) CellwiseSourceEllipticPde3 (class in chaste.cell_based) chaste (module) chaste.cell_based (module) chaste.core (module) chaste.mesh (module) chaste.ode (module) chaste.pde (module) chaste.tutorial (module) chaste.visualization (module) chaste.visualization.fortests (module) ChasteBuildInfo (class in chaste.core) ChastePoint2 (class in chaste.mesh) ChastePoint3 (class in chaste.mesh) CheckAndLabelCellsForApoptosisOrDeath() (chaste.cell_based.AbstractCellKiller2 method) (chaste.cell_based.AbstractCellKiller3 method) (chaste.cell_based.ApoptoticCellKiller2 method) (chaste.cell_based.ApoptoticCellKiller3 method) (chaste.cell_based.PlaneBasedCellKiller2 method) (chaste.cell_based.PlaneBasedCellKiller3 method) (chaste.cell_based.RandomCellKiller2 method) (chaste.cell_based.RandomCellKiller3 method) CheckAndLabelSingleCellForApoptosis() (chaste.cell_based.ApoptoticCellKiller2 method) (chaste.cell_based.ApoptoticCellKiller3 method) (chaste.cell_based.RandomCellKiller2 method) (chaste.cell_based.RandomCellKiller3 method) CheckForIntersections() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) CheckForRosettes() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) CheckForSwapsFromShortEdges() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) CheckForT2Swaps() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) CheckIsConforming() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) CheckIsVoronoi() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) CheckOutwardNormals() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method)

Clear() (chaste.cell_based.CellPropertyRegistry method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) ClearAppliedForce() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) ClearBoxCollection() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) ClearHaloNodes() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) ClearLocationsOfT1Swaps() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) ClearLocationsOfT3Swaps() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) ClearNeighbours() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) Complain() (chaste.tutorial.Hello method) ComputeConstantInUSourceTerm() (chaste.cell_based.AbstractLinearEllipticPde2_2 method) (chaste.cell_based.AbstractLinearEllipticPde3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) (chaste.pde.AbstractLinearEllipticPde2_2 method) (chaste.pde.AbstractLinearEllipticPde3_3 method) ComputeConstantInUSourceTermAtNode() (chaste.cell_based.AbstractLinearEllipticPde2_2 method) (chaste.cell_based.AbstractLinearEllipticPde3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) (chaste.pde.AbstractLinearEllipticPde2_2 method) (chaste.pde.AbstractLinearEllipticPde3_3 method) ComputeDiffusionTerm() (chaste.cell_based.AbstractLinearEllipticPde2_2 method) (chaste.cell_based.AbstractLinearEllipticPde3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) (chaste.pde.AbstractLinearEllipticPde2_2 method) (chaste.pde.AbstractLinearEllipticPde3_3 method) ComputeLinearInUCoeffInSourceTerm() (chaste.cell_based.AbstractLinearEllipticPde2_2 method) (chaste.cell_based.AbstractLinearEllipticPde3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) (chaste.pde.AbstractLinearEllipticPde2_2 method) (chaste.pde.AbstractLinearEllipticPde3_3 method) ComputeLinearInUCoeffInSourceTermAtNode() (chaste.cell_based.AbstractLinearEllipticPde2_2 method) (chaste.cell_based.AbstractLinearEllipticPde3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) (chaste.pde.AbstractLinearEllipticPde2_2 method) (chaste.pde.AbstractLinearEllipticPde3_3 method) ConstBoundaryCondition2 (class in chaste.pde) ConstBoundaryCondition3 (class in chaste.pde) ConstructCuboid() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) ConstructFromMesh() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) ConstructFromMeshReader() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) ConstructLinearMesh() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) ConstructNodesWithoutMesh() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) ConstructRectangularMesh() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) ConstructRegularSlabMesh() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) ConstructRegularSlabMeshWithDimensionSplit() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) container_id (chaste.visualization.fortests.JupyterNotebookManager attribute) ContainingBoundaryElementsBegin() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) ContainingBoundaryElementsEnd() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) ContainingElementsBegin() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) ContainingElementsEnd() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) CopyFileTo() (chaste.core.OutputFileHandler method) CopyTo() (chaste.core.FileFinder method) CreateAndSetVec() (chaste.core.PetscTools static method) CreateCellCycleModel() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) CreateVec() (chaste.core.PetscTools static method) Cylindrical2dVertexMesh (class in chaste.mesh)

D

DangerousRemove() (chaste.core.FileFinder method) DecrementCellCount() (chaste.cell_based.AbstractCellProperty method) DefaultCellProliferativeType (class in chaste.cell_based) DeleteBoundaryNodeAt() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) DeleteElement() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) DeleteElementPriorToReMesh() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) DeleteMovedNode() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) DeleteNode() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) DeleteNodePriorToReMesh() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) Destroy() (chaste.cell_based.SimulationTime static method) (chaste.core.PetscTools static method) (chaste.core.RandomNumberGenerator static method) DifferentialAdhesionPottsUpdateRule2 (class in chaste.cell_based)

DifferentialAdhesionPottsUpdateRule3 (class in chaste.cell_based) DifferentiatedCellProliferativeType (class in chaste.cell_based) DiffusionCaUpdateRule2 (class in chaste.cell_based) DiffusionCaUpdateRule3 (class in chaste.cell_based) Divide() (chaste.cell_based.Cell method) DivideEdge() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) DivideElement() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) DivideElementAlongGivenAxis() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) DivideElementAlongShortAxis() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) DoCellBirth() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) DoCellRemoval() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) DumpPetscObject() (chaste.core.PetscTools static method)

