Efficient molecular dynamics simulations with many-body potentials on graphics processing units
文献类型：期刊论文
| 作者 | Fan, Zheyong1,2,3; Chen, Wei4; Vierimaa, Ville2,3; Harju, Ari2,3 |
| 刊名 | Computer physics communications
 |
| 出版日期 | 2017-09-01 |
| 卷号 | 218页码:10-16 |
| 关键词 | Molecular dynamics simulation Many-body potential Tersoff potential Stillinger-weber potential Graphics processing units Virial stress Heat current |
| ISSN号 | 0010-4655 |
| DOI | 10.1016/j.cpc.2017.05.003 |
| 通讯作者 | Fan, zheyong(brucenju@gmail.com) ; Chen, wei(weichen@cnic.cn) |
| 英文摘要 | Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. however, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. in the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a cuda kernel. in this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (fan et al., 2015). in our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. we discuss the formulations and algorithms and evaluate their performance. a new open-source code, gpumd, is developed based on the proposed formulations. for the tersoff many-body potential, the double precision performance of gpumd using a tesla k40 card is equivalent to that of the lammps (large-scale atomic/molecular massively parallel simulator) molecular dynamics code running with about 100 cpu cores (intel xeon cpu x5670 @ 2.93 ghz). (c) 2017 elsevier b.v. all rights reserved. |
| WOS关键词 | THERMAL-CONDUCTIVITY ; PERFORMANCE ; GPU ; ORDER ; IMPLEMENTATION ; SYSTEMS |
| WOS研究方向 | Computer Science ; Physics |
| WOS类目 | Computer Science, Interdisciplinary Applications ; Physics, Mathematical |
| 语种 | 英语 |
| WOS记录号 | WOS:000404204800002 |
| 出版者 | ELSEVIER SCIENCE BV |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2374218 |
| 专题 | 计算机网络信息中心 |
| 通讯作者 | Fan, Zheyong; Chen, Wei |
| 作者单位 | 1.Bohai Univ, Sch Math & Phys, Jinzhou, Peoples R China 2.Aalto Univ, COMP Ctr Excellence, Helsinki, Finland 3.Aalto Univ, Dept Appl Phys, Helsinki Inst Phys, Helsinki, Finland 4.Chinese Acad Sci, Comp Network Informat Ctr, POB 349, Beijing 100190, Peoples R China |
| 推荐引用方式 GB/T 7714 | Fan, Zheyong,Chen, Wei,Vierimaa, Ville,et al. Efficient molecular dynamics simulations with many-body potentials on graphics processing units[J]. Computer physics communications,2017,218:10-16. |
| APA | Fan, Zheyong,Chen, Wei,Vierimaa, Ville,&Harju, Ari.(2017).Efficient molecular dynamics simulations with many-body potentials on graphics processing units.Computer physics communications,218,10-16. |
| MLA | Fan, Zheyong,et al."Efficient molecular dynamics simulations with many-body potentials on graphics processing units".Computer physics communications 218(2017):10-16. |
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