Supercomputer molecular modeling of thermodynamic equilibrium in gas-metal microsystems

Authors

DOI:

https://doi.org/10.26089/NumMet.v16r113

Keywords:

molecular dynamics, parallel computing, supercomputing simulation, nitrogen and nickel surface interaction, thermodynamic equilibrium

Abstract

This paper is devoted to the supercomputer modeling of thermodynamic equilibrium in microsystems containing different substances in various aggregate states. As an example, a nitrogen-nickel system is considered. This choice is due to the fact that such a microsystem is the basis of many technical applications, including the devices of supersonic cold gas-dynamic sputtering using nanoparticles on the surfaces of perspective carbonaceous materials. At the first stage of studies, the equilibrium state of a nitrogen-nickel microsystems is of interest. The molecular dynamic approach is used to model the thermodynamic equilibrium in this microsystem. The chosen numerical algorithm of its implementation is based on the Verlet finite-difference scheme. In order to increase the computational speedup, a parallel algorithm is proposed; its implementation is performed using the MPI and OpenMP technologies. The developed parallel solver is employed to study the establishment of thermodynamic equilibrium in the pure components (nitrogen and nickel) at several temperatures, including room temperature, and in the nitrogen-nickel microsystem. In the numerical experiments, the optimum parameters of the calculation procedure (including the efficiency of parallelization using processors of different architecture) and the physical parameters of the modeled process are found.

Author Biographies

V.O. Podryga

S.V. Polyakov

D.V. Puzyrkov

References

  1. I. G. Kaplan, Theory of Molecular Interactions (Nauka, Moscow, 1982; Amsterdam, Elsevier, 1986).
  2. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (McGraw-Hill, New York, 1981; Mir, Moscow, 1987).
  3. J. M. Haile, Molecular Dynamics Simulations. Elementary Methods (Wiley, New-York, 1992).
  4. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithm to Applications (Academic, San Diego, 2002).
  5. M. P. Allen, “Introduction to Molecular Dynamics Simulation,” in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, NIC Series (John von Neumann Inst. for Computing, Jülich, 2004), Vol. 23, pp. 1-28.
  6. G. Sutmann, “Classical Molecular Dynamics,” in Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, Lecture Notes, NIC Series (John von Neumann Inst. for Computing, Jülich, 2002), Vol. 10, pp. 211-254.
  7. D. C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge Univ. Press, Cambridge, 2004; Inst. Komp’yut. Issled., Izhevsk, 2012).
  8. G. E. Norman and V. V. Stegailov, “Stochastic Theory of the Classical Molecular Dynamics Method,” Mat. Model. 24 (6), 3-44 (2012) [Math. Models Comput. Simul. 5 (4), 305-333 (2013)].
  9. R. G. Winkler, H. Morawitz, and D. Y. Yoon, “Novel Molecular Dynamics Simulations at Constant Pressure,” Mol. Phys. 75 (3), 669-688 (1992).
  10. H. Schlacken, “Molecular-Dynamics Simulation of Statistical-Mechanical Systems,” Acta Polym. 39 (3), 151-152 (1988).
  11. A. P. Alkhimov, S. V. Klinkov, V. F. Kosarev, and V. M. Fomin, Cold Gas Dynamic Spraying: Theory and Practice (Fizmatlit, Moscow, 2010; Cambridge Int. Sci. Pub., Cambridge, 2011).
  12. D. Resnick, “Nanoimprint Lithography,” in Nanolithography. The Art of Fabricating Nanoelectronic and Nanophotonic Devices and Systems (Woodhead Publ., Cambridge, 2014), pp. 315-347.
  13. V. O. Podryga, “Molecular Dynamics Method for Heated Metal’s Simulation of Thermodynamic Equilibrium,” Mat. Model. 23 (9), 105-119 (2011).
  14. L. Verlet, “Computer, “Experiments’’ on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules,” Phys. Rev. 159 (5), 98-103 (1967).
  15. J. E. Lennard-Jones, “Cohesion,” Proc. Phys. Soc. 43 (5), 461-482 (1931).
  16. L. R. Fokin and A. N. Kalashnikov, “The Transport Properties of an N_2-H_2 Mixture of Rarefied Gases in the EPIDIF Database,” Teplofiz. Vys. Temp. 47 (5), 675-687 (2009) [High Temp. 47 (5), 643-655 (2009)].
  17. M. S. Daw and M. I. Baskes, “Embedded-Atom Method: Derivation and Application to Impurities, Surfaces, and Other Defects in Metals,” Phys. Rev. B 29 (12), 6443-6453 (1984).
  18. X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, “Misfit-Energy-Increasing Dislocations in Vapor-Deposited CoFe/NiFe Multilayers,” Phys. Rev. B 69 (14), 144113-1-144113-10 (2004).
  19. V. O. Podryga and S. V. Polyakov, Molecular Dynamic Simulation of Thermodynamic Equilibrium Problem for Heated Nickel , Preprint No. 41 (Keldysh Inst. Appl. Math., Moscow, 2014).
  20. A. N. Lagarkov and V. M. Sergeev, “Molecular Dynamics Method in Statistical Physics,” Usp. Fiz. Nauk 125 (3), 409-448 (1978) [Sov. Phys. Usp. 21 (7), 566-588 (1978)].
  21. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, et al., “Molecular Dynamics with Coupling to an External Bath,” J. Chem. Phys. 81 (8), 3684-3690 (1984).
  22. A. I. Kitaigorodsky, Molecular Crystals and Molecules (Nauka, Moscow, 1971; Academic, New York, 1973).
  23. C. Kittel, Introduction to Solid State Physics (Wiley, New York, 1976; Nauka, Moscow, 1978).
  24. S. V. Polyakov, Yu. N. Karamzin, O. A. Kosolapov, et al., “Hybrid Supercomputer Platform and Application Programming for the Solution of Continuous Mechanics Problems by Grid Methods,” Izv. Southern Federal Univ., Tekh. Nauki, No. 6, 105-115 (2012).
  25. V. V. Voevodin and Vl. V. Voevodin, Parallel Computing (BHV-Petersburg, St. Petersburg, 2002) [in Russian].
  26. The Message Passing Interface (MPI) standard.
    http://www.mcs.anl.gov/research/projects/mpi . Cited February 5, 2015.
  27. The OpenMP API specification for parallel programming. Tutorials.
    http://www.openmp.org,
    http://www.llnl.gov/computing/tutorials/openMP . Cited February 5, 2015.
  28. CUDA Toolkit Documentation.
    http://docs.nvidia.com/cuda/index.html . Cited February 5, 2015.

Published

16-03-2015

How to Cite

Подрыга В., Поляков С., Пузырьков Д. Supercomputer Molecular Modeling of Thermodynamic Equilibrium in Gas-Metal Microsystems // Numerical Methods and Programming (Vychislitel’nye Metody i Programmirovanie). 2015. 16. 123-138. doi 10.26089/NumMet.v16r113

Issue

Section

Section 1. Numerical methods and applications