Performance analysis of parallel algorithms in physics simulation for molecular dynamics simulation liquid metals solidification processes

摘要

In this work, a parallel arithmetic program for the MD (molecular dynamics) simulation study of a large-sized system is proposed and reformed, based on the previous program with PVM (Parallel Virtual Machine) model applied in a small-sized system for liquid metals. Our methodology is combined with the MPI (message passing interface) and OpenMP (Open Multiple Processing) programming model using the spatial domain decomposition method, conquering the problems occurred in PVM model and enlarging the scale of simulated system. Comparing with the previous small-sized system consisting of 50,000-100,000 atoms, the large-sized system is consist of 5,000,000-10,000,000 atoms and the simulation results are more closely to the real situation of the simulated system. In this paper, the performance of parallel program using MPI + OpenMP model is analyzed, showing better speedup, parallel efficiency, and scalability. Finally, we adopt many physical evaluation methods to verify the validity of the simulation results, including pair distribution function, bond-type index analysis, atomic clusters analysis and visualizing analysis. From these physical results, it is clear that the simulation results are in good agreement with the experimental results, which confirm the correctness of the program in simulation. (C) 2014 Elsevier Ltd. All rights reserved.