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Monte Carlo strategies for first-principles simulations of elemental systems

Published:16 July 2012Publication History

ABSTRACT

We discuss the application of atomistic Monte Carlo simulation based on electronic structure calculations to elemental systems such as metals and alloys. As in prior work in this area, an approximate "pre-sampling" potential is used to generate large moves with a high probability of acceptance. Even with such a scheme, however, such simulations are extremely expensive and may benefit from algorithmic developments that improve acceptance rates and/or enable additional parallelization.

Here we consider several such developments. The first of these is a three-level hybrid algorithm in which two pre-sampling potentials are used. The lowest level is an empirical potential, and the "middle" level uses a low-quality density functional theory. The efficiency of the multistage algorithm is analyzed and an example application is given.

Two other schemes for reducing overall run-time are also considered. In the first, the Multiple-try Monte Carlo algorithm, a series of moves are attempted in parallel, with the choice of the next state in the chain made by using all the information gathered. This is found to be a poor choice for simulations of this type. In the second scheme, "tree sampling," multiple trial moves are made in parallel such that if the first is rejected, the second is ready and can be considered immediately. Performance of this scheme is shown to be quite effective under certain reasonable run parameters.

References

  1. D. Frenkel and B. Smit. Understanding Molecular Simulation. Acad. Press., San Diego, 1996. Google ScholarGoogle ScholarDigital LibraryDigital Library
  2. A. D. Sokal. Monte Carlo methods for the self-avoiding walk. In K. Binder, editor, Monte Carlo and Molecular Dynamics Simulations in Polymer Science, pages 47--124. Oxford U. Press., New York, 1995.Google ScholarGoogle Scholar
  3. R. H. Swendsen and J.-S. Wang. Nonuniversal critical dynamics in Monte Carlo simulations. Phys. Rev. Letts., 58:86--88, 1987.Google ScholarGoogle ScholarCross RefCross Ref
  4. T. Schlick. Molecular modeling and simulation: an interdisciplinary guide. Springer-Verlag, New York, 2002. Google ScholarGoogle ScholarDigital LibraryDigital Library
  5. C. J. Cramer. Essentials of Computational Chemistry: Theories and Models. John Wiley & Sons, Chichester, UK, 2002.Google ScholarGoogle Scholar
  6. F. Jensen. Introduction to Computational Chemistry. John Wiley & Sons, Ltd., Chichester, UK, 2nd edition, 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  7. R. M. Martin. Electronic structure: basic theory and practical methods. Cambridge U. Press, Cambridge, UK, 2004.Google ScholarGoogle ScholarCross RefCross Ref
  8. R. Dronskowski. Computational Chemistry of Solid State Materials. Wiley-VCH Verlag GmbH & Co., Weinheim, 2005.Google ScholarGoogle Scholar
  9. D. S. Sholl and J. A. Steckel. Density Functional Theory: A Practical Introduction. Wiley, Hoboken, NJ, 2009.Google ScholarGoogle Scholar
  10. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov. New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles. J. Chem. Phys., 96(3):1776--1783, 1992.Google ScholarGoogle ScholarCross RefCross Ref
  11. U. H. E. Hansmann. Parallel tempering for conformational studies of biological molecules. Chem. Phys. Letts., 281(1-3):140--150, 1997.Google ScholarGoogle ScholarCross RefCross Ref
