  simulator.AgentContainer | Class to store all the agents, call them, and manage shoving/erosion of located agents |
 simulator.geometry.boundaryConditions.AllBC | Group all methods expected by the interface but common to most of the boundary classes |
 simulator.geometry.boundaryConditions.BoundaryBulk | Defines the bulk boundary: the concentration on the boundary is fixed by a dynamical bulk, the agents crossing this line die |
| simulator.geometry.boundaryConditions.BoundaryConstant | BoundaryConstant : the concentration on the boundary is fixed by a constant bulk, the agents crossing this line die |
| simulator.geometry.boundaryConditions.BoundaryCyclic | BoundaryCyclic : close the system along a dimension |
| simulator.geometry.boundaryConditions.BoundaryGasMembrane | BoundaryMembrane : defines a boundary impermeable to everything except to gas |
 simulator.geometry.boundaryConditions.BoundaryZeroFlux | Defines an impermeable boundary to solutes and agents |
| simulator.geometry.Bulk | Define the bulk: an object used to define the environment connected to the simulated system |
| simulator.geometry.FluctEnv | |
| soft_update.Check_Release_Status | Checks if a new release of iDynomics is available |
| Cloneable | |
 simulator.agent.Agent | Major class of iDynoMiCS - defines the agents that are involved in an iDynoMiCS simulation. Extended by a number of agent types |
 simulator.agent.SpecialisedAgent | Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation |
 simulator.agent.ActiveAgent | Extension of Agent and SpecialisedAgent - adds reaction information to model agent involvement in reactions |
| simulator.agent.LocatedAgent | Extends ActiveAgent by adding functionality to control agent grid location, agent shoving, agent death and division, and agent movement |
| simulator.agent.zoo.Bacterium | Creates an object of the Bacterium Species. Acts as a superclass for all current species with the exception of ParticulateEPS |
| simulator.agent.zoo.BactEPS | Creates an object of the Bacterium EPS Species: a bacterium with a permanent hydrolytic activity of its EPS capsule |
| simulator.agent.zoo.BactAdaptable | Creates a Bacterium agent object that can change its reaction based on local conditions |
| simulator.agent.zoo.ParticulateEPS | Creates an object of the Particulate EPS species |
| simulator.agent.InfoAgent | Abstract class used for declaring Episome and MultiEpisome objects |
| simulator.agent.zoo.Episome | |
| simulator.agent.zoo.MultiEpisome | |
| simulator.agent.LocatedAgent | Extends ActiveAgent by adding functionality to control agent grid location, agent shoving, agent death and division, and agent movement |
| simulator.agent.SpecialisedAgent | Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation |
| simulator.agent.zoo.Bacterium | Creates an object of the Bacterium Species. Acts as a superclass for all current species with the exception of ParticulateEPS |
| simulator.geometry.ContinuousVector | Implements 3D vector of continuous spatial coordinates. Can be used to store Continuous coordinates or Movement vectors |
| simulator.geometry.DiscreteVector | Implements 3D vector of discrete spatial coordinates |
| utils.Complex | Class for storing complex numbers as two doubles representing real and imaginary part, respectively |
| utils.ComplexArray | Class for storing an 1- to 3-dimensional array of complex numbers as an 1D array of alternating real and imaginary parts in double precision |
| simulator.detachment.ConnectedVolume | Implements connected volume filtration operation. Provides a base class for geometry specific connected volume filtrators |
| simulator.diffusionSolver.DiffusionSolver | An abstract class used as a parent for all diffusion solvers that could be defined |
| simulator.diffusionSolver.Solver_chemostat | |
| simulator.diffusionSolver.Solver_multigrid | |
| simulator.diffusionSolver.Solver_pressure | Initialises and calculates pressure affect on the simulation domain |
| utils.ExtraMath | Abstract class with some extra useful math functions |
| utils.FftOperations | Tool for performing fast fourier transform (FFT) on grids of Complex and real numbers |
| FilenameFilter | |
| utils.Jfilter | Used in simulation initialisation to ensure onky XML files are read as protocol files and previous results files are excluded |
| simulator.geometry.GridElementFloat | Implements a reference to a grid element |
