Parallel molecular dynamics simulations for short-ranged many-body potentials

Abstract

A new method is described that permits the efficient execution of parallel molecular dynamics simulations for irregular problems with several thousands of atoms on Single-Instruction Multiple-Data computers. The approach is based on a data-parallel atomic decomposition scheme and has overall time-complexity O(N) , where N is the size of the system. The method has been implemented on a MasPar MP-1 computer and was found to obey theoretical timing estimates. The methodology has wide applicability and can be ported to other architectures in a straightforward manner.