  12. Q. Yan and J. J. de Pablo. Hyper-parallel tempering Monte Carlo: Application to the Lennard-Jones fluid and the restricted primitive model. J. Chem. Phys., 111(21):9509--9516, 1999.Google ScholarGoogle ScholarCross RefCross Ref
  13. R. H. Swendsen, B. Diggs, J.-S. Wang, S.-T. Li, C. Genovese, and J. B. Kadane. Transition matrix Monte Carlo. Int. J. Mod. Phys. C, 10:1563--1569, 1999.Google ScholarGoogle ScholarCross RefCross Ref
  14. Y. Sugita, A. Kitao, and Y. Okamoto. Multidimensional replica-exchange method for free-energy calculations. J. Chem. Phys., 113(15):6041--6051, 2000.Google ScholarGoogle ScholarCross RefCross Ref
  15. T. Rodinger, P. L. Howell, and R. Pomès. Distributed replica sampling. J. Chem. Theory. Comput., 2:725--731, 2006.Google ScholarGoogle ScholarCross RefCross Ref
  16. J. S. Liu and R. Chen. Sequential Monte Carlo methods for dynamic systems. J. Am. Stat. Assoc., 93(443):1032--1044, 1998.Google ScholarGoogle ScholarCross RefCross Ref
  17. J. S. Liu. Monte Carlo Strategies in Scientific Computing. Springer, New York, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  18. R. Iftimie, D. Salahub, D. Wei, and J. Schofield. Using a classical potential as an efficient importance function for sampling from an ab initio potential. J. Chem. Phys., 113(12):4852--4862, 2000.Google ScholarGoogle ScholarCross RefCross Ref
  19. R. Iftimie and J. Schofield. Reaction mechanism and isotope effects derived from centroid transition state theory in intramolecular proton transfer reactions. J. Chem. Phys., 115(13):5891--5902, 2001.Google ScholarGoogle ScholarCross RefCross Ref
  20. R. Iftimie, D. Salahub, and J. Schofield. An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution. J. Chem. Phys., 119(21):11285--11297, 2003.Google ScholarGoogle ScholarCross RefCross Ref
  21. B. Hetényi, K. Bernacki, and B. J. Berne. Multiple "time step" Monte Carlo. J. Chem. Phys., 117(18):8203--8207, 2002.Google ScholarGoogle ScholarCross RefCross Ref
  22. L. D. Gelb. Monte Carlo simulations using sampling from an approximate potential. J. Chem. Phys., 118(17):7747--7750, 2003.Google ScholarGoogle ScholarCross RefCross Ref
  23. T. Z. Lwin and R. Luo. Overcoming entropic barrier with coupled sampling at dual resolutions. J. Chem. Phys., 123:194904, 2005.Google ScholarGoogle ScholarCross RefCross Ref
  24. C. H. Mak. Stochastic potential switching algorithm for Monte Carlo simulations of complex systems. J. Chem. Phys., 122:214110, 2005.Google ScholarGoogle ScholarCross RefCross Ref
  25. S. Wang, S. J. Mitchell, and P. A. Rikvold. Ab initio Monte Carlo simulations for finite-temperature properties: application to lithium clusters and bulk liquid lithium. Comp. Mater. Sci., 29:145--151, 2004.Google ScholarGoogle ScholarCross RefCross Ref
  26. L. D. Gelb and T. Carnahan. Isothermal-isobaric Monte Carlo simulations of liquid lithium using density functional theory. Chem. Phys. Letts., 417:283--287, 2006.Google ScholarGoogle ScholarCross RefCross Ref
  27. M. J. McGrath, J. I. Siepmann, I-F. W. Kuo, C. J. Mundy, J. VandeVondele, M. Sprik, J. Hutter, F. Mohamed, M. Krack, and M. Parrinello. Toward a Monte Carlo program for simulating vapor-liquid equilibria from first principles. Comp. Phys. Comm., 169:289--294, 2005.Google ScholarGoogle ScholarCross RefCross Ref
  28. M. J. McGrath, I.-F. W. Kuo, and J. I. Siepmann. Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional. Phys. Chem. Chem. Phys., 13:19943--19950, 2011.Google ScholarGoogle ScholarCross RefCross Ref
  29. S. Duane, A. D. Kennedy, B. J. Pendleton, and D. Roweth. Hybrid Monte Carlo. Phys. Lett. B, 195(2):216--222, 1987.Google ScholarGoogle ScholarCross RefCross Ref
