Clusters is a program that has been used to model energy transfer in crystal lattices. The source code is available here. Notes: The Technical Details are just that - there is little additional exposition included, but they should be self-explanatory. Most of the files exist to support the interface, and much of the main code is enumeration of cases. The code is Java version J2SE 5.0. Author unless otherwise stated: Alastair Douglas. All rights reserved.
Technical Details (PDF)

Executable JAR file
(If you have have Java installed on your system, you can download and double-click this to run the program.)