Implementation properties of many-body potentials on heteroheneous computing systems
Matematičeskoe modelirovanie, Tome 25 (2013) no. 10, pp. 123-136.

Voir la notice de l'article provenant de la source Math-Net.Ru

One way to improve the performance of atomistic modeling algorithms is to transform them for running on heterogeneous computing systems that combine the CPU and GPU. Adequate calculation of the mechanical and transport properties of nanostructures using many-body interatomic potentials require significantly more processing power. The article describes the features of the implementation of GPU algorithm for calculating many-body Tersoff and embedded atom potential by means of the OpenCL technology. The performance of different algorithms for GPU computing is compared.
Keywords: general purpose computation, graphics processing units, OpenCL, many-body interatomic potentials, Tersoff potential, embedded-atom potential.
@article{MM_2013_25_10_a9,
     author = {A. A. Knizhnik and A. S. Minkin and B. V. Potapkin},
     title = {Implementation properties of many-body potentials on heteroheneous computing systems},
     journal = {Matemati\v{c}eskoe modelirovanie},
     pages = {123--136},
     publisher = {mathdoc},
     volume = {25},
     number = {10},
     year = {2013},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MM_2013_25_10_a9/}
}
TY  - JOUR
AU  - A. A. Knizhnik
AU  - A. S. Minkin
AU  - B. V. Potapkin
TI  - Implementation properties of many-body potentials on heteroheneous computing systems
JO  - Matematičeskoe modelirovanie
PY  - 2013
SP  - 123
EP  - 136
VL  - 25
IS  - 10
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MM_2013_25_10_a9/
LA  - ru
ID  - MM_2013_25_10_a9
ER  - 
%0 Journal Article
%A A. A. Knizhnik
%A A. S. Minkin
%A B. V. Potapkin
%T Implementation properties of many-body potentials on heteroheneous computing systems
%J Matematičeskoe modelirovanie
%D 2013
%P 123-136
%V 25
%N 10
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MM_2013_25_10_a9/
%G ru
%F MM_2013_25_10_a9
A. A. Knizhnik; A. S. Minkin; B. V. Potapkin. Implementation properties of many-body potentials on heteroheneous computing systems. Matematičeskoe modelirovanie, Tome 25 (2013) no. 10, pp. 123-136. http://geodesic.mathdoc.fr/item/MM_2013_25_10_a9/

[1] Car R., Parrinello M., “Unified Approach for Molecular Dynamics and Density Functional Theory”, Phys. Rev. Lett., 55:22 (1985), 2471–2474 | DOI

[2] Allen M. P., Tildesley D. J., Computer simulation of liquids, Oxford University Press, N.-Y., 1990 | Zbl

[3] Sutmann G., “Classical molecular dynamics”, Quantum Simulations of Complex Many-Body Systems. From Theory to Algorithms, NIC series, 10, eds. J. Grotendorst et al., NIC, Julich, 2002, 211–254

[4] Tersoff J., “Modeling solid-state chemistry: Interatomic potentials for multicomponent systems”, Phys. Rev. B, 39:8 (1989), 5566–5568 | DOI

[5] Brenner D. W., “Empirical Potential for Hydrocarbons for Use in Simulating the Chemical Vapor-Deposition of Diamond Films”, Physical Review B, 42:15 (1990), 9458–9471 | DOI

[6] Kumagai T., Hara S., Choi J., Izumi S., Kato T., “Development of empirical bond-order-type interatomic potential for amorphous carbon structures”, Journal of Applied Physics, 105:6 (2009), 064310 | DOI

[7] Lebedeva I. V., Knizhnik A. A., Popov A. M., Potapkin B. V., “Ni-Assisted Transformation of Graphene Flakes to Fullerenes”, J. Phys. Chem. C, 116:11 (2012), 6572–6584 | DOI

[8] Foiles S. M., Adams J. M., “Thermodynamic properties of fcc transition metals as calculated with the embedded-atom model”, Physical Review B, 40 (1989), 5909–5915 | DOI

