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

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-...

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Bibliographic Details
Published in:Chinese science bulletin 2009-05, Vol.54 (9), p.1463-1469
Main Authors: Cui, ZhiWei, Sun, Yi, Qu, JianMin
Format: Article
Language:English
Subjects:
Articles/Solid-State Mechanics
Chemistry/Food Science
Earth Sciences
Engineering
Humanities and Social Sciences
Life Sciences
multidisciplinary
Physics
Science
Science (multidisciplinary)
三次系统
分子动力学模拟
度量张量
计算效率
负载条件
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Summary: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.
ISSN:1001-6538
2095-9273
1861-9541
2095-9281
DOI:10.1007/s11434-009-0197-0