Distributed 2-D Molecular Dynamics Simulation on Networked Workstations and Multiprocessors

摘要

In the paper we present a parallel program for molecular dynamics simulation of 2-D Lennard-Jones systems with large number of particles (10~6+). The parallel algorithm is based on geometric decomposition and it was implemented on networked workstations and on the CONVEX Exemplar SPP 1000 and SPP 1200 under PVM. The program was written in C language and optimised for the execution time and memory requirements. The computational complexity is reduced by use of distributed neighbor (Verlet) and link (Hockney) lists. On heterogeneous or loaded networks load balance is obtained by and adaptive repartitioning of the computational box during a simulation run. The load balancing procedure is based on the assumption that time of computation scales linearly with the number of particles. Sample results of a simulation of a flow around a cylinder are reported.