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A multilevel-skin neighbor list algorithm for molecular dynamics simulation
Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei
2018
Source PublicationCOMPUTER PHYSICS COMMUNICATIONS
ISSN0010-4655
Volume222Issue:00Pages:59
Abstract

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists. (C) 2017 Elsevier B.V. All rights reserved.

KeywordHigh Performance Computing Molecular Dynamics Simulation Neighbor-list-based Algorithm Searching Efficiency
SubtypeArticle
DOI10.1016/j.cpc.2017.09.017
Language英语
WOS IDWOS:000418969900005
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ipe.ac.cn/handle/122111/23467
Collection研究所(批量导入)
Corresponding AuthorGe, Wei
Recommended Citation
GB/T 7714
Zhang, Chenglong,Zhao, Mingcan,Hou, Chaofeng,et al. A multilevel-skin neighbor list algorithm for molecular dynamics simulation[J]. COMPUTER PHYSICS COMMUNICATIONS,2018,222(00):59.
APA Zhang, Chenglong,Zhao, Mingcan,Hou, Chaofeng,&Ge, Wei.(2018).A multilevel-skin neighbor list algorithm for molecular dynamics simulation.COMPUTER PHYSICS COMMUNICATIONS,222(00),59.
MLA Zhang, Chenglong,et al."A multilevel-skin neighbor list algorithm for molecular dynamics simulation".COMPUTER PHYSICS COMMUNICATIONS 222.00(2018):59.
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