Parallelization of a molecular dynamics simulation of an ion-surface collision


ATİŞ M., Ozdogan C., Guvenc Z.

INTERNATIONAL JOURNAL OF MODERN PHYSICS C, vol.16, no.6, pp.969-990, 2005 (Journal Indexed in SCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 16 Issue: 6
  • Publication Date: 2005
  • Doi Number: 10.1142/s0129183105007649
  • Title of Journal : INTERNATIONAL JOURNAL OF MODERN PHYSICS C
  • Page Numbers: pp.969-990

Abstract

Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar-Ni(100) collision system and calculated physical quantities are presented.