Go to the 'scripts' directory and find the 'optimise.py' file, it reads and loads a TPD (ToPy Problem Definition) file.
You can (obviously) change optimise.py to suit your needs.
The 'mbb_beam' directory is probably the best place to start experimenting.
You have to copy the 'optimise.py' type files to each example directory. Under Linux (and I suspect OS X too) you can make use of symbolic links - I don't know if there's a similar mechanism in Windows to accomplish this.
In a terminal/console, type:
python optimise.py <filename>.tpd
in the relevant example directory.
All 3D animations were created with the help of ParaView 3 and ImageMagick. In ParaView, save the animation as a sequence of PNGs, or directly as an AVI (produces larger files). gifsicle is another option to produce GIFs from stills.
I found the least painful way to get animations to be via convert (or gifsicle).
Create with: ImageMagick's convert, a command-line tool.
View with: Just about any web browser should display GIFs without any problem.
A typical command:
convert -delay 35 *.png anim.gif
This will convert all the PNGs in the folder into a single GIF. Job done!