Global optimization of parameters in the reactive force field ReaxFF for SiOH

Journal of Computational Chemistry

Volumn 34, Issue 25, 2013, Pages 2178-2189

  Larsson, Henrik R ^a   Van Duin, Adri C T ^b   Hartke, Bernd ^a  

^a UNIVERSITY OF KIEL   (Germany)

^b The Pennsylvania State University   (United States)

Author keywords

evolutionary algorithms; force field fitting; genetic algorithms; global optimization; reactive force fields

Indexed keywords

FORCE-FIELD FITTING; GA OPTIMIZATION; MESSAGE PASSING INTERFACE; OPTIMIZATION APPROACH; OPTIMIZATION EFFICIENCY; OPTIMIZATION OF PARAMETERS; PARAMETER VECTORS; REACTIVE FORCE FIELD;

EVOLUTIONARY ALGORITHMS; GENETIC ALGORITHMS; MESSAGE PASSING; OPTIMIZATION;

GLOBAL OPTIMIZATION;

EID: 84882661113     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23382     Document Type: Article

References (76)

1. P. Vashishta, R. K. Kalia, A. Nakano, J. Nanopart. Res. 2003, 5, 119.
2. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. Shan, W. Wriggers, Science 2010, 330, 341.
3. T. J. Lane, D. Shukla, K. A. Beauchamp, V. S. Pande, Curr. Opin. Struct. Biol. 2013, 23, 58.
4. D. W. Brenner, Phys. Rev. B 1990, 42, 9458.
5. Y. T. Chang, W. H. Miller, J. Phys. Chem. 1990, 94, 5884.
6. J. Aqvist, A. Warshel, Chem. Rev. 1993, 93, 2523.
7. Y. Kim, J. C. Corchado, J. Villa, J. Xing, D. G. Truhlar, J. Chem. Phys. 2000, 112, 2718.
8. S. C. L. Kamerlin, J. Cao, E. Rosta, A. Warshel, J. Phys. Chem. B 2009, 113, 10905.
9. S. C. L. Kamerlin, A. Warshel, Faraday Discuss. 2010, 145, 71.
10. H. S. Johnston, Adv. Chem. Phys. 1961, 3, 131.
11. B. C. Bolding, H. C. Andersen, Phys. Rev. B 1990, 41, 10568.
12. L. Ojamae, I. Shavitt, S. J. Singer, J. Phys. Chem. 1998, 109, 5547.
13. P. Ballone, R. O. Jones, J. Chem. Phys. 2004, 121, 8147.
14. A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard, III,., J. Phys. Chem. A 2001, 105, 9396.
15. S. S. Han, J. K. Kang, H. M. Lee, A. C. T. van Duin, W. A. Goddard, III, J. Chem. Phys. 123, 2005, 114703.
16. K. D. Nielson, A. C. T. van Duin, J. Oxgaard, W. Q. Deng, W. A. Goddard, III, J. Phys. Chem. A 2005, 109, 493.
17. K. Chenoweth, A. C. T. van Duin, P. Persson, M. J. Cheng, J. Oxgaard, W. A. Goddard, III, J. Phys. Chem. C 2008, 112, 14645.
18. J. A. Keith, D. Fantauzzi, T. Jacob, A. C. T. van Duin, Phys. Rev. B 2010, 81, 235404.
19. A. Nakano, R. K. Kalia, K. Nomura, A. Sharma, P. Vashishta, F. Shimojo, A. C. T. van Duin, W. A. Goddard, III, R. Biswas, D. Srivastava, Comput. Mater. Sci. 2007, 38, 642.
20. A. Neumaier, Acta Numer. 2004, 13, 271.
21. A. Neumaier, O. Shcherbina, W. Huyer, T. Vinkõ, Math. Program. Ser. B 2005, 103, 335.
22. J. H. Holland, Adaption in Natural and Artificial Systems, University of Michigan Press: Ann Arbor, MI, 1975.
23. D. E. Goldberg, Genetic Algorithms in Search, Optimization and Machine Learning, Addison-Wesley: Reading, MA, 1989.
24. Y. A. Arnautova, J. Pillardy, C. Czaplewski, H. A. Scheraga, J. Phys. Chem. B 2003, 107, 712.
25. E. R. Hatcher, O. Guvench, A. D. MacKerell, Jr., J. Chem. Theor. Comput. 2009, 5, 1315.
26. W. Yu, P. E. M. Lopes, B. Roux, A. D. MacKerell, Jr., J. Chem. Phys. 2013, 138, 034508.
27. H. M. Marques, I. Cukrowski, Phys. Chem. Chem. Phys. 2002, 4, 5878.
28. V. Blum, A. Zunger, Phys. Rev. B 2005, 72, 020104.
29. B. Arnold, A. D. Ortiz, G. L. W. Hart, H. Dosch, Phys. Rev. B 2010, 81, 094116.
30. J. Hunger, S. Beyreuther, G. Huttner, K. Allinger, U. Radelof, L. Zsolnai, Eur. J. Inorg. Chem. 1998, 693.
31. J. Hunger, G. Huttner, J. Comput. Chem. 1999, 20, 455.
32. T. R. Cundari, W. T. Wi, Inorg. Chim. Acta 2000, 300, 113.
33. B. Courcot, A. J. Bridgeman, J. Comput. Chem. 2011, 32, 240.
34. T. Strassner, M. Busold, W. A. Herrmann, J. Comput. Chem. 2002, 23, 282.
