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.
Eduardo H. M. Cruz, Matheus S. Serpa, Arthur M. Krause, Philippe O. A. Navaux
Apply the concepts of parallelism and distributed memory computing to your code to improve software performance. This paper expands on concepts discussed in Part 1, to consider parallelism, both vectorization (single instruction multiple data SIMD) as well as shared memory parallelism (threading), and distributed memory computing.
This article focuses on the steps to improve software performance with vectorization. Included are examples of full applications along with some simpler cases to illustrate the steps to vectorization.