Atomsmith is a really cool program, but doesn't seem to work for everyone. A very computer-savvy student could probably contact the authors and help to de-bug it for multiple platforms. It really is a program that should be used in every science class.
Since many of my students have had problems with it, and my non-student readers don't have access to the program, I recorded a screencast of some of the important parts of the summer assignment I wrote. Here it is:
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