THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND
Yıl: 2018 Cilt: 4 Sayı: 2 Sayfa Aralığı: 224 - 230 Metin Dili: İngilizce DOI: 10.22531/muglajsci.466173 İndeks Tarihi: 29-05-2019
THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND
Öz: Event-driven molecular dynamics (EDMD) is a special application of Molecular Dynamics (MD) derived from kinetic theory of gases. While classical solution of Navier-Stokes equations fails at high Knudsen (Kn) number flows, EDMD is valid on entire regime. Interaction potentials are considered discrete and exist only at the moment of impact. Hence, molecule trajectories are linear. Unlike the classical MD, this helps to simulate bigger systems. Molecular interactions, interaction times and partners can be predicted deterministically. Diatomic and polyatomic molecules are handled by an implemented energy relaxation scheme. Calculation of possible event times and determination of the earliest are the most timeconsuming steps of the simulation. In order to improve computational speed, a cell partitioning methodology and a priority queue structure are implemented in this study. The effect of the implementations on the performance is investigated and optimum simulation parameters are determined; when using PQ, number of cells must be greater than the number of molecules for maximum computational speed. Robustness assessments for the implementations are conducted with a realworld problem. Extreme density difference in confined geometries has vast usage in engineering and is also a good example of stress test because of its complex nature. This paper addresses the calculation of sound speed in a shock tube filled with a diatomic gas by using EDMD simulations. The robustness is validated since the results agrees perfectly with the theoretical values.
Anahtar Kelime: OLAY GÜDÜMLÜ MOLEKÜLER DİNAMİĞİN SES HIZI HESABINA DAYALI SAĞLAMLIK DEĞERLENDİRMESİ
Öz: Olay güdümlü moleküler dinamik (OGMD) gazların kinetik teorisinden türetilen moleküler dinamiğin (MD) özel bir uygulamasıdır. Navier-Stokes denklemlerinin klasik çözümü yüksek Knudsen (Kn) akışlarında başarısız olurken, OGMD tüm akış rejimi için geçerlidir. Etkileşim potansiyellerinin süreksiz ve sadece temas anında mevcut olduğu kabul edilir. Bu sayede molekül yörüngeleri doğrusaldır. Bu klasik MD’nin aksine büyük sistemlerin simülasyonunu mümkün kılar. Molekül etkileşimleri, etkileşim zamanları ve çiftleri deterministik olarak öngörülebilirdir. Diatomik ve poliatomik moleküller uyarlanan bir enerji gevşeme düzeni ile modellenir. Muhtemel olay zamanlarının hesabı ve en erken olanın seçimi simülasyonun en çok zaman alan adımlarıdır. Hesaplama hızını geliştirmek amacıyla bu çalışmada bir hücre bölümleme metodolojisi ve öncelik kuyruğu yapısı simülasyona uyarlanmıştır. Uyarlamaların performans üzerine etkileri incelenmiş ve optimum süreç parametreleri belirlenmiştir; öncelik kuyruğunun kullanılması durumunda maksimum hesaplama performansı için hücre sayısının molekül sayısından fazla olması gerekmektedir. Uyarlamaların sağlamlık değerlendirmesi gerçek bir problem ile yapılmıştır. Kapalı geometrilerdeki aşırı yoğunluk farkı mühendislikte geniş bir kullanım alanı bulmakla birlikte karmaşık doğasından dolayı stres testi için uygun bir örnektir. Bu çalışma OGMD simülasyonları kullanarak diatomik bir gaz ile doldurulmuş şok tüpünde ses hızının hesaplanmasını ele almaktadır. Sonuçların teorik değerlerle mükemmel olarak uyum göstermiş olması sağlamlığı doğrulamaktadır.
Anahtar Kelime: Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık
- M. Gad-el-Hak, “The Fluid Mechanics of Microdevices—The Freeman Scholar Lecture,” J. Fluids Eng., vol. 121, no. 1, p. 5, Mar. 1999.
- S. Chapman and T. G. Cowling, The Mathematical Theory of Non-uniform Gases: An Account of the Kinetic Theory of Viscosity, Thermal Conduction and Diffusion in Gases, 3rd ed. Cambridge University Press, 1970.
- J. J. Martin, Atmospheric reentry: an introduction to its science and engineering. Prentice-Hall, 1966.
- B. Alder and T. Wainwright, “Phase Transition for a Hard Sphere System,” J. Chem. Phys., vol. 27, no. 5, pp. 1208–1211, 1957.
- B. J. Alder and T. E. Wainwright, “Studies in molecular dynamics. I. General method,” J. Chem. Phys., vol. 31, no. 2, pp. 459–466, 1959.
- B. J. Alder and T. E. Wainwright, “Studies in molecular dynamics. II. Behavior of a small number of elastic spheres,” J. Chem. Phys., vol. 33, no. 5, pp. 1439–1451, 1960.
