IDEAS home Printed from https://ideas.repec.org/a/wsi/ijmpcx/v04y1993i01ns0129183193000069.html
   My bibliography  Save this article

An Approach To Data Parallel Molecular Dynamics For Liquids

Author

Listed:
  • FREDRIK HEDMAN

    (Center for Parallel Computers (PDC), Royal Institute of Technology, S-100 44 Stockholm, Sweden)

  • AATTO LAAKSONEN

    (Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden)

Abstract

An efficient approach to large scale data parallel short-range molecular dynamics for liquids is presented. The method is based on the coarse-grained cell method in which the simulation cell is decomposed into equally sized subcells, with the shortest side being larger than the cut-off radius. To avoid a large fraction of the nonproductive calculations we develop a geometric sorting procedure based on particle distances to subcell boundaries. Due to particle migration, the contents of the subcells need to be updated. This is done with a method based only on nearest-neighbor communications. Special "null-particles" are introduced, which act as buffers during periodic updates and allow for a globally uniform algorithm during the force calculations. The method should be easy to implement on most massively parallel computers of SIMD or MIMD type. We have implemented our code in CM Fortran on an 8K CM200. Communication cost is around 7% of the total cpu time. The overall speed for one million particles is approximately5.9μsper MD time step and per particle and5.5μsfor five million particles.

Suggested Citation

  • Fredrik Hedman & Aatto Laaksonen, 1993. "An Approach To Data Parallel Molecular Dynamics For Liquids," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 4(01), pages 41-48.
    • Handle: RePEc:wsi:ijmpcx:v:04:y:1993:i:01:n:s0129183193000069
    DOI: 10.1142/S0129183193000069
    as

    Download full text from publisher

    File URL: http://www.worldscientific.com/doi/abs/10.1142/S0129183193000069
    Download Restriction: Access to full text is restricted to subscribers
    File URL: https://libkey.io/10.1142/S0129183193000069?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:wsi:ijmpcx:v:04:y:1993:i:01:n:s0129183193000069. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Tai Tone Lim (email available below). General contact details of provider: http://www.worldscinet.com/ijmpc/ijmpc.shtml .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.