JCGrid is an easy-to-use tools for real-world grid-computing. It requires only to install Java Runtime and you can easy split your cpu-intensive task among several Workstations/PC/Mac/etc. It includes support for POVRay and MandelGrid as usage examples.
EyesRay render a 3D scene with the raytracing algorithm. Some specifics points are: a scene loader, the support of transparency, avaibility to generate images (ppm format)...
The Graph Visualization Framework is a set of Java 2 packages that can
serve as a foundation for applications that manipulate or visualize graph structures. "Royere" is built on the GVF and includes XML
support, SVG output, pluggable layouts, editing.
A Java based molecular modeling program. Has support for generating movies by interpolating between given positions, interactive display and manipulation of atoms and bonds, and dynamic modeling of substance formation.
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ASSET is an open source Java application providing support to the modelling of maritime tactics. User-defined performance files can be used to replace the generic data used for ships, submarines, weapons, sensors, and helos.