View in EDS

Pseudo-Verlet lists: a new, compact neighbour list representation.

Saved in:
Bibliographic Details
Title: Pseudo-Verlet lists: a new, compact neighbour list representation.
Authors: Gonnet, Pedro1
Source: Molecular Simulation. Aug2013, Vol. 39 Issue 9, p721-727. 7p.
Subjects: Molecular dynamics, Simulation methods & models, Cache memory, Nonbonded molecular interactions, Bandwidths, Graphics processing units, Geometry
Abstract: Verlet lists, or neighbour lists, are a popular device to speed up the computation of non-bonded interactions in molecular dynamics and other particle-based simulations, in which a list of interacting particles for a given geometry is computed once and reused over several time steps until the geometry changes significantly. The size of the Verlet list is generallyindices in the range, whereNis the total number of particles, ρNis the particle number density andrcandrsare the cutoff and skin distances, respectively. Due to their memory requirements, Verlet lists are not always an optimal choice on multi-core or graphics processing unit systems in which the memory bandwidth per core is limited. This paper introducespseudo-Verlet lists, an alternative neighbour list representation which requires only 13Nindices in the range, thus requiring less storage, and resulting in better cache reuse. [ABSTRACT FROM AUTHOR]
Copyright of Molecular Simulation is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
FullText Text:
  Availability: 0
Header DbId: egs
DbLabel: Engineering Source
An: 89100771
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Pseudo-Verlet lists: a new, compact neighbour list representation.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Gonnet%2C+Pedro%22">Gonnet, Pedro</searchLink><relatesTo>1</relatesTo>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22Molecular+Simulation%22">Molecular Simulation</searchLink>. Aug2013, Vol. 39 Issue 9, p721-727. 7p.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Cache+memory%22">Cache memory</searchLink><br /><searchLink fieldCode="DE" term="%22Nonbonded+molecular+interactions%22">Nonbonded molecular interactions</searchLink><br /><searchLink fieldCode="DE" term="%22Bandwidths%22">Bandwidths</searchLink><br /><searchLink fieldCode="DE" term="%22Graphics+processing+units%22">Graphics processing units</searchLink><br /><searchLink fieldCode="DE" term="%22Geometry%22">Geometry</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Verlet lists, or neighbour lists, are a popular device to speed up the computation of non-bonded interactions in molecular dynamics and other particle-based simulations, in which a list of interacting particles for a given geometry is computed once and reused over several time steps until the geometry changes significantly. The size of the Verlet list is generallyindices in the range, whereNis the total number of particles, ρNis the particle number density andrcandrsare the cutoff and skin distances, respectively. Due to their memory requirements, Verlet lists are not always an optimal choice on multi-core or graphics processing unit systems in which the memory bandwidth per core is limited. This paper introducespseudo-Verlet lists, an alternative neighbour list representation which requires only 13Nindices in the range, thus requiring less storage, and resulting in better cache reuse. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Molecular Simulation is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=89100771
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1080/08927022.2012.762097
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 7
        StartPage: 721
    Subjects:
      – SubjectFull: Molecular dynamics
        Type: general
      – SubjectFull: Simulation methods & models
        Type: general
      – SubjectFull: Cache memory
        Type: general
      – SubjectFull: Nonbonded molecular interactions
        Type: general
      – SubjectFull: Bandwidths
        Type: general
      – SubjectFull: Graphics processing units
        Type: general
      – SubjectFull: Geometry
        Type: general
    Titles:
      – TitleFull: Pseudo-Verlet lists: a new, compact neighbour list representation.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Gonnet, Pedro
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 08
              Text: Aug2013
              Type: published
              Y: 2013
          Identifiers:
            – Type: issn-print
              Value: 08927022
          Numbering:
            – Type: volume
              Value: 39
            – Type: issue
              Value: 9
          Titles:
            – TitleFull: Molecular Simulation
              Type: main
ResultId 1