[9] Daw M. S., Baskes M. I., “Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals”, Physical Review B (American Physical Society), 29:12 (1984), 6443–6453 | DOI

[10] Daw M. S., Foiles S., “The embedded-atom method: a review of theory and applications”, Mat. Sci. Reports, 9 (1993) | Zbl

[11] Bielajew A. F., Fundamentals of the Monte Carlo method for neutral and charged particle transport, http://www-personal.umich.edu/b̃ielajew/MCBook/book.pdf

[12] Flynn M., “Some Computer Organizations and Their Effectiveness”, IEEE Trans. Comput., 21:9 (1972), 948–960 | DOI | MR | Zbl

[13] Shpakovskii G. I., Realizatsiya parallelnykh vychislenii: klastery, mnogoyadernye protsessory, grid, kvantovye kompyutery, BGU, Minsk, 2010, 155 pp.

[14] Plimpton S., “Fast parallel algorithms for short-range molecular dynamics”, J. Comp. Phys., 117:1 (1995), 1–19 | DOI | Zbl

[15] Berendsen H. J. C., van der Spoel D., van Drunen R., “Gromacs: a message-passing parallel molecular dynamics implementation”, Comp. Phys. Comm., 91 (1995), 43–56 | DOI

[16] Phillips J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kale L., Schulten K., “Scalable molecular dynamics with NAMD”, J. Comput. Chem., 26:16 (2005), 1781–1802 | DOI

[17] Anderson J. A., Lorenz C. D., Travesset A., “General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units”, J. Comp. Phys., 227:10 (2008), 5342–5359 | DOI | Zbl

[18] Ivanova E. A., Krivtsov A. M., Morozov N. F., Firsova A. D., Teoreticheskaya mekhanika. Opredelenie ekvivalentnykh uprugikh kharakteristik diskretnykh sistem, Izd-vo SPbGPU, SPb., 2004

[19] Byzov A. P., Ivanova E. A., “Potentsialy vzaimodeistviya chastits s vraschatelnymi stepenyami svobody”, Sovremennye problemy mekhaniki sploshnoi sredy, Trudy IX Mezhdunarodnoi konferentsii, posvyaschennoi 85-letiyu so dnya rozhdeniya akademika RAN I. I. Vorovicha (g. Rostov-na-Donu, 11–15 oktyabrya 2005 g.), v. 2, 47–51 http://www.ipme.ru/ipme/labs/dms/prive/ivanova/Home_page_Elena_Ivanova/PDF/By_Iv.pdf

[20] Erkoc S., “Empirical Many-Body Potential Energy Function Used In Computer Simulations Of Condensed Matter Properties”, Physics Reports, 278:2 (1997), 79–105 | DOI

[21] Brenner D. W., “Relationship between the embedded-atom method and Tersoff potentials”, Phys. Rev. Lett., 63:9 (1989), 1022 | DOI

[22] Boreskov A. V., Kharlamov A. A., Osnovy raboty s tekhnologiei CUDA, DMK-Press, M., 2010, 232 pp.

[23] Gaster B., Howes L., Kaeli D. R., Mistry P., Schaa D., Heterogeneous Computing with OpenCL, Morgan Kaufmann, San Fransisco, 2011

[24] Colberg P. H., Hofling F., Accelerating glassy dynamics using graphics processing units, arXiv: 0912.3824 [cond-mat.soft]

[25] Kider J. T., GPU as a Parallel Machine: Sorting on the GPU. CIS 700/010: 3/17/05, http://www.cis.upenn.edu/s̃uvenkat/700/lectures/19/sorting-kider.pdf

[26] Morozov I. V., Kazennov A. M., Bystryi R. G., Norman G. E., Pisarev V. V., Stegailov V. V., “Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs”, Comp. Phys. Comm., 182:9 (2011), 1974–1978 | DOI