  30. B. Mehlig, D. W. Heermann, and B. M. Forrest. Hybrid Monte Carlo method for condensed-matter systems. Phys. Rev. B, 45(2):679--685, 1992.Google ScholarGoogle ScholarCross RefCross Ref
  31. V. Weber and D. Asthagiri. Thermodynamics of water modeled using ab initio simulations. J. Chem. Phys., 133:141101, 2010.Google ScholarGoogle ScholarCross RefCross Ref
  32. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. Equation of state calculations by fast computing machines. J. Chem. Phys., 21:1087--1092, 1953.Google ScholarGoogle ScholarCross RefCross Ref
  33. M. E. Clamp, P. G. Baker, C. J. Stirling, and A. Brass. Hybrid Monte Carlo: An efficient algorithm for condensed matter simulation. J. Comp. Chem., 15(8):838--846, 1994. Google ScholarGoogle ScholarDigital LibraryDigital Library
  34. B. Chen and J. I. Siepmann. A novel Monte Carlo algorithm for simulating strongly associating fluids: Applications to water, hydrogen fluoride, and acetic acid. J. Phys. Chem. B, 104:8725--8734, 2000.Google ScholarGoogle ScholarCross RefCross Ref
  35. B. Chen and J. I. Siepmann. Improving the efficiency of the aggregation-volume-bias Monte Carlo algorithm. J. Phys. Chem. B, 105:11275--11282, 2001.Google ScholarGoogle ScholarCross RefCross Ref
  36. A. M. Ferrenberg and R. H. Swendsen. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett., 61(23):2635--2638, 1988.Google ScholarGoogle ScholarCross RefCross Ref
  37. G. Orkoulas and A. Z. Panagiotopoulos. Phase behavior of the restricted primitive model and square-well fluids from Monte Carlo simulations in the grand canonical ensemble. J. Chem. Phys., 110:1581--1590, 1999.Google ScholarGoogle ScholarCross RefCross Ref
  38. M. Valiev, E. J. Bylaska, N. Govind, K. Kowalski, T. P. Straatsma, H. J. J. Van Dam, D. Wang, J. Nieplocha, E. Apra, T. L. Windus, and W. A. de Jong. NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comp. Phys. Comm., 181:1477--1489, 2010.Google ScholarGoogle ScholarCross RefCross Ref
  39. G. van Rossum. http://www.python.org.Google ScholarGoogle Scholar
  40. http://pympi.sourceforge.net.Google ScholarGoogle Scholar
  41. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. Numerical Recipes in C. Cambridge University Press, Cambridge, 2 edition, 1988.Google ScholarGoogle Scholar
  42. S.-N. Luo, T. J. Ahrens, T. Çağin, A. Strachan, W. A. Goddard III, and D. C. Swift. Maximum superheating and undercooling: Systematics, molecular dynamics simulations, and dynamic experiments. Phys. Rev. B, 68:134206, 2003.Google ScholarGoogle ScholarCross RefCross Ref
  43. M. S. Daw, S. M. Foiles, and M. I. Baskes. The Embedded-Atom Method - a review of theory and applications. Mat. Sci. Rep., 9(7-8):251--310, 1993.Google ScholarGoogle ScholarCross RefCross Ref
  44. A. P. Sutton and J. Chen. Long-range Finnis-Sinclair potentials. Phil. Mag. Letts., 61(3):139--146, 1990.Google ScholarGoogle ScholarCross RefCross Ref
  45. H. Rafii-Tabar and A. P. Sutton. Long-range Finnis-Sinclair potentials for f. c. c. metallic alloys. Phil. Mag. Letts., 63:217--224, 1991.Google ScholarGoogle ScholarCross RefCross Ref

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                cover image ACM Other conferences
                XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond
                July 2012
                423 pages
                ISBN:9781450316026
                DOI:10.1145/2335755

                Copyright © 2012 ACM

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                Publication History

                • Published: 16 July 2012

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