E

EdgesBegin() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) EdgesEnd() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) ElementIncludesPoint() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) EllipticGrowingDomainPdeModifier2 (class in chaste.cell_based) EllipticGrowingDomainPdeModifier3 (class in chaste.cell_based) End() (chaste.cell_based.CellPropertyCollection method) (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) EndRoundRobin() (chaste.core.PetscTools static method) EvaluateHamiltonianContribution() (chaste.cell_based.AbstractPottsUpdateRule2 method) (chaste.cell_based.AbstractPottsUpdateRule3 method) (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method)

EvaluateProbability() (chaste.cell_based.AbstractCaUpdateRule2 method) (chaste.cell_based.AbstractCaUpdateRule3 method) (chaste.cell_based.DiffusionCaUpdateRule2 method) (chaste.cell_based.DiffusionCaUpdateRule3 method) EvaluateYDerivatives() (chaste.ode.AbstractOdeSystem method) Exists() (chaste.core.FileFinder method) ExponentialRandomDeviate() (chaste.core.RandomNumberGenerator method)

F

FakePath() (chaste.core.FileFinder static method)

FileFinder (class in chaste.core) FindFile() (chaste.core.OutputFileHandler method)

G

GammaRandomDeviate() (chaste.core.RandomNumberGenerator method) GeneralisedLinearSpringForce2_2 (class in chaste.cell_based) GeneralisedLinearSpringForce3_3 (class in chaste.cell_based) GenerateFeMesh() (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) GenerateVerticesFromElementCircumcentres() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetAbsolutePath() (chaste.core.FileFinder method) GetAdhesionParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) GetAge() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.Cell method) GetAncestor() (chaste.cell_based.Cell method) (chaste.cell_based.CellAncestor method) GetAngleBetweenNodes() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetAnyVariableIndex() (chaste.ode.AbstractOdeSystemInformation method) GetAnyVariableUnits() (chaste.ode.AbstractOdeSystemInformation method) GetApoptosisTime() (chaste.cell_based.Cell method) GetAreaGradientOfElementAtNode() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetAttribute() (chaste.ode.AbstractOdeSystemInformation method) GetAverageStemCellCycleTime() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetAverageTransitCellCycleTime() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetBirthTime() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.Cell method) GetBoundaryCondition() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) GetBoundaryElementIteratorBegin() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) GetBoundaryElementIteratorEnd() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) GetBoundaryNodeIteratorBegin() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetBoundaryNodeIteratorEnd() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetBuilderUnameInfo() (chaste.core.ChasteBuildInfo static method) GetBuildInformation() (chaste.core.ChasteBuildInfo static method) GetBuildTime() (chaste.core.ChasteBuildInfo static method) GetCell() (chaste.cell_based.AbstractCellCycleModel method) GetCellBoundaryAdhesionEnergy() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) GetCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) GetCellCellAdhesionEnergy() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) GetCellCellAdhesionEnergyParameter() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) GetCellCount() (chaste.cell_based.AbstractCellProperty method) GetCellCycleDuration() (chaste.cell_based.AbstractSimpleCellCycleModel method) GetCellCycleModel() (chaste.cell_based.Cell method) GetCellData() (chaste.cell_based.Cell method) GetCellId() (chaste.cell_based.Cell method) (chaste.cell_based.CellId method) GetCellPopulation() (chaste.cell_based.AbstractCellKiller2 method) (chaste.cell_based.AbstractCellKiller3 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition2_2 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition3_3 method) GetCellPopulationActorGenerator() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) GetCellProliferativeType() (chaste.cell_based.Cell method) GetCellRearrangementRatio() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetCellRearrangementThreshold() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetCellVecData() (chaste.cell_based.Cell method) GetCentroidOfElement() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetChasteTestOutputDirectory() (chaste.core.OutputFileHandler static method) GetCheckForInternalIntersections() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetCoefficient() (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) GetColorTransferFunction() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) GetColour() (chaste.cell_based.AbstractCellMutationState method) (chaste.cell_based.AbstractCellProliferativeType method) (chaste.cell_based.CellLabel method) GetCompilerFlags() (chaste.core.ChasteBuildInfo static method) GetCompilerType() (chaste.core.ChasteBuildInfo static method) GetCompilerVersion() (chaste.core.ChasteBuildInfo static method) GetContainingElementIndex() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) GetContainingElementIndexWithInitialGuess() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetContainingElementIndices() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetCriticalHypoxicDuration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) GetCurrentCellCyclePhase() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) GetCurrentHypoxiaOnsetTime() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) GetCurrentHypoxicDuration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) GetCurrentTime() (chaste.core.ChasteBuildInfo static method) GetCutOffLength() (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) GetDeathProbabilityInAnHour() (chaste.cell_based.RandomCellKiller2 method) (chaste.cell_based.RandomCellKiller3 method) GetDeformationEnergyParameter() (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method) GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetDerivedQuantityIndex() (chaste.ode.AbstractOdeSystemInformation method) GetDerivedQuantityUnits() (chaste.ode.AbstractOdeSystemInformation method) GetDiffusionParameter() (chaste.cell_based.DiffusionCaUpdateRule2 method) (chaste.cell_based.DiffusionCaUpdateRule3 method) GetDimension() (chaste.cell_based.AbstractCellCycleModel method) GetDiscreteColorTransferFunction() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) GetDistanceBetweenNodes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetDt() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetEdgeLength() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetElapsedTime() (chaste.core.Timer static method) GetElement() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetElementIteratorBegin() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetElementIteratorEnd() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetElongationShapeFactorOfElement() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetExtension() (chaste.core.FileFinder method) GetFreeVariableName() (chaste.ode.AbstractOdeSystemInformation method) GetFreeVariableUnits() (chaste.ode.AbstractOdeSystemInformation method) GetG1Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetG2Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetGeneration() (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) GetGrowthDuration() (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) GetHaloNodeIndices() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetHypoxicConcentration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) GetIdentifier() (chaste.cell_based.Identifiable method) GetIndex() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) GetInitialConditions() (chaste.ode.AbstractOdeSystemInformation method) GetInverseJacobianForElement() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetItem() (chaste.cell_based.CellData method) GetJacobianForElement() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetKeys() (chaste.cell_based.CellData method) GetLabelledCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) GetLabelledCellCellAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) GetLabelledCellLabelledCellAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) GetLastT2SwapLocation() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetLeafName() (chaste.core.FileFinder method) GetLeafNameNoExtension() (chaste.core.FileFinder method) GetLicenceText() (chaste.core.ChasteBuildInfo static method) GetLocalIndexForElementEdgeClosestToPoint() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetLocationsOfT1Swaps() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetLocationsOfT3Swaps() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetMajorReleaseNumber() (chaste.core.ChasteBuildInfo static method) GetMatureCellTargetSurfaceArea() (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) GetMatureCellTargetVolume() (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method) GetMaxCellCycleDuration() (chaste.cell_based.UniformCellCycleModel method) GetMaxCellId() (chaste.cell_based.CellId method) GetMaximumInteractionDistance() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) GetMaximumNodeIndex() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetMaxTransitGenerations() (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) GetMDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetMeinekeDivisionRestingSpringLength() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) GetMeinekeSpringGrowthDuration() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) GetMeinekeSpringStiffness() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) GetMeshFileBaseName() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetMessage() (chaste.tutorial.Hello method) GetMinCellCycleDuration() (chaste.cell_based.UniformCellCycleModel method) GetMinimumGapDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) GetMinorReleaseNumber() (chaste.core.ChasteBuildInfo static method) GetMooreNeighbouringNodeIndices() (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) GetMutationState() (chaste.cell_based.Cell method) GetMyRank() (chaste.core.PetscTools static method) GetNagaiHondaCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) GetNagaiHondaCellCellAdhesionEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) GetNagaiHondaDeformationEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) GetNagaiHondaMembraneSurfaceEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) GetNearestElementIndex() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetNearestElementIndexFromTestElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) GetNearestNodeIndex() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNeighbouringElementIndices() (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNeighbouringNodeIndices() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method)

