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    Parallelization of a molecular dynamics simulation of an ion-surface collision
    (World Scientific Publ Co Pte Ltd, 2005) Atiş, Murat; Özdoğan, Cem; Güvenç, Ziya B.
    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.
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    Öğe
    Structure and Energetic of Bn (n = 2–12) Clusters: Electronic Structure Calculations
    (Wiley, 2007) Atis, Murat; Özdoğan, Cem; Güvenç, Ziya B.
    The electronic and geometric structures, total and binding energies, first and second energy differences, harmonic frequencies, point symmetries, and highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps of small and neutral B-n (n = 2-12) clusters have been investigated using density functional theory (DFT), B3LYP with 6-311 + + G(d,p) basis set. Linear, planar, convex, quasi-planar, three-dimensional (3D) cage, and open-cage structures have been found. None of the lowest energy structures and their isomers has an inner atom; i.e., all the atoms are positioned at the surface. Within this size range, the planar and quasi-planar (convex) structures have the lowest energies. The first and the second energy differences are used to obtain the most stable sizes. A simple growth path is also discussed with the studied sizes and isomers. The results have been compared with previously available theoretical and experimental works. (C) 2006 Wiley Periodicals, Inc.