| utils.GridOperations | Collection of static methods to deal with spatial grids that are used in the MicroCoSm model |
| simulator.agent.HasReaction | Interface of methods that should be implemented for agent classes that are involved in solute reactions |
| simulator.agent.ActiveAgent | Extension of Agent and SpecialisedAgent - adds reaction information to model agent involvement in reactions |
| simulator.agent.HasSpecies | Interface for species classes, stating the methods that these classes should include |
| simulator.agent.InfoAgent | Abstract class used for declaring Episome and MultiEpisome objects |
| simulator.agent.SpecialisedAgent | Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation |
| idyno.Idynomics | Main class to run to launch the iDynoMiCS tool |
| utils.InitialisationErrorLog | Creates and updates a simulation initialisation error log file for the initialising simulation |
| simulator.geometry.boundaryConditions.IsBC | Interface for the boundary conditions on the system's margins. To be used in solvers and agent move |
| simulator.geometry.IsComputationDomain | Interface describing mandatory methods for a computation domain object. The default class is "ComputationDomain" but other can be defined |
| simulator.geometry.Domain | Define the computation domain: an evenly spaced rectilinear grid described by its dimensionality (2D or 3D) |
| simulator.geometry.shape.IsShape | Interface class used by boundary condition classes. Defines the methods used to monitor the boundaries of the computation domain |
| simulator.geometry.shape.Planar | Create a planar shaped boundary |
| simulator.detachment.LevelSet | Solver used for modelling detachment |
| simulator.detachment.DS_Biomass | Biomass detachment method. Function: kDet*L^2/X, where L is the local biomass thickness and X the local biomass concentration |
| simulator.detachment.DS_Proportional | Proportional detachment method. Function: kDet*L, where L is the local biomass thickness |
| simulator.detachment.DS_Quadratic | Quadratic detachment method. Function: kDet*L^2, where L is the local biomass thickness |
| simulator.detachment.DS_SolGrad | SolGrad detachment method. Loop through solutes to find the maximum gradient and use this as a multiplier to calculate detachment rate |
| simulator.agent.LocatedGroup | Object to hold a group of agents in one location on the agent grid |
| utils.LogFile | Creates and updates a log file for the running simulation |
| utils.MatrixOperations | Implements static utility functions for used in multigrid method |
| simulator.diffusionSolver.multigrid.MultigridSolute | Implements static utility functions for used in multigrid method |
| simulator.diffusionSolver.multigrid.MultigridUtils | |
| utils.ResultFile | Class used to create auto-zipping result files. At each iteration, the file is added to an archive |
| RuntimeException | |
| exceptions.ModelRuntimeException | Creates the runtime exceptions that are generated by iDynoMiCS when an error is encountered |
| idyno.SimTimer | Class to create and keep track of the timestep and simulation time course |
| simulator.Simulator | Top-level class of the simulation core. Used to create and run a simulation |
| simulator.diffusionSolver.multigrid.SinglegridPressure | |
| simulator.agent.SpeciesParam | Class used to store and set parameters specific for a species. Can be extended to add additional parameters |
| simulator.agent.ActiveParam | Extends SpeciesParam, adding parameters used to simulate an agents involvement in a reaction |
| simulator.agent.LocatedParam | Extends ActiveParam by adding location and behaviour parameters to a defined agent |
| simulator.agent.zoo.BacteriumParam | Extends LocatedParam to create an object that can store all common parameters for Bacteria-based species |
| simulator.agent.zoo.BactEPSParam | Extends Bacterium Param for use by BactEPS species, a bacterium with a permanent hydrolytic activity of its EPS capsule |
| simulator.agent.zoo.BactAdaptableParam | Creates a parameter object for BactAdaptable, a Bacterium agent object that can change its reaction based on local conditions |
| simulator.agent.zoo.ParticulateEPSParam | Stores parameters common to the Particulate EPS species - representing generic extracellular polymers and contains only the 'capsule' type |
| simulator.agent.zoo.EpisomeParam | |
| simulator.agent.zoo.MultiEpisomeParam | |
