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PARALLELIZATION OF A MOLECULAR DYNAMICS SIMULATION OF AN ION-SURFACE COLLISION SYSTEM: Ar–Ni(100)

Author

Listed:
  • MURAT ATİŞ

    (Department of Physics, Kırıkkale University, Yahşihan, 71451, Kırıkkale, Turkey)

  • CEM ÖZDOĞAN

    (Department of Computer Engineering, Çankaya University, Balgat, 06530, Ankara, Turkey)

  • ZİYA B. GÜVENÇ

    (Department of Electronic and Communication Engineering, Çankaya University, Balgat, 06530, Ankara, Turkey)

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 theAr–Ni(100)collision system and calculated physical quantities are presented.

Suggested Citation

  • Murat Ati̇ş & Cem Özdoğan & Zi̇ya B. Güvenç, 2005. "PARALLELIZATION OF A MOLECULAR DYNAMICS SIMULATION OF AN ION-SURFACE COLLISION SYSTEM: Ar–Ni(100)," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 16(06), pages 969-990.
    • Handle: RePEc:wsi:ijmpcx:v:16:y:2005:i:06:n:s0129183105007649
    DOI: 10.1142/S0129183105007649
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