In my Master's work I'm using NumPy and SciPy, which are Python packages to do very fast numerics, but there is indeed a lot of Fortran, and there's also a lot of Mathematica.
It's not completely related, but the idea of expressing complicated physics ideas in simpler code form has been handled in Scheme in the book Structure and Interpretation of Classical Mechanics, free to read from here:
http://mitpress.mit.edu/SICM/book.html
You might also look up the textbook
Computational Physics by J.K. Thijssen (full disclosure: I am working underneath this professor at the TU Delft), but it's not quite for your particular niche -- I don't think in my physics education proper I was ever really taught about chaos or bifurcation diagrams or solitons, except to mention that it existed.