LAMMPS is an open-source software package that simulates classical molecular dynamics. As it supports many energy models and simulation options, its versatility has made it a popular choice. It was first developed at Sandia National Laboratories to use large-scale parallel computation.
An article addressing thread and task parallelism. This article can be used to optimize framework methodology. Written by Andrew Binstock--Principal Analyst at Pacific Data Works LLC and lead author of "Practical Algorithms for Programmers."
FreeFEM++ is a package that targeted for researchers who needs a powerful tool for solving partial differential equations.