An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities

摘要

We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5 x overall speedup and good scaling to large problem sizes and processor counts. (C) 2019 The Author(s). Published by Elsevier Inc.