DL-FIND: An open-source geometry optimizer for atomistic simulations*

Journal of Physical Chemistry A

Volumn 113, Issue 43, 2009, Pages 11856-11865

  Kästner, Johannes ^a,c   Carr, Joanne M ^a   Keal, Thomas W ^a,b   Thiel, Walter ^b   Wander, Adrian ^a   Sherwood, Paul ^a  

^a DARESBURY LABORATORY   (United Kingdom)

^b MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^c UNIVERSITY OF STUTTGART   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC STRUCTURE; ATOMISTIC SIMULATIONS; BFGS ALGORITHM; CARTESIAN COORDINATE; CLASSICAL FORCE FIELDS; CO-ORDINATE TRANSFORMATION; CONICAL INTERSECTION; CONJUGATE GRADIENT; CPU TIME; DIMER METHOD; GEOMETRY OPTIMIZATION; GRADIENT PROJECTIONS; INTERNAL COORDINATES; LAGRANGE; MINIMIZATION METHODS; NEWTON METHODS; NUDGED ELASTIC BAND; OPEN-SOURCE; OPTIMIZATION ALGORITHMS; OPTIMIZERS; PENALTY FUNCTION; QUASI-NEWTON; RATIONAL FUNCTION OPTIMIZATION; STEEPEST DESCENT; STOCHASTIC SEARCH METHODS; SURFACE SCIENCE; TRANSITION-STATE;

CONJUGATE GRADIENT METHOD; FUNCTION EVALUATION; MOLECULAR DYNAMICS; NEWTON-RAPHSON METHOD; OPTIMIZATION; PARALLEL ALGORITHMS;

COMPUTATIONAL GEOMETRY;

EID: 70350381537     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9028968     Document Type: Article

References (70)

