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