- G. A. Bird, Molecular Gas Dynamics and the Direct Simulation of Gas Flows. Oxford: Clarendon Press, 1994.
- W. Wagner, “A convergence proof for Bird’s direct simulation Monte Carlo method for the Boltzmann equation,” J. Stat. Phys., vol. 66, no. 3–4, pp. 1011– 1044, Feb. 1992.
- D. Rapaport, “The event scheduling problem in molecular dynamic simulation,” J. Comput. Phys., vol. 34, no. 2, pp. 184–201, Feb. 1980.
- W. T. Tang, R. S. M. Goh, and I. L.-J. Thng, “Ladder queue,” ACM Trans. Model. Comput. Simul., vol. 15, no. 3, pp. 175–204, Jul. 2005.
- I. Kandemir, “A multicell molecular dynamics method,” Case Western Reserve University, Ann Arbor, 1999.
- V. R. Akkaya, “Fiziksel ve kimyasal moleküler gaz dinamiğisimülasyonu,”GebzeTechnical University, 2015.
- A. Donev, A. L. Garcia, and B. J. Alder, “Stochastic Event-Driven Molecular Dynamics,” J. Comput. Phys., vol. 227, no. 4, pp. 2644–2665, Feb. 2008.
- C. Borgnakke and P. S. Larsen, “Statistical Collision Model for Monte Carlo Simulation of Polyatomic Gas Mixture,” J. Comput. Phys., vol. 18, no. 4, pp.405–420, 1975.
- G. Paul, “A Complexity O(1) priority queue for event driven molecular dynamics simulations,” J. Comput. Phys., vol. 221, no. 2, pp. 615–625, Feb. 2007.
- M. Marín and P. Cordero, “An empirical assessment of priority queues in event-driven molecular dynamics simulation,” Comput. Phys. Commun., vol. 92, no. 2–3, pp. 214–224, Dec. 1995.
- M. Marín, “Event-driven hard-particle molecular dynamics using bulk-synchronous parallelism,” Comput. Phys. Commun., vol. 102, no. 1–3, pp. 81– 96, May 1997.
- A. T. Krantz, “Analysis of an efficient algorithm for the hard-sphere problem,” ACM Trans. Model. Comput. Simul., vol. 6, no. 3, pp. 185–209, Jul. 1996.
- R. Brown, “Calendar queues: a fast 0(1) priority queue implementation for the simulation event set problem,” Communications of the ACM, vol. 31. pp. 1220–1227, 1988.
| APA | Akkaya V, kandemir i (2018). THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. , 224 - 230. 10.22531/muglajsci.466173 |
| Chicago | Akkaya Volkan Ramazan,kandemir ilyas THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. (2018): 224 - 230. 10.22531/muglajsci.466173 |
| MLA | Akkaya Volkan Ramazan,kandemir ilyas THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. , 2018, ss.224 - 230. 10.22531/muglajsci.466173 |
| AMA | Akkaya V,kandemir i THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. . 2018; 224 - 230. 10.22531/muglajsci.466173 |
| Vancouver | Akkaya V,kandemir i THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. . 2018; 224 - 230. 10.22531/muglajsci.466173 |
| IEEE | Akkaya V,kandemir i "THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND." , ss.224 - 230, 2018. 10.22531/muglajsci.466173 |
| ISNAD | Akkaya, Volkan Ramazan - kandemir, ilyas. "THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND". (2018), 224-230. https://doi.org/10.22531/muglajsci.466173 |
| APA | Akkaya V, kandemir i (2018). THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. Mugla Journal of Science and Technology, 4(2), 224 - 230. 10.22531/muglajsci.466173 |
| Chicago | Akkaya Volkan Ramazan,kandemir ilyas THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. Mugla Journal of Science and Technology 4, no.2 (2018): 224 - 230. 10.22531/muglajsci.466173 |
| MLA | Akkaya Volkan Ramazan,kandemir ilyas THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. Mugla Journal of Science and Technology, vol.4, no.2, 2018, ss.224 - 230. 10.22531/muglajsci.466173 |
| AMA | Akkaya V,kandemir i THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. Mugla Journal of Science and Technology. 2018; 4(2): 224 - 230. 10.22531/muglajsci.466173 |
| Vancouver | Akkaya V,kandemir i THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND. Mugla Journal of Science and Technology. 2018; 4(2): 224 - 230. 10.22531/muglajsci.466173 |
| IEEE | Akkaya V,kandemir i "THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND." Mugla Journal of Science and Technology, 4, ss.224 - 230, 2018. 10.22531/muglajsci.466173 |
| ISNAD | Akkaya, Volkan Ramazan - kandemir, ilyas. "THE ROBUSTNESS ASSESSMENT FOR EVENT DRIVEN MOLECULAR DYNAMICS BY CALCULATING SPEED OF SOUND". Mugla Journal of Science and Technology 4/2 (2018), 224-230. https://doi.org/10.22531/muglajsci.466173 |
