Extrema, originally developed in the fields of nuclear and particle physics, is a powerful visualization and data analysis tool that enables researchers to quickly distill their large, complex data sets into meaningful information. Its flexibility, sophistication, and power allow you to easily develop your own commands and create highly customized graphs.
Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results (populations and reaction counts) in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. Solvers are implemented as command line executables, which makes it easy to launch batch jobs and simplifies the process of adding new solvers. Solvers include Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, and Hybrid direct/tau-leaping.
MBDyn features the integrated multidisciplinary analysis of multi-body, multi-physics systems, including nonlinear mechanics of rigid and flexible constrained bodies, smart materials, electric networks, active control, hydraulic networks, and essential fixed-wing and rotorcraft aerodynamics. It allows you to simulate the behavior of heterogeneous mechanical, aero-servo-elastic systems based on first principles equations. It is being actively developed and used in the aerospace and automotive fields for dynamics analysis and simulation of complex systems. The extension of available analysis domains to new models, and new analysis domains, is planned and problem-driven.
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.