Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
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DOI：
10.1557/jmr.2017.456
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发表时间：
2018-04-13
影响因子：
2.7
通讯作者：
Voter, Arthur F.
中科院分区：
文献类型：
--
作者：
Perez, Danny;Huang, Rao;Voter, Arthur F.
分子动力学是计算材料科学中应用最广泛的技术之一。通过提供完全解析的轨迹，它允许对静态、热力学和动力学属性进行自然描述。阻碍MD使用的一个主要障碍是，即使在使用大规模并行计算机时，可以直接模拟的时间尺度也非常有限。在这项研究中，我们比较了两种时间并行化方法，并行副本动力学(ParRep)和并行轨迹拼接(ParSplice)，这两种方法是专门为稀有事件系统设计的，利用并行计算资源来解决这一问题，并通过模拟小无序铂纳米粒子的弛豫，对两种方法的性能进行了比较分析。结果表明，在轨迹在构型空间的某一区域内长时间停留，但在该区域内发生快速结构转变的常见情况下，ParSplice的性能明显优于ParRep。
Molecular dynamics (MD) is one of the most widely used techniques in computational materials science. By providing fully resolved trajectories, it allows for a natural description of static, thermodynamic, and kinetic properties. A major hurdle that has hampered the use of MD is the fact that the timescales that can be directly simulated are very limited, even when using massively parallel computers. In this study, we compare two time-parallelization approaches, parallel replica dynamics (ParRep) and parallel trajectory splicing (ParSplice), that were specifically designed to address this issue for rare event systems by leveraging parallel computing resources.Using simulations of the relaxation of small disordered platinum nanoparticles, a comparative performance analysis of the two methods is presented. The results show that ParSplice can significantly outperform ParRep in the common case where the trajectory remains trapped for a long time within a region of configuration space but makes rapid structural transitions within this region.