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Smoothed Molecular Dynamics for Large Step Time Integration

Yan Liu1, Xiong Zhang1, K. Y. Sze2, Min Wang1

Department of Engineering Mechanics, Tsinghua University, Beijing 100084, P. R. China
Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, P. R. China

Computer Modeling in Engineering & Sciences 2007, 20(3), 177-192.


In molecular simulations, the frequencies of the low-frequency modes are many orders of magnitude lower than those of the high-frequency 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.


Cite This Article

Liu, Y., Zhang, X., Sze, K. Y., Wang, M. (2007). Smoothed Molecular Dynamics for Large Step Time Integration. CMES-Computer Modeling in Engineering & Sciences, 20(3), 177–192.

This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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