Please use this identifier to cite or link to this item: https://doi.org/10.1016/j.cpc.2004.04.004
DC FieldValue
dc.titleImproved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method
dc.contributor.authorYao, Z.
dc.contributor.authorWang, J.-S.
dc.contributor.authorLiu, G.-R.
dc.contributor.authorCheng, M.
dc.date.accessioned2014-04-24T09:34:22Z
dc.date.available2014-04-24T09:34:22Z
dc.date.issued2004-08-01
dc.identifier.citationYao, Z., Wang, J.-S., Liu, G.-R., Cheng, M. (2004-08-01). Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method. Computer Physics Communications 161 (1-2) : 27-35. ScholarBank@NUS Repository. https://doi.org/10.1016/j.cpc.2004.04.004
dc.identifier.issn00104655
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/51435
dc.description.abstractAn improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition approach to accelerate the neighbor list construction speed, and data sorting method to lower the CPU data cache miss rate, as well as partial updating method to minimize the unnecessary reconstruction of the neighbor list. Both serial and parallel performance of molecular dynamics simulation are evaluated using the proposed algorithm and compared with those using conventional Verlet table and cell linked list algorithms. Results show that the new algorithm outperforms the conventional algorithms by a factor of 2∼3 in cases of both small and large number of atoms. © 2004 Elsevier B.V. All rights reserved.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1016/j.cpc.2004.04.004
dc.sourceScopus
dc.subjectCell linked list
dc.subjectMolecular dynamics
dc.subjectNeighbor list
dc.subjectVerlet table
dc.typeArticle
dc.contributor.departmentMECHANICAL ENGINEERING
dc.contributor.departmentSINGAPORE-MIT ALLIANCE
dc.contributor.departmentCOMPUTATIONAL SCIENCE
dc.description.doi10.1016/j.cpc.2004.04.004
dc.description.sourcetitleComputer Physics Communications
dc.description.volume161
dc.description.issue1-2
dc.description.page27-35
dc.description.codenCPHCB
dc.identifier.isiut000223043300003
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