Parallel molecular dynamics for short-short-ranged many-body potentials using MPI

摘要

In this paper we describe an algorithm to perform molecular dynamics (MD) simulations on MIMD parallel computers using Message Passing interface (MPI). The scheme for performing the geometrical decomposition and communication between processes is presented with timing comparison made between several parallel platforms. The modules needed to perform the MD calculations are independent of the modules that perform the communication between processors. That is, there are no MPI function calls within the MD calculation modules. As a result, the code used to perform the communication between processors can be used for a wide range of many-body potentials provided the potentials use a cut-off scheme to limit the range of the interactions.