@article{Atis2005,
Author = {Murat Atiş and Cem Özdoğan and Ziya Burhanettin Güvenç},
Title = {Parallelization of a molecular dynamics simulation of an ion-surface
   collision},
Journal = {International Journal of Modern Physics C},
Volume = {16},
Number = {6},
Month = {JUN},
Publisher = {WORLD SCIENTIFIC PUBL CO PTE LTD},
ISSN = {0129-1831},
DOI = {10.1142/S0129183105007649},
Pages = {969-990},
Keywords = {parallel; molecular dynamics; linear scaling; ion-surface collision;
   sputtering; PVM},
Keywords-Plus = {DOMAIN DECOMPOSITION; SPUTTERING YIELDS; COMPUTER; AR; CU; BOMBARDMENT;
   PROCESSORS; POTENTIALS; ALGORITHMS; DEPOSITION},
Year = {2005},
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.},
}