35. M. Tafipolsky, R. Schmid, J. Phys. Chem. B 2009, 113, 1341.
36. J. M. Wang, P. A. Kollman, J. Comput. Chem. 2001, 22, 1219.
37. A. Globus, M. Menon, D. Srivastava, Comput. Model. Eng. Sci. 2002, 3, 557.
38. C. R. Herbers, K. Johnston, N. F. A. van der Vegt, Phys. Chem. Chem. Phys. 2011, 13, 10577.
39. B. Hartke, Chem. Phys. Lett. 1996, 258, 144.
40. B. Hartke, Theor. Chem. Acc. 1998, 99, 241.
41. B. Hartke, M. Schütz, H.-J. Werner, Chem. Phys. 1998, 239, 561.
42. J. M. Dieterich, B. Hartke, J. Comput. Chem. 2011, 32, 1377.
43. B. C. Barnes, L. D. Gelb, J. Chem. Theor. Comput. 2007, 3, 1749.
44. C. M. Handley, R. J. Deeth, J. Chem. Theor. Comput. 2012, 8, 194.
45. A. Slepoy, M. D. Peters, A. P. Thompson, J. Comput. Chem. 2007, 28, 2465.
46. W. M. Brown, A. P. Thompson, P. A. Schultz, J. Chem. Phys. 2010, 132, 024108.
47. L. Angibaud, L. Briquet, P. Philipp, T. Wirtz, J. Kieffer, Nucl. Instrum. Methods B 2011, 269, 1559.
48. L. Huang, J. Kieffer, J. Chem. Phys. 2003, 118, 1487.
49. L. G. V. Briquet, A. Jana, L. Mether, K. Nordlund, G. Henrion, P. Philipp, T. Wirtz, J. Phys. Condens. Matter 2012, 24, 395004.
50. P. Pahari, S. Chaturvedi, J. Mol. Model. 2012, 18, 1049.
51. I. Rossi, D. G. Truhlar, Chem. Phys. Lett. 1994, 233, 231.
52. A. Gonzalez-Lafont, T. N. Truong, D. G. Truhlar, J. Phys. Chem. 1991, 95, 4618.
53. S. E. Schönborn, S. Goedecker, S. Roy, A. R. Oganov, J. Chem. Phys. 2009, 130, 144108.
54. A. C. T. van Duin, J. M. A. Baas, B. van de Graaf, J. Chem. Soc. Faraday Trans. 1994, 90, 2881.
55. H. R. Larsson, B. Hartke, Comput. Methods Mater. Sci. 2013, 13, 120.
56. J. M. Dieterich, B. Hartke, Mol. Phys. 2010, 108, 279; Available at http://www.ogolem.org/, last accessed: 6 July 2013.
57. B. Bandow, B. Hartke, J. Phys. Chem. A 2006, 110, 5809.
58. B. Hartke, Angew. Chem. Int. Ed. 2002, 41, 1468.
59. B. Hartke, In Computational Molecular Science;, P. R. Schreiner, W. D. Allen, M. Orozco, W. Thiel, P. Willett, Eds.; Wiley Interdisciplinary Reviews, WIREs Comput. Mol. Sci. 2011, 1, 879.
60. W. H. Press, B. P. Flannery, S. A. Teukolsky, W. T. Vetterling, Numerical Recipes-The Art of Scientific Computing, 2nd ed.; Cambridge University Press, Cambridge, UK, 2003.
61. M. J. D. Powell, IMA J. Numer. Anal. 2008, 28, 649.
62. M. J. D. Powell, Report No. DAMTP 2009/NA06, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK.
63. A. C. T. van Duin, W. A. Goddard, III, A. L. Yakovlev, ReaxFF 2012, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, Available at: http://www.scm.com/, last accessed: 6 July 2013.
64. W. Gropp, E. Lusk, A. Skjellum, Using MPI, MIT Press: Cambridge, MA, 1999.
65. M. R. LaBrosse, J. K. Johnson, A. C. T. van Duin, J. Phys. Chem. A 2010, 114, 5855.
66. A. C. T. van Duin, A. Strachan, S. Stewman, Q. Zhang, X. Xu, W. A. Goddard, III,., J. Phys. Chem. A 2003, 107, 3803.
67. J. C. Fogarty, H. M. Aktulga, A. Y. Grama, A. C. T. van Duin, S. A. Pandit, J. Phys. Chem. A 2010, 132, 174704.
68. C. A. Brewer, Available at: http://www.ColorBrewer2.org, 2012, last accessed: 6 July 2013.
69. T. Weise, Global Optimization Algorithms-Theory and Application, Available at: http://www.it-weise.de/, 2011, last accessed: 6 July 2013.
70. L. Davis, Ed. Genetic Algorithms and Simulated Annealing, Pitman Publishing: London, 1987.
71. L. Davis, Ed. Handbook of Genetic Algorithms, Van Nostrand Reinhold: New York, 1991.
72. L. Spector, Ed. Gecco-2001, In Proceedings of the Genetic and Evolutionary Computation Conference; Morgan Kaufmann Publishers: San Francisco, 2001.
73. J. Lässig, K. H. Hoffmann, Phys. Rev. E 2009, 79, 046702.
74. H. R. Larsson, BSc thesis, University of Kiel, May/June 2012.
75. O. Rahaman, A. C. T. van Duin, W. A. Goddard, III, D. J. Doren, J. Phys. Chem. B 2011, 115, 249.
76. K. Michaelian, Chem. Phys. Lett. 1998, 293, 202.