GetNeighbouringNodeNotAlsoInElement() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNeighboursSetUp() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) GetNextEdgeGradientOfElementAtNode() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNode() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetNodeIteratorBegin() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetNodeIteratorEnd() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetNodeLocation() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetNumAllBoundaryElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) GetNumAllElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNumAllNodes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNumberOfAttributes() (chaste.ode.AbstractOdeSystemInformation method) GetNumberOfDerivedQuantities() (chaste.ode.AbstractOdeSystemInformation method) GetNumberOfParameters() (chaste.ode.AbstractOdeSystemInformation method) GetNumBirths() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetNumBoundaryElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetNumBoundaryNodes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) GetNumCableElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetNumContainingElements() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) GetNumDeaths() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetNumElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNumericalMethod() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) GetNumFaces() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNumItems() (chaste.cell_based.CellData method) GetNumLocalBoundaryElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetNumLocalElements() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetNumNodeAttributes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) GetNumNodes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetNumProcs() (chaste.core.PetscTools static method) GetNumVertices() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetOutputCellVelocities() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetOutputDirectory() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetOutputDirectoryFullPath() (chaste.core.OutputFileHandler method) GetOutputDivisionLocations() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetOutputGradient() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) GetParameterIndex() (chaste.ode.AbstractOdeSystemInformation method) GetParameterUnits() (chaste.ode.AbstractOdeSystemInformation method) GetParent() (chaste.core.FileFinder method) GetPde() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) GetPerimeterGradientOfElementAtNode() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetPoint() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) GetPreviousEdgeGradientOfElementAtNode() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetProperty() (chaste.cell_based.CellPropertyCollection method) GetProtorosetteFormationProbability() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetProtorosetteResolutionProbabilityPerTimestep() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetProvenanceString() (chaste.core.ChasteBuildInfo static method) GetQuiescentConcentration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) GetRadius() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) GetRadiusOfSphere() (chaste.cell_based.SphereGeometryBoundaryCondition2 method) (chaste.cell_based.SphereGeometryBoundaryCondition3 method) GetReferenceTargetArea() (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) GetRegion() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) GetRelativePath() (chaste.core.FileFinder method) (chaste.core.OutputFileHandler method) GetRenderer() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) GetRevisionNumber() (chaste.core.ChasteBuildInfo static method) GetRootDir() (chaste.core.ChasteBuildInfo static method) GetRosetteRankOfElement() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetRosetteResolutionProbabilityPerTimestep() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetSceneAsCharBuffer() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) GetSDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) GetSG2MDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) GetShortAxisOfElement() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetSize() (chaste.cell_based.CellPropertyCollection method) (chaste.core.ReplicatableVector method) GetStartOfApoptosisTime() (chaste.cell_based.Cell method) GetStateVariableIndex() (chaste.ode.AbstractOdeSystemInformation method) GetStateVariableUnits() (chaste.ode.AbstractOdeSystemInformation method) GetStemCellG1Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) GetSurfaceArea() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetSurfaceAreaOfElement() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetSystemName() (chaste.ode.AbstractOdeSystemInformation method) GetT2Threshold() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) GetTime() (chaste.cell_based.SimulationTime method) GetTimeStep() (chaste.cell_based.SimulationTime method) GetTimeStepsElapsed() (chaste.cell_based.SimulationTime method) GetTimeUntilDeath() (chaste.cell_based.Cell method) GetTransitCellG1Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) GetUpdateCellPopulationRule() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) GetUseAnalyticJacobian() (chaste.ode.AbstractOdeSystem method) GetUseCutOffLength() (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) GetUseJiggledNodesOnPlane() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) GetValue() (chaste.pde.AbstractBoundaryCondition2 method) (chaste.pde.AbstractBoundaryCondition3 method) (chaste.pde.ConstBoundaryCondition2 method) (chaste.pde.ConstBoundaryCondition3 method) GetVector() (chaste.tutorial.Hello method) GetVectorFromAtoB() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetVersionString() (chaste.core.ChasteBuildInfo static method) GetVolume() (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetVolumeOfElement() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetVonNeumannNeighbouringNodeIndices() (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex() (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetVtkScene() (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) GetWallTime() (chaste.core.Timer static method) GetWeightedDirectionForBoundaryElement() (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetWeightedDirectionForElement() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) GetWidth() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) GetWithDefault() (chaste.mesh.ChastePoint2 method) (chaste.mesh.ChastePoint3 method) GetXsdVersion() (chaste.core.ChasteBuildInfo static method)

