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Agents (A Game theoretic Evolutionary Network Traffic Simulation) is a toolkit for the analysis of selfish agents in networks by means of evolutionary game theory. Simulations of replicator and other dynamics can be plotted, visualised and analysed.
ODE for Java is a binding between C dynamics library ODE (Open Dynamics Engine, http://ode.org) and Java. Separate packages provide among other things a Java3D integration and thus a scenegraph representation of selected ODE objects.
JRVFSim (Jarvis) is a simulator of a fluid dynamics phenomenon known as radial viscous fingering. Its main feature consists of taking jordan curves and simulating their evolution subject to various parameters. Includes a partial API for numerical methods