Quasi-Newton parallel geometry optimization methods

Journal of Chemical Physics

Volumn 133, Issue 3, 2010, Pages

  Burger, Steven K ^a   Ayers, Paul W ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARTESIANS; CYCLIC ADENOSINE; DIPEPTIDE; FINITE DIFFERENCE; GEOMETRY OPTIMIZATION; LANCZOS ALGORITHM; LANCZOS METHODS; MOLECULAR SYSTEMS; NEWTON METHODS; QUASI-NEWTON; SECANT UPDATE; SPEED-UPS; TRIPEPTIDE; UNCONSTRAINED MINIMIZATION; UNIT VECTORS;

FETAL MONITORING; NEWTON-RAPHSON METHOD; PHOSPHATASES;

OPTIMIZATION;

EID: 77956240093     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3455719     Document Type: Article

References (36)

1. C. L. Janssen and I. M. B. Nielsen, Parallel Computing in Quantum Chemistry (Taylor & Francis, Boca Raton, FL, 2008).
2. J. Baker, L. Fusti-Molnar, and P. Pulay, J. Phys. Chem. A JPCAFH 1089-5639 108, 3040 (2004). 10.1021/jp036926l
3. P. Brown, C. Woods, S. McIntosh-Smith, and F. R. Manby, J. Chem. Theory Comput. JCTCCE 1549-9618 4, 1620 (2008). 10.1021/ct800261j
4. T. Furlani, J. Kong, and P. Gill, Comput. Phys. Commun. CPHCBZ 0010-4655 128, 170 (2000). 10.1016/S0010-4655(00)00059-X
5. C. Gan, C. Tymczak, and M. Challacombe, J. Chem. Phys. JCPSA6 0021-9606 121, 6608 (2004). 10.1063/1.1790891
6. J. Baker and P. Pulay, J. Comput. Chem. JCCHDD 0192-8651 23, 1150 (2002). 10.1002/jcc.10071
7. J. Baker and M. Shirel, Parallel Comput. ZZZZZZ 0167-8191 26, 1011 (2000). 10.1016/S0167-8191(00)00024-7
8. M. W. Feyereisen, R. A. Kendall, J. Nichols, D. Dame, and J. T. Golab, J. Comput. Chem. JCCHDD 0192-8651 14, 818 (1993). 10.1002/jcc.540140708
9. J. Kästner, J. M. Carr, T. W. Keal, W. Thiel, A. Wander, and P. Sherwood, J. Phys. Chem. A JPCAFH 1089-5639 113, 11856 (2009). 10.1021/jp9028968
10. B. Peters, A. Heyden, and A. T. Bell, J. Chem. Phys. JCPSA6 0021-9606 120, 7877 (2004). 10.1063/1.1691018
11. W. N. E, W. Q. Ren, and E. Vanden-Eijnden, Phys. Rev. B PRBMDO 0163-1829 66, 052301 (2002). 10.1103/PhysRevB.66.052301
12. S. K. Burger and W. T. Yang, J. Chem. Phys. JCPSA6 0021-9606 124, 054109 (2006). 10.1063/1.2163875
13. G. Henkelman and H. Jonsson, J. Chem. Phys. JCPSA6 0021-9606 113, 9978 (2000). 10.1063/1.1323224
14. J. Nocedal and S. Wright, Numerical Optimization (Springer, New York, 1999). 10.1007/b98874
15. R. Fletcher, Practical Methods of Optimization (Wiley-Interscience, NY, 1987).
16. S. Nash and A. Sofer, Math. Program. MHPGA4 0025-5610 45, 529 (1989). 10.1007/BF01589117
17. R. Schnabel, Parallel Comput. ZZZZZZ 0167-8191 21, 875 (1995). 10.1016/0167-8191(95)00004-8
18. R. Byrd, R. Schnabel, and G. Shultz, Math. Program. MHPGA4 0025-5610 42, 273 (1988). 10.1007/BF01589407
19. R. Schnabel, " Quasi-Newton methods using multiple secant equations.," Department of Computer Science, University of Colorado at Boulder Technical Report No. CU-CS-247-83, 1983.
20. G. Golub and C. Van Loan, Matrix Computations (The Johns Hopkins University Press, Baltimore, MD, 1996).
21. L. Liberti and N. Maculan, Global Optimization: From Theory to Implementation (Springer, New York, 2009).
22. S. L. Ho, S. Yang, G. Ni, E. W. C. Lo, and H. C. Wong, IEEE Trans. Magn. IEMGAQ 0018-9464 41, 1756 (2005). 10.1109/TMAG.2005.846033
23. J. Baker and W. Hehre, J. Comput. Chem. JCCHDD 0192-8651 12, 606 (1991). 10.1002/jcc.540120510
24. J. Baker, J. Comput. Chem. JCCHDD 0192-8651 14, 1085 (1993). 10.1002/jcc.540140910
25. G. Fogarasi, X. Zhou, P. W. Taylor, and P. Pulay, J. Am. Chem. Soc. JACSAT 0002-7863 114, 8191 (1992). 10.1021/ja00047a032
26. C. Peng, P. Y. Ayala, H. B. Schlegel, and M. J. Frisch, J. Comput. Chem. JCCHDD 0192-8651 17, 49 (1996). 10.1002/(SICI)1096-987X(19960115)17:1<49:: AID-JCC5>3.0.CO;2-0
27. V. Bakken and T. Helgaker, J. Chem. Phys. JCPSA6 0021-9606 117, 9160 (2002). 10.1063/1.1515483
28. D. Xie and T. Schlick, SIAM J. Optim. SJOPE8 1052-6234 10, 132 (1999). 10.1137/S1052623497313642
29. E. Koslover and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 127, 234105 (2007). 10.1063/1.2807227
30. A. Ghysels, D. Van Neck, V. Van Speybroeck, T. Verstraelen, and M. Warquier, J. Chem. Phys. JCPSA6 0021-9606 126, 224102 (2007). 10.1063/1.2737444
31. A. Ghysels, D. Van Neck, and