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The neighbor list algorithm for a parallelepiped box in molecular dynamics simulations

  • Articles/Solid-State Mechanics
  • Published:
Chinese Science Bulletin

Abstract

In classic molecular dynamics (MD) simulations, the conventional Verlet table, cell linked list and many other techniques have been adopted to increase the computational efficiency. However, these methods are only applicable in cubic systems. In this work, the above techniques along with the metric-tensor method are extended to handle NP ensembles, so that MD simulations can be carried out under the most general loading conditions. In order to do so, a particular spatial Cartesian reference frame is proposed to determine the scaling matrix. Also, a combination method, taking the advantages of the improved Verlet table and cell linked list, is established to identify the neighbor atoms very quickly in a parallelepiped box. An example using Lennard-Jones potential is presented to verify the validity of the proposed algorithm.

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Author information

Authors and Affiliations

  1. Department of Astronautic Science and Mechanics, Harbin Institute of Technology, Harbin, 150001, China

    ZhiWei Cui & Yi Sun

  2. G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, 30332-0405, USA

    JianMin Qu

Authors
  1. ZhiWei Cui
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  2. Yi Sun
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  3. JianMin Qu
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Corresponding author

Correspondence to Yi Sun.

Additional information

Supported by the National Natural Science Foundation of China (Grant No. 10472028) and Excellent Youth Foundation of Heilongjiang Province

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Cui, Z., Sun, Y. & Qu, J. The neighbor list algorithm for a parallelepiped box in molecular dynamics simulations. Chin. Sci. Bull. 54, 1463–1469 (2009). https://doi.org/10.1007/s11434-009-0197-0

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  • DOI: https://doi.org/10.1007/s11434-009-0197-0

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