Packages

Here are the packages with brief descriptions (if available):

[detail level 123]

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
idyno	Package of classes used to launch iDynomics
povray	Package of classes used to create output files that can be processed using POV-Ray software
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
detachment	Package of classes that capture detachment of agents from the biomass
diffusionSolver
multigrid
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
shape	Package of utilities that assist with managing the boundary conditions in iDynoMiCS
reaction
kinetic	Package of kinetic factors that comprise the multiplicative terms that make up the reaction kinetics in iDynoMiCS
soft_update	Package of classes required to detect whether a new release of iDynomics is available, and to perform the update
test	Package of classes used to test methods within iDynoMiCS
utils	Package of classes that perform utility functions in the process of running an iDynoMiCS Simulation