Open DESIRE is a modeling/simulation language for dynamic systems and neural networks, a runtime compiler, and an experiment-protocol script for simulation studies. It supports up to 40,000 differential equations or neural networks, in scalar and/or vector form. It also supports very fast Monte Carlo studies and complex frequency-response plots.
Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems. It supports distributed-memory parallel simulations, nonlinear, anisotropic, and dispersive media, PML absorbing boundaries, and 1D/2D/3D and cylindrical problems. It is completely scriptable from either C++ or a Scheme (GNU Guile) interface.
pyFormex is a tool for generating, manipulating, and transforming large geometrical models of 3D structures by sequences of mathematical transformations. Thanks to a powerful (Python based) scripting language, it is very well suited for the automated design of spatial frame structures. It provides a wide range of operations on surface meshes, like STL type triangulated surfaces. There are provisions to import medical scan images. pyFormex can also be used as a pre- and post-processor for Finite Element analysis programs. Finally, it might be used just for creating some nice graphics.