分子动力学模拟的优化与并行研究  

Research of Optimization and Parallelization for Molecular Dynamics Simulation

作　　者：张勤勇[1] 蒋洪川[2] 刘翠华[1] 

机构地区：[1]西华大学材料学院,四川成都610039 [2]电子科技大学微电子与固体电子学院,四川成都610054

出　　处：《计算机应用研究》2005年第8期84-85,91,共3页Application Research of Computers

摘　　要：分析讨论了分子动力学模拟的算法特征和计算特点,对串行程序作了优化,并使之适合于作并行化。对模拟体系使用区域分解的方法,在计算节点间保留了部分重叠区域,采用基于消息传递的MPI设计平台,在可扩展机群上实现了并行化,获得了90%以上的并行效率。Analyzes the algorithmic character of molecular dynamics simulation, and optimizes the serial program. In the task decompose for parallelization, spatial decomposition method is adopted, and part of area is keeping as overlap in neighbor subarea. On the basis of the message passing parallel programming platform MPI, and on the network of workstation, parallelization is implemented. In the parallel environment, the parallel efficiency is above 90%.

关 键 词：分子动力学模拟 优化 并行 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构]