1. Murrell, J. N.; Laidler, K. J. J. Chem. Soc, Faraday Trans. 1968, 64, 371.
2. http://www.gnu.org/licenses/lgpl.html.
3. http://ccpforge.cse.rl.ac.uk/projects/dl-flnd.
4. http://www.mpi-forum.org.
5. Guest, M. F.; Bush, I. J.; van Dam, H. J. J.; Sherwood, P.; Thomas, J. M. H.; van Lenthe, J. R; Havenith, R. W. A.; Kendrick, J. Mol. Phys. 2005, 103, 719.
6. GAMESS-UK is a package of ab initio programs. See: http:// www.rfs.dl.ac.uk/gamess-uk/index.shtml and http://ccpfa-ge.cse.rl.ac.uk/ projects/ gamess-uk/.
7. ChemShell, a Computational Chemistry Shell, see www.chemshell.org.
8. Sherwood, P.; de Vries, A. R; Guest, M. F.; Schreckenbach, G.; Catlow, C. R. A.; French, S. A.; Sokol, A. A.; Bromley, S. T.; Thiel, W.; Turner, A. J.; Billeter, S.; Terstegen, F.; Thiel, S.; Kendrick, J.; Rogers, S. C; Casci, J.; Watson, M.; King, F.; Karlsen, E.; Sjøvoll, M.; Fahmi, A.; Schäfer, A.; Lennartz, C. J. Mol. Struct. (THEOCHEM) 2003, 632, 1.
9. Dovesi, R.; Saunders, V. R.; Roetti, C; Orlando, R.; Zicovich-Wilson, C. M.; Pascale, F.; Civalleri, B.; Doll, K.; Harrison, N. M.; Bush, I. J.; D'Arco, Ph.; Llunell, M.; Crystal06 user's manual; http://www.crystal.un.ito.it/, 2006.
10. Thiel, W.; MNDO program, version 6.1, Mülheim, 2008.
11. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M..; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; .Dapprich, S.; Daniels, A. D.; Strain, M. C; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, L; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C; Pople, J. A.; Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
12. Werner, R-J.; Knowles, P. J.; Lindh, R; Manby, F. R.; Schütz, M.; et al. MOLPRO, version 2006.1, a package of ab initio programs; see http:// www.molpro.net.
13. Peng, C; Ayala, P. Y.; Schlegel, R. B.; Frisch, M. J. J. Comput. Chem. 1996, 17, 49.
14. Pulay, P.; Fogarasi, G. J. Chem. Phys. 1992, 96, 2856.
15. Baker, J.; Kessi, A.; Delley, B. Chem. Phys. 1996, 105, 192.
16. Billeter, S. R; Turner, A. J.; Thiel, W. Phys. Chem. Chem. Phys. 2000, 2, 2177.
17. Polak. E; Ribière, G. Ref. Fra. Inf. Rech. Op. 1969, 3, 35.
18. Verlet, L. Phys. Rev. 1967, 159, 98.
19. Broyden, C. G. IMA J. Appl, Math. 1970, 6. 76.
20. Fletcher, R. Comput. J. 1970, 13, 317.
21. Goldfarb, D. Mgth. Comp. 1970, 24, 23.
22. Shanno, D. F. Math. Comp. 1970, 24, 647.
23. Boflll, J. M. J. Comput. Chem. 1994, 15, 1.
24. Powell, M. J. D. Math. Prog. 1971, 26, 1.
25. Liu, D. C; Nocedal, J. Math. Program. 1989, 45, 503.
26. Nocedal, J. Math. Comp. 1980, 35, 773.
27. Holland, J. H. Adaptation in Natural and Artificial, Systems; University of Michigan. Press: Ann. Arbor, MI, 1975.
28. Goldberg, D. Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley: New York, 1989.
29. Haupt, R. L.; Haupt, S. E. Practical genetic algorithms; Wiley: New York, 1998.
30. De Jong, K. A. An analysis of the behavior of a class of genetic adaptive systems; PhD thesis, University of Michigan, 1975.
31. Goldberg, D. E. Sizing populations for serial and parallel genetic algorithms. In Proceedings of the third international conference on Genetic algorithms; Morgan Kaufmann Publishers, Inc.: San. Mateo, CA, 1989; p 70.
32. Grefenstette, J. J. Parallel adaptive algorithms for function optimization; Tech. rep. no.cs-81-19; Vanderbilt University, Computer Science Department, Nashville, TN, 1981.
33. Anderson, R. L. J. Am. Stat. Assoc. 1953, 48, 789.
34. Brooks, S. H. Overations Res. 1957, 6, 244.
35. Luus, R.; Jaakola, T. H. I. AIChe J. 1973, 19, 760.
36. Cerjan, C. J.; Miller, W. H. J. Chem. Phys. 1981, 75, 2800.
37. Simons, J.; Jørgensen, P.; Taylor, H.; Ozment, J. J. Phys. Chem. 1983, 87, 2745.
38. Banerjee, A.; Adams, N.; Simons, J.; Shepard, R. J. Phys. Chem. 1985, 89, 52.
39. Baker, J. J. Comput. Chem. 1986, 7, 385.
40. Murtagh, B. A.; Sargent, R. W. H. Comput. J. 1970, 13, 185.
41. Jónsson, R; Mills, G.; Jacobsen, K. W. Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions. In Classical and Quantum Dynamics in Condensed Phase Simulations; World Scientific: Singapore, 1998; Chapter 16, p 385.
42. Henkelman, G.; Uberuaga, B. P.; Jónsson, R. J. Chem. Phys. 2000, 113, 9901.
43. Henkelman, G.; Jónsson, H. J. Chem. Phys. 2000, 113, 9978.
44. Goumans, T. P. M.; Catlow, C. R. A.; Brown, W. A.; Kästner, J.; Sherwood, P. Phys. Chem. Chem. Phys. 2009, 11, 5431.
45. Henkelman, G.; Jónsson, H. J. Chem. Phys. 1999, 111, 7010.
46. Olsen, R. A.; Kroes, G. J.; Henkelman, G.; Arnaldsson, A.; Jónsson, H. J. Chem. Phys. 2004, 121, 9776.
47. Heyden, A.; Bell, A. T.; Keil, F. J. J. Chem. Phys. 2005, 123, 224101.
48. Kästner, J.; Sherwood, P. J. Chem. Phys. 2008, 128, 014106.
49. Keal, T. W.; Koslowski, A.; Thiel, W. Theor. Chem. Acc 2007, 118, 837.
50. Yarkony, D. R. J. Phys. Chem. A 2004, 108, 3200.
51. Senn, H. M.; Thiel, W. Angew Chem. 2009, 48, 1198.
52. Senn, H. M.; Thiel, W. Top. Curr. Chem. 2007, 268, 173.
53. Wu, R. B.; Xie, H. J.; Cao, Z. X.; Mo, Y. R. J. Am. Chem. Soc. 2008, 130, 7022.
54. Mladenovic, M.; Fink, R. F.; Thiel, W.; Schirmeister, T.; Engels, B. J. Am. Chem. Soc. 2008, 130, 8696.
55. Sadeghian, K.; Bocola, M.; Schütz, M. J. Am. Chem. Soc. 2008, 130, 12501.
56. Goumans, T. P. M.; Catlow, C. R. A.; Brown, W. A. Mon. Not. R. Astron Soc. 2009, 393, 1403.
57. Metz, S.; Thiel, W. To be published.
58. Keal, T. W.; Wanko, M.; Thiel, W. Theor. Chem. Acc 2009, 123, 145.
59. Silva-Junior., M. R; Thiel, W. To be published.
60. Fabiano, E.; Thiel, W. J. Phys. Chem. A 2008, 112, 6859.
61. Lan, Z.; Fabiano, E.; Thiel, W. J. Phys. Chem 2009, 10, 1225.
62. Lan., Z.; Fabiano, E.; Thiel, W. J. Phys. Chem. B 2009, 113, 3548.
63. Toniolo, A.; Granucci, G.; Martínez, T. J. J. Phys. Chem. A 2003, 107, 3822.
64. Dang, L. X.; Pettitt, B. M. J. Phys. Chem. 1987, 91, 3349.
65. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. G; Ghio, C; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
66. Weber, W. PhD thesis, Universität Zürich, 1996.
67. Weber, W.; Thiel, W. Theor. Chem, Acc. 2000, 103, 495.
68. Koslowski, A.; Beck, M. E.; Thiel, W. J. Comput. Chem. 2003, 24, 714.
69. Toniolo, A.; Ben-Nun, M.; Martinez, T. J. J. Phys. Chem. A 2002, 106, 4679.
70. Lan, Z; Fabiano, E.; Thiel, W. To be published.