H

HandleHighOrderJunctions() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) HasAnyVariable() (chaste.ode.AbstractOdeSystemInformation method) HasApoptosisBegun() (chaste.cell_based.Cell method) HasAttribute() (chaste.ode.AbstractOdeSystemInformation method) HasAveragedSourcePde() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) HasCellVecData() (chaste.cell_based.Cell method)

HasDerivedQuantity() (chaste.ode.AbstractOdeSystemInformation method) HasNodeAttributes() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) HasOrderingBeenSpecified() (chaste.cell_based.CellPropertyRegistry method) HasParameter() (chaste.ode.AbstractOdeSystemInformation method) HasParMetis() (chaste.core.PetscTools static method) HasProperty() (chaste.cell_based.CellPropertyCollection method) HasStateVariable() (chaste.ode.AbstractOdeSystemInformation method) Hello (class in chaste.tutorial)

I

Identifiable (class in chaste.cell_based) IdentifySwapType() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) ImposeBoundaryCondition() (chaste.cell_based.AbstractCellPopulationBoundaryCondition2_2 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition3_3 method) (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) (chaste.cell_based.SphereGeometryBoundaryCondition2 method) (chaste.cell_based.SphereGeometryBoundaryCondition3 method) IncrementCellCount() (chaste.cell_based.AbstractCellProperty method) IncrementTimeOneStep() (chaste.cell_based.SimulationTime method) init() (in module chaste) Initialise() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) (chaste.ode.AbstractOdeSystemInformation method) (chaste.ode.AbstractPythonOdeSystemInformation method) InitialiseCellCycleModel() (chaste.cell_based.Cell method) InitialiseDaughterCell() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) InitialiseSrnModel() (chaste.cell_based.Cell method) Instance() (chaste.cell_based.CellPropertyRegistry static method) (chaste.cell_based.SimulationTime static method) (chaste.core.RandomNumberGenerator static method)

interactive_plot_init() (chaste.visualization.fortests.JupyterNotebookManager method) interactive_plot_show() (chaste.visualization.fortests.JupyterNotebookManager method) interactive_plotting_loaded (chaste.visualization.fortests.JupyterNotebookManager attribute) IsAbsolutePath() (chaste.core.FileFinder static method) IsBoundaryNode() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) IsDead() (chaste.cell_based.Cell method) IsDeleted() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) IsDir() (chaste.core.FileFinder method) IsEmpty() (chaste.core.FileFinder method) IsEndTimeAndNumberOfTimeStepsSetUp() (chaste.cell_based.SimulationTime method) IsFile() (chaste.core.FileFinder method) IsFinished() (chaste.cell_based.SimulationTime method) IsInitialised() (chaste.core.PetscTools static method) IsInternal() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) IsIsolated() (chaste.core.PetscTools static method) IsLogged() (chaste.cell_based.Cell method) IsMeshChanging() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) IsMeshOnDisk() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) IsNeumannBoundaryCondition() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) IsNewerThan() (chaste.core.FileFinder method) IsolateProcesses() (chaste.core.PetscTools static method) IsOwned() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) IsParallel() (chaste.core.PetscTools static method) IsParticle() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) IsPathSet() (chaste.core.FileFinder method) IsSame() (chaste.cell_based.AbstractCellProperty method) IsSamePoint() (chaste.mesh.ChastePoint2 method) (chaste.mesh.ChastePoint3 method) IsSequential() (chaste.core.PetscTools static method) IsStartTimeSetUp() (chaste.cell_based.SimulationTime method) IsWorkingCopyModified() (chaste.core.ChasteBuildInfo static method)

