Smoothed molecular dynamics for large step time integration
Smoothed molecular dynamics for large step time integration
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DOI：
10.3970/cmes.2007.020.177
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发表时间：
2007-08
影响因子：
2.4
通讯作者：
Yan Liu;Xiong Zhang;K. Sze;Min Wang
中科院分区：
文献类型：
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作者：
Yan Liu;Xiong Zhang;K. Sze;Min Wang
在分子模拟中，低频模式的频率比高频模式的频率低许多数量级。与低频模式的振幅相比，高频模式的振幅通常可以忽略不计，因此最不受关注。如最高频率模式的周期所指示的，稳定时间积分的临界时间步长可以通过抑制可忽略的高频模式而显著增加，而解决方案几乎保持不变。在此基础上，提出了一种平滑分子动力学（SMD）方法，通过使用规则的背景网格来消除动力学系统中的高频模式。通过控制网格尺寸，可以相对于常规分子动力学（MD）的临界时间步长显著增加临界时间步长。SMD的实现与传统MD非常相似。在SMD中可以采用常规MD中使用的任何时间积分器和原子间相互作用势。MD和SMD方法的耦合进行了简要的研究，和MD和SMD方法之间的相似性，使一个简单而简洁的耦合。一维原子链和三维单晶拉压问题的算例表明，本文提出的SMD方法与传统的MD方法计算结果相近，但前者的时间步长比后者高一个数量级。通过一个裂纹单晶的拉伸实验验证了耦合方法的有效性，耦合方法可以准确地捕捉到屈服点。关键词：分子动力学，临界时间1清华大学工程力学系，北京100084。中国2香港大学机械工程系，香港特别行政区，中国。中国步，物质点法，背景网格。
In molecular simulations, the frequencies of the low-frequency modes are many orders of magnitude lower than those of the highfrequency modes. Compared with the amplitudes of the low-frequency modes, the amplitudes of the high-frequency modes are often negligible and, thus, least interesting. As dictated by the period of the highest frequency mode, the critical time step for stable time integration can be significantly increased by suppressing the negligible high-frequency modes yet the solution remains virtually intact. In this light, a smoothed molecular dynamics (SMD) approach is proposed to eliminate the high-frequency modes from the dynamical system through the use of a regular background grid. By manipulating the grid size, it is possible to increase the critical time step significantly with respect to that of the conventional molecular dynamics (MD). The implementation of SMD is very similar to the conventional MD. Any time integrators and inter-atomic potentials used in the conventional MD can be equally adopted in SMD. The coupling of MD and SMD methods is briefly investigated, and the similarity between MD and SMD methods enables a simple and concise coupling. Examples on 1D atom chains and 3D tension/compression of single crystal show that the proposed SMD method and the conventional MD method yield close results yet the time step of the former can be one order higher than that of the latter. Tension of a cracked single crystal is examined to verify the coupling method, and the yield point can be captured precisely by the coupling method. Keyword: Molecular dynamics, Critical time 1 Department of Engineering Mechanics, Tsinghua University, Beijing 100084, P. R. China 2 Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, P. R. China step, Material point method, Background grid.