AN APPROACH TO DATA PARALLEL MOLECULAR DYNAMICS FOR LIQUIDS

Fredrik Hedman and Aatto Laaksonen
Additional contact information
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

International Journal of Modern Physics C (IJMPC), 1993, vol. 04, issue 01, 41-48

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.

Date: 1993
References: Add references at CitEc
Citations:

Downloads: (external link)
http://www.worldscientific.com/doi/abs/10.1142/S0129183193000069
Access to full text is restricted to subscribers

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:wsi:ijmpcx:v:04:y:1993:i:01:n:s0129183193000069

Ordering information: This journal article can be ordered from

DOI: 10.1142/S0129183193000069

Access Statistics for this article

International Journal of Modern Physics C (IJMPC) is currently edited by H. J. Herrmann

More articles in International Journal of Modern Physics C (IJMPC) from World Scientific Publishing Co. Pte. Ltd.
Bibliographic data for series maintained by Tai Tone Lim ().