- r -

radiusOfACylinder() : utils.ExtraMath
radiusOfASphere() : utils.ExtraMath
readBulk() : simulator.diffusionSolver.multigrid.MultigridSolute
readConcentrationSeen() : simulator.reaction.Reaction
readGeometry() : simulator.geometry.boundaryConditions.IsBC , simulator.geometry.boundaryConditions.AllBC , simulator.geometry.boundaryConditions.BoundaryCyclic
readShape() : simulator.geometry.shape.IsShape , simulator.geometry.shape.Planar
readSoluteGrid() : simulator.diffusionSolver.multigrid.MultigridSolute
readSquareMatrixFromFile() : simulator.diffusionSolver.multigrid.MultigridUtils
readyToFollowBoundary() : simulator.geometry.shape.IsShape , simulator.geometry.shape.Planar
readyToSwitch() : simulator.agent.zoo.BactAdaptable
receivedPlasmid() : simulator.agent.zoo.MultiEpisome
recordGenealogy() : simulator.agent.Agent
recreateBulkConditions() : simulator.Simulator
recreateSpecies() : simulator.Simulator
refreshBioFilmGrids() : simulator.geometry.Domain , simulator.geometry.IsComputationDomain
refreshBorder() : simulator.detachment.LevelSet
refreshBoundary() : simulator.geometry.boundaryConditions.AllBC , simulator.geometry.boundaryConditions.BoundaryBulk , simulator.geometry.boundaryConditions.BoundaryConstant , simulator.geometry.boundaryConditions.BoundaryCyclic , simulator.geometry.boundaryConditions.BoundaryGasMembrane , simulator.geometry.boundaryConditions.BoundaryZeroFlux , simulator.geometry.boundaryConditions.IsBC , simulator.SoluteGrid
refreshCarrier() : simulator.detachment.LevelSet
refreshDiffBoundaries() : simulator.diffusionSolver.multigrid.MultigridSolute
refreshDiffBoundary() : simulator.geometry.boundaryConditions.AllBC , simulator.geometry.boundaryConditions.BoundaryGasMembrane , simulator.geometry.boundaryConditions.IsBC
refreshElement() : simulator.agent.LocatedGroup
refreshGroupStatus() : simulator.AgentContainer
refreshVolume() : simulator.agent.LocatedGroup
register() : simulator.agent.Species , simulator.diffusionSolver.DiffusionSolver , simulator.reaction.Reaction
registerBirth() : simulator.agent.zoo.MultiEpisome , simulator.agent.ActiveAgent , simulator.agent.Agent , simulator.agent.LocatedAgent , simulator.agent.SpecialisedAgent , simulator.agent.zoo.Episome , simulator.AgentContainer
registerDeath() : simulator.AgentContainer
registerMove() : simulator.AgentContainer
registerOnAllActiveReaction() : simulator.agent.ActiveAgent
relax() : simulator.diffusionSolver.multigrid.MultigridSolute , simulator.diffusionSolver.multigrid.SinglegridPressure , simulator.diffusionSolver.Solver_multigrid
relaxGrid() : simulator.AgentContainer
remove() : simulator.agent.LocatedGroup
removeAgent() : simulator.reaction.Reaction
removeAllDead() : simulator.AgentContainer
removeLocated() : simulator.AgentContainer
removeOnBorder() : simulator.AgentContainer
removeReaction() : simulator.agent.HasReaction , simulator.agent.ActiveAgent
reopenFile() : utils.LogFile
repaintAndSave() : utils.Chart
replication() : simulator.agent.zoo.MultiEpisome
reset() : idyno.SimTimer , simulator.geometry.ContinuousVector , simulator.agent.zoo.MultiEpisome , simulator.geometry.DiscreteVector
resetFinest() : simulator.diffusionSolver.multigrid.MultigridSolute
resetMove() : simulator.agent.LocatedGroup
resetMultigridCopies() : simulator.diffusionSolver.multigrid.MultigridSolute , simulator.diffusionSolver.multigrid.SinglegridPressure
resetReaction() : simulator.diffusionSolver.multigrid.MultigridSolute
resetSoluteGrid() : simulator.diffusionSolver.multigrid.SinglegridPressure
reshapeArray() : utils.GridOperations
respondToConditions() : simulator.agent.zoo.BactAdaptable
restrict() : simulator.diffusionSolver.multigrid.MultigridUtils
restrict2() : simulator.diffusionSolver.multigrid.MultigridUtils
restrictBoundaryLayer() : simulator.diffusionSolver.multigrid.MultigridUtils
restrictBoundaryLayer2() : simulator.diffusionSolver.multigrid.MultigridUtils
restrictToCoarsest() : simulator.diffusionSolver.multigrid.MultigridSolute
ResultFile() : utils.ResultFile
returnGroupInVoxel() : simulator.AgentContainer
returnSimulationLength() : idyno.SimTimer
run() : simulator.Simulator