| test.TestUtils | |
| utils.UnitConverter | Static class used to convert units (mass, length, time) |
| utils.VectorizedArray | Creates a 2D or 3D Vectorized array of a set size, and provides utilities to set and get values from this array |
| simulator.World | Class containing methods to create and query the simulation world (bulk and computational domains) |
| utils.ZipArchive | Class to create and update zip archives that contain simulation result files |
| ApplicationFrame | |
| utils.Chart | Class used to represent simulation output on a graph. Assumed deprecated as never called in iDynoMiCS 1.2 |
| JFrame | |
| soft_update.Update_IDynomics | Performs an update to the iDynomics tool if a new version has been detected |
| Random | |
| utils.MTRandom | An implementation of the original java mersenne twister class by Makoto Matsumoto and Takuji Nishimura |
 Serializable | |
| povray.Background | Specifies the background that will be used in the POV-Ray images |
| povray.Biofilm3D | Creates a union with a box (the biofilm carrier) and spheres (the bacteria), creating a 3D scene for the PovRay rendering engine |
| povray.Box | Class used to set the properties of the box used in POV-Ray output |
| povray.Camera | Creates the 'camera' settings required to produce POV-Ray output |
| povray.ColorMaps | Class containing methods to adjust POV-Ray display colours if necessary |
| povray.LightSource | Class used to specify the light source information for POV-Ray images |
| povray.ParticleWithCapsule | Used by Povray3DScene to create a capsule object in a format that can be displayed graphically in POV-Ray output |
| povray.Povray3DScene | Create a POV-Ray 3D scene object for use in visualising 3D Biofilms (with class Biofilm3D) |
| povray.PovRayWriter | Class that writes POV-Ray files that can be used to visualise simulation results |
| povray.VectorProperty | Class used by the majority of POV-Ray scripts to represent coordinates and colours as vector properties for use in POV-Ray |
| simulator.agent.Species | Creates and manages the species that are to be included in an iDynoMiCS simulation |
| simulator.geometry.ContinuousVector | Implements 3D vector of continuous spatial coordinates. Can be used to store Continuous coordinates or Movement vectors |
| simulator.geometry.DiscreteVector | Implements 3D vector of discrete spatial coordinates |
| simulator.geometry.shape.Planar | Create a planar shaped boundary |
| simulator.reaction.kinetic.IsKineticFactor | Interface for all kinetic reactions that can be defined in iDynoMiCS |
| simulator.reaction.kinetic.FirstOrderKinetic | Model a reaction using First Order Kinetics. Use of this kinetic is discouraged (Rob 071211) |
| simulator.reaction.kinetic.HaldaneKinetic | Model a reaction using Haldane Kinetics |
| simulator.reaction.kinetic.HillKinetic | Model a reaction using Hill Kinetics |
| simulator.reaction.kinetic.LinearKinetic | |
| simulator.reaction.kinetic.MonodKinetic | Model a reaction using a monod kinetic factor |
| simulator.reaction.kinetic.SimpleInhibition | Model a reaction using a simple inhibition kinetic factor |
| simulator.reaction.Reaction | Class containing methods to create and query reactions that occur in the simulation |
| simulator.reaction.FirstOrder | Modelled First-Order reactions. This class is deprecated |
| simulator.reaction.ReactionFactor | Allows creation of a Reaction object whose the reaction rate can be decomposed in several kinetic factors (one factor by solute) |
| simulator.reaction.ReactionFactorWithConstant | Allows creation of a Reaction object whose the reaction rate can be decomposed in several kinetic factor (one factor by solute), but adds a constant factor to the calculation |
| simulator.reaction.ReactionGrowthFitness | Captures the fitness cost associated with the carriage of a plasmid |
| simulator.reaction.SingleMonod | Deprecated. Was used to create pathways described by a simple Monod kinetic y1 S1 -> y2 S2+X where ยต=muMax*S1/(Ks+S1) |
| simulator.SpatialGrid | Class defining a spatial grid, i.e. a matrix of double. The grid is padded, 3D grid |
| simulator.EpithelialGrid | Grid that will hold the epithelial cells on the bottom of a boundary (if specified) |
| simulator.SoluteGrid | Class for containing chemical solutes, that are represented by a grid |
| utils.XMLParser | Class providing methods of parsing the XML simulation protocol file |
1.8.3.1