J

JupyterNotebookManager (class in chaste.visualization.fortests)

JupyterSceneModifier2 (class in chaste.visualization.fortests) JupyterSceneModifier3 (class in chaste.visualization.fortests)

K

Kill() (chaste.cell_based.Cell method)

L

LoadBalanceMesh() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method)

M

MarkAsDeleted() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) MarkAsInternal() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) MoveMergeNode() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method)

MutableMesh2_2 (class in chaste.mesh) MutableMesh3_3 (class in chaste.mesh) MutableVertexMesh2_2 (class in chaste.mesh) MutableVertexMesh3_3 (class in chaste.mesh)

N

NagaiHondaForce2 (class in chaste.cell_based) NagaiHondaForce3 (class in chaste.cell_based) NeighboursIsEmpty() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) NoCellCycleModel (class in chaste.cell_based)

Node2 (class in chaste.mesh) Node3 (class in chaste.mesh) NodeAttributes2 (class in chaste.mesh) NodeAttributes3 (class in chaste.mesh) NodesOnlyMesh2 (class in chaste.mesh) NodesOnlyMesh3 (class in chaste.mesh) NormalRandomDeviate() (chaste.core.RandomNumberGenerator method)

O

OffLatticeSimulation2_2 (class in chaste.cell_based) OffLatticeSimulation3_3 (class in chaste.cell_based) OnLatticeSimulation2 (class in chaste.cell_based) OnLatticeSimulation3 (class in chaste.cell_based) OutputAdditionalSimulationSetup() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) OutputCellCycleModelInfo() (chaste.cell_based.AbstractCellCycleModel method) OutputCellCycleModelParameters() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) OutputCellKillerInfo() (chaste.cell_based.AbstractCellKiller2 method) (chaste.cell_based.AbstractCellKiller3 method) OutputCellKillerParameters() (chaste.cell_based.AbstractCellKiller2 method) (chaste.cell_based.AbstractCellKiller3 method) (chaste.cell_based.ApoptoticCellKiller2 method) (chaste.cell_based.ApoptoticCellKiller3 method) (chaste.cell_based.PlaneBasedCellKiller2 method) (chaste.cell_based.PlaneBasedCellKiller3 method) (chaste.cell_based.RandomCellKiller2 method) (chaste.cell_based.RandomCellKiller3 method) OutputCellPopulationBoundaryConditionInfo() (chaste.cell_based.AbstractCellPopulationBoundaryCondition2_2 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition3_3 method) OutputCellPopulationBoundaryConditionParameters() (chaste.cell_based.AbstractCellPopulationBoundaryCondition2_2 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition3_3 method) (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) (chaste.cell_based.SphereGeometryBoundaryCondition2 method) (chaste.cell_based.SphereGeometryBoundaryCondition3 method) OutputFileHandler (class in chaste.core) OutputForceInfo() (chaste.cell_based.AbstractForce2_2 method) (chaste.cell_based.AbstractForce3_3 method) OutputForceParameters() (chaste.cell_based.AbstractForce2_2 method) (chaste.cell_based.AbstractForce3_3 method) (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method)

OutputSimulationModifierInfo() (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) OutputSimulationModifierParameters() (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier2 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) OutputSimulationParameters() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) OutputSimulationSetup() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) OutputUpdateRuleInfo() (chaste.cell_based.AbstractUpdateRule2 method) (chaste.cell_based.AbstractUpdateRule3 method) OutputUpdateRuleParameters() (chaste.cell_based.AbstractCaUpdateRule2 method) (chaste.cell_based.AbstractCaUpdateRule3 method) (chaste.cell_based.AbstractPottsUpdateRule2 method) (chaste.cell_based.AbstractPottsUpdateRule3 method) (chaste.cell_based.AbstractUpdateRule2 method) (chaste.cell_based.AbstractUpdateRule3 method) (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) (chaste.cell_based.DiffusionCaUpdateRule2 method) (chaste.cell_based.DiffusionCaUpdateRule3 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method)

P

PerformIntersectionSwap() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformNodeMerge() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformProtorosetteResolution() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformRosetteRankDecrease() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformRosetteRankIncrease() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformT1Swap() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformT2Swap() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformT3Swap() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) PerformVoidRemoval() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method)

PermuteNodes() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) PetscTools (class in chaste.core) PlaneBasedCellKiller2 (class in chaste.cell_based) PlaneBasedCellKiller3 (class in chaste.cell_based) PlaneBoundaryCondition2_2 (class in chaste.cell_based) PlaneBoundaryCondition3_3 (class in chaste.cell_based) PottsMesh2 (class in chaste.mesh) PottsMesh3 (class in chaste.mesh) Print() (chaste.core.Timer static method) PrintAndReset() (chaste.core.Timer static method)

R

randMod() (chaste.core.RandomNumberGenerator method) RandomCellKiller2 (class in chaste.cell_based) RandomCellKiller3 (class in chaste.cell_based) RandomNumberGenerator (class in chaste.core) ranf() (chaste.core.RandomNumberGenerator method) ReadNodesPerProcessorFile() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) ReadPetscObject() (chaste.core.PetscTools static method) ReadyToDivide() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.Cell method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) RefineElement() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) RefreshJacobianCachedData() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) RefreshMesh() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) ReIndex() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) RelativeTo (class in chaste.core) ReMesh() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) Remove() (chaste.core.FileFinder method) RemoveAllCellKillers() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) RemoveAllCellPopulationBoundaryConditions() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) RemoveAllForces() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) RemoveAllUpdateRules() (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) RemoveBoundaryElement() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) RemoveDeletedElements() (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) RemoveDeletedNodes() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) RemoveDeletedNodesAndElements() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) RemoveDuplicateNeighbours() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method)

RemoveElement() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) RemoveProperty() (chaste.cell_based.CellPropertyCollection method) ReplaceSpacesWithUnderscores() (chaste.core.FileFinder static method) ReplaceUnderscoresWithSpaces() (chaste.core.FileFinder static method) ReplicatableVector (class in chaste.core) Replicate() (chaste.core.ReplicatableVector method) ReplicateBool() (chaste.core.PetscTools static method) ReplicateException() (chaste.core.PetscTools static method) ReplicatePetscVector() (chaste.core.ReplicatableVector method) Reseed() (chaste.core.RandomNumberGenerator method) Reset() (chaste.core.Timer static method) ResetCache() (chaste.core.PetscTools static method) ResetEndTimeAndNumberOfTimeSteps() (chaste.cell_based.SimulationTime method) ResetForDivision() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) ResetMaxCellId() (chaste.cell_based.CellId static method) ResetRenderer() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) Resize() (chaste.core.ReplicatableVector method) ResizeBoxCollection() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) RevertToOldLocations() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) rGetAppliedForce() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) rGetCellPopulation() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.CellwiseSourceEllipticPde2 method) (chaste.cell_based.CellwiseSourceEllipticPde3 method) rGetCentreOfSphere() (chaste.cell_based.SphereGeometryBoundaryCondition2 method) (chaste.cell_based.SphereGeometryBoundaryCondition3 method) rGetConstStateVariables() (chaste.ode.AbstractOdeSystem method) rGetDerivedQuantityNames() (chaste.ode.AbstractOdeSystemInformation method) rGetDerivedQuantityUnits() (chaste.ode.AbstractOdeSystemInformation method) rGetLocation() (chaste.mesh.ChastePoint2 method) (chaste.mesh.ChastePoint3 method) (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) rGetNormalToPlane() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBasedCellKiller2 method) (chaste.cell_based.PlaneBasedCellKiller3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) rGetParameterNames() (chaste.ode.AbstractOdeSystemInformation method) rGetParameterUnits() (chaste.ode.AbstractOdeSystemInformation method) rGetPointOnPlane() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBasedCellKiller2 method) (chaste.cell_based.PlaneBasedCellKiller3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) rGetProjectVersions() (chaste.core.ChasteBuildInfo static method) rGetStateVariableNames() (chaste.ode.AbstractOdeSystemInformation method) rGetStateVariableUnits() (chaste.ode.AbstractOdeSystemInformation method) Rotate() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) RotateX() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) RotateY() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) RotateZ() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method)

S

Scale() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SetAncestor() (chaste.cell_based.Cell method) SetApoptosisTime() (chaste.cell_based.Cell method) SetArchiveDirectory() (chaste.core.OutputFileHandler method) SetAsBoundaryNode() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) SetAttractionThreshold() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) SetBirthTime() (chaste.cell_based.AbstractCellCycleModel method) (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.Cell method) (chaste.cell_based.NoCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) SetCalculateNodeNeighbours() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) SetCell() (chaste.cell_based.AbstractCellCycleModel method) SetCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) SetCellCellAdhesionEnergyParameter() (chaste.cell_based.AdhesionPottsUpdateRule2 method) (chaste.cell_based.AdhesionPottsUpdateRule3 method) SetCellCycleDuration() (chaste.cell_based.AbstractSimpleCellCycleModel method) (chaste.cell_based.UniformCellCycleModel method) SetCellCycleModel() (chaste.cell_based.Cell method) SetCellPopulation() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) SetCellProliferativeType() (chaste.cell_based.Cell method) SetCellPropertyRegistry() (chaste.cell_based.CellPropertyCollection method) SetCellRearrangementRatio() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetCellRearrangementThreshold() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetCheckForInternalIntersections() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetColorByCellData() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetColorByCellType() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetColorByUserDefined() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetCoordinate() (chaste.mesh.ChastePoint2 method) (chaste.mesh.ChastePoint3 method) SetCriticalHypoxicDuration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) SetCurrentHypoxiaOnsetTime() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) SetCutOffLength() (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) SetDataLabel() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetDefaultInitialCondition() (chaste.ode.AbstractOdeSystemInformation method) SetDefaultInitialConditions() (chaste.ode.AbstractOdeSystemInformation method) SetDeformationEnergyParameter() (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method) SetDependentVariableName() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) SetDiffusionParameter() (chaste.cell_based.DiffusionCaUpdateRule2 method) (chaste.cell_based.DiffusionCaUpdateRule3 method) SetDimension() (chaste.cell_based.AbstractCellCycleModel method) SetDistributedVectorFactory() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SetDt() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetEdgeColor() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetEdgeSize() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetElementOwnerships() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SetEndTime() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetEndTimeAndNumberOfTimeSteps() (chaste.cell_based.SimulationTime method) SetG1Duration() (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) SetG2Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) SetGeneration() (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) SetGrowthDuration() (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) SetHypoxicConcentration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) SetIndex() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) SetInitialBoxCollection() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) SetIsInitialised() (chaste.ode.AbstractPythonOdeSystemInformation method) SetIsInteractive() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) SetIsParticle() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) SetItem() (chaste.cell_based.CellData method) SetLabelledCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) SetLabelledCellCellAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) SetLabelledCellLabelledCellAdhesionEnergyParameter() (chaste.cell_based.DifferentialAdhesionPottsUpdateRule2 method) (chaste.cell_based.DifferentialAdhesionPottsUpdateRule3 method) SetLogged() (chaste.cell_based.Cell method) SetMatureCellTargetSurfaceArea() (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule2 method) (chaste.cell_based.SurfaceAreaConstraintPottsUpdateRule3 method) SetMatureCellTargetVolume() (chaste.cell_based.VolumeConstraintPottsUpdateRule2 method) (chaste.cell_based.VolumeConstraintPottsUpdateRule3 method) SetMaxCellCycleDuration() (chaste.cell_based.UniformCellCycleModel method) SetMaximumInteractionDistance() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) SetMaxTransitGenerations() (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) SetMDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) SetMeinekeDivisionRestingSpringLength() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) SetMeinekeSpringGrowthDuration() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) SetMeinekeSpringStiffness() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) SetMeshHasChangedSinceLoading() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) SetMinCellCycleDuration() (chaste.cell_based.UniformCellCycleModel method) SetMinimumGapDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) SetMinimumNodeDomainBoundarySeparation() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) SetMutationState() (chaste.cell_based.Cell method) SetNagaiHondaCellBoundaryAdhesionEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) SetNagaiHondaCellCellAdhesionEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) SetNagaiHondaDeformationEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) SetNagaiHondaMembraneSurfaceEnergyParameter() (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method) SetNeighboursSetUp() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) SetNoBirth() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetNode() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method)

SetNumericalMethod() (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) SetOption() (chaste.core.PetscTools static method) SetOutputCellVelocities() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetOutputDirectory() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetOutputDivisionLocations() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetOutputFilePath() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) SetOutputGradient() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) SetOutputSolutionAtPdeNodes() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) SetPath() (chaste.core.FileFinder method) SetPoint() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) SetPointColor() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetPointOnPlane() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) SetPointSize() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetProtorosetteFormationProbability() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetProtorosetteResolutionProbabilityPerTimestep() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetQuiescentConcentration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) SetRadius() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) SetReferenceTargetArea() (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) SetRegion() (chaste.mesh.Node2 method) (chaste.mesh.Node3 method) (chaste.mesh.NodeAttributes2 method) (chaste.mesh.NodeAttributes3 method) SetRosetteResolutionProbabilityPerTimestep() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetSamplingTimestepMultiple() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetSaveAsAnimation() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) SetSaveAsImages() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) SetSDuration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) SetShowCellCentres() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetShowEdges() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetShowMutableMeshEdges() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetShowPoints() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetShowPottsMeshEdges() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetShowPottsMeshOutlines() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetShowVolume() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetShowVoronoiMeshEdges() (chaste.visualization.CellPopulationPyChasteActorGenerator2 method) (chaste.visualization.CellPopulationPyChasteActorGenerator3 method) SetSrnModel() (chaste.cell_based.Cell method) SetStartTime() (chaste.cell_based.SimulationTime method) SetStemCellG1Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) SetT2Threshold() (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) SetTransitCellG1Duration() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) SetUpBoxCollection() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) SetUpdateCellPopulationRule() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SetUpdateFrequency() (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) SetupMat() (chaste.core.PetscTools static method) SetupSolve() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier2 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) SetUpSourceTermsForAveragedSourcePde() (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) SetUseJiggledNodesOnPlane() (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) SetVector() (chaste.tutorial.Hello method) SetVolumeColor() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetVolumeOpacity() (chaste.visualization.AbstractPyChasteActorGenerator2 method) (chaste.visualization.AbstractPyChasteActorGenerator3 method) SetVtkScene() (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) Shuffle() (chaste.core.RandomNumberGenerator method) SimpleOxygenBasedCellCycleModel (class in chaste.cell_based) SimpleTargetAreaModifier2 (class in chaste.cell_based) SimpleTargetAreaModifier3 (class in chaste.cell_based) SimulationTime (class in chaste.cell_based) Solve() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) SolveBoundaryElementMapping() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SolveElementMapping() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SolveNodeMapping() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method) SpecifyOrdering() (chaste.cell_based.CellPropertyRegistry method) SphereGeometryBoundaryCondition2 (class in chaste.cell_based) SphereGeometryBoundaryCondition3 (class in chaste.cell_based) SplitEdge() (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) StandardNormalRandomDeviate() (chaste.core.RandomNumberGenerator method) Start() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) StartApoptosis() (chaste.cell_based.Cell method) StartInteractiveEventHandler() (chaste.visualization.VtkScene2 method) (chaste.visualization.VtkScene3 method) StemCellProliferativeType (class in chaste.cell_based) StopFaking() (chaste.core.FileFinder static method) StoppingEventHasOccurred() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) SurfaceAreaConstraintPottsUpdateRule2 (class in chaste.cell_based) SurfaceAreaConstraintPottsUpdateRule3 (class in chaste.cell_based)

T

TetrahedralMesh2_2 (class in chaste.mesh) TetrahedralMesh3_3 (class in chaste.mesh) three_js_dir (chaste.visualization.fortests.JupyterNotebookManager attribute) Timer (class in chaste.core) TransitCellProliferativeType (class in chaste.cell_based) Translate() (chaste.mesh.AbstractMesh2_2 method) (chaste.mesh.AbstractMesh3_3 method) (chaste.mesh.AbstractTetrahedralMesh2_2 method) (chaste.mesh.AbstractTetrahedralMesh3_3 method) (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableMesh2_2 method) (chaste.mesh.MutableMesh3_3 method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) (chaste.mesh.PottsMesh2 method) (chaste.mesh.PottsMesh3 method) (chaste.mesh.TetrahedralMesh2_2 method) (chaste.mesh.TetrahedralMesh3_3 method) (chaste.mesh.VertexMesh2_2 method) (chaste.mesh.VertexMesh3_3 method)

U

UniformCellCycleModel (class in chaste.cell_based) UniformG1GenerationalCellCycleModel (class in chaste.cell_based) UpdateAtEndOfOutputTimeStep() (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier2 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) UpdateAtEndOfSolve() (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier2 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) UpdateAtEndOfTimeStep() (chaste.cell_based.AbstractCellBasedSimulationModifier2_2 method) (chaste.cell_based.AbstractCellBasedSimulationModifier3_3 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.AbstractPdeModifier2 method) (chaste.cell_based.AbstractPdeModifier3 method) (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier2 method) (chaste.cell_based.EllipticGrowingDomainPdeModifier3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) (chaste.visualization.fortests.JupyterSceneModifier2 method) (chaste.visualization.fortests.JupyterSceneModifier3 method)

UpdateBoxCollection() (chaste.mesh.NodesOnlyMesh2 method) (chaste.mesh.NodesOnlyMesh3 method) UpdateCellCyclePhase() (chaste.cell_based.AbstractPhaseBasedCellCycleModel method) (chaste.cell_based.AbstractSimpleGenerationalCellCycleModel method) (chaste.cell_based.AbstractSimplePhaseBasedCellCycleModel method) (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) (chaste.cell_based.UniformG1GenerationalCellCycleModel method) UpdateCellData() (chaste.cell_based.AbstractGrowingDomainPdeModifier2 method) (chaste.cell_based.AbstractGrowingDomainPdeModifier3 method) (chaste.cell_based.VtkSceneModifier2 method) (chaste.cell_based.VtkSceneModifier3 method) UpdateCellLocationsAndTopology() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) UpdateCellPopulation() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method) UpdateHypoxicDuration() (chaste.cell_based.SimpleOxygenBasedCellCycleModel method) UpdateTargetAreaOfCell() (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method) (chaste.cell_based.SimpleTargetAreaModifier2 method) (chaste.cell_based.SimpleTargetAreaModifier3 method) UpdateTargetAreas() (chaste.cell_based.AbstractTargetAreaModifier2 method) (chaste.cell_based.AbstractTargetAreaModifier3 method)

V

VariableSpringConstantMultiplicationFactor() (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) VerifyBoundaryCondition() (chaste.cell_based.AbstractCellPopulationBoundaryCondition2_2 method) (chaste.cell_based.AbstractCellPopulationBoundaryCondition3_3 method) (chaste.cell_based.AttractingPlaneBoundaryCondition2_2 method) (chaste.cell_based.AttractingPlaneBoundaryCondition3_3 method) (chaste.cell_based.PlaneBoundaryCondition2_2 method) (chaste.cell_based.PlaneBoundaryCondition3_3 method) (chaste.cell_based.SphereGeometryBoundaryCondition2 method) (chaste.cell_based.SphereGeometryBoundaryCondition3 method)

VertexMesh2_2 (class in chaste.mesh) VertexMesh3_3 (class in chaste.mesh) VolumeConstraintPottsUpdateRule2 (class in chaste.cell_based) VolumeConstraintPottsUpdateRule3 (class in chaste.cell_based) vtk_show() (chaste.visualization.fortests.JupyterNotebookManager method) vtk_show_basic() (in module chaste.visualization.fortests) VtkScene2 (class in chaste.visualization) VtkScene3 (class in chaste.visualization) VtkSceneModifier2 (class in chaste.cell_based) VtkSceneModifier3 (class in chaste.cell_based)

W

WidenEdgeOrCorrectIntersectionLocationIfNecessary() (chaste.mesh.Cylindrical2dVertexMesh method) (chaste.mesh.MutableVertexMesh2_2 method) (chaste.mesh.MutableVertexMesh3_3 method) WildTypeCellMutationState (class in chaste.cell_based) WriteDataToVisualizerSetupFile() (chaste.cell_based.AbstractForce2_2 method) (chaste.cell_based.AbstractForce3_3 method) (chaste.cell_based.AbstractTwoBodyInteractionForce2_2 method) (chaste.cell_based.AbstractTwoBodyInteractionForce3_3 method) (chaste.cell_based.GeneralisedLinearSpringForce2_2 method) (chaste.cell_based.GeneralisedLinearSpringForce3_3 method) (chaste.cell_based.NagaiHondaForce2 method) (chaste.cell_based.NagaiHondaForce3 method)

WriteVisualizerSetupFile() (chaste.cell_based.AbstractCellBasedSimulation2_2 method) (chaste.cell_based.AbstractCellBasedSimulation3_3 method) (chaste.cell_based.OffLatticeSimulation2_2 method) (chaste.cell_based.OffLatticeSimulation3_3 method) (chaste.cell_based.OnLatticeSimulation2 method) (chaste.cell_based.OnLatticeSimulation3 method)