Journal of Frontiers of Computer Science and Technology ›› 2017, Vol. 11 ›› Issue (3): 355-364.DOI: 10.3778/j.issn.1673-9418.1512050

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Comparison of Large-Scale Molecular Dynamics Software for Materials Microstucture Evolution

NIE Ningming1+, HU Changjun2, ZHANG Yunquan3, HE Xinfu4, ZHANG Boyao1, LI Shigang3   

  1. 1. Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
    2. School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
    3. Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
    4. China Institute of Atomic Energy, Beijing 102413, China
  • Online:2017-03-01 Published:2017-03-09



  1. 1. 中国科学院 计算机网络信息中心,北京 100190
    2. 北京科技大学 计算机与通信工程学院,北京 100083
    3. 中国科学院 计算技术研究所,北京 100190
    4. 中国原子能科学研究院,北京 102413

Abstract:  Molecular dynamics simulation is an important tool for studying materials microstructure evolution under radiation effects. This paper introduces four kinds of mainstream large-scale molecular dynamics open source software for materials computing, LAMMPS, Ls1-MarDyn, IMD and CoMD, and compares and analyzes data structures, computational methods, parallel decomposition methods and atomic storage, etc. By the design examples, this paper tests computational efficiency, parallel performance and memory usage. A new idea of less memory-used data structure design for the single crystal is prepared for the simulation characteristics of metal materials evolution under irradiation defects. It provides the basis for subsequent research to realize large temporal and spatial scale molecular dynamics simulation.

Key words: molecular dynamics, data structure, material irradiation damage

摘要: 分子动力学模拟是研究材料辐照效应下微观结构演化的重要工具。对4款主流材料计算大规模分子动力学开源软件LAMMPS、Ls1-MarDyn、IMD和CoMD进行了详细的介绍,从数据结构、计算方法、并行分解方式、原子存储等多个方面进行了横向分析比较。通过设计算例测试了各软件的计算效率、并行性能和内存使用情况。针对压力容器关键材料辐照缺陷演化计算特点,提出了设计节省存储空间的面向单晶的新型数据结构的设想,为后续实现大时空尺度分子动力学模拟研究提供了研究基础。

关键词: 分子动力学模拟, 数据结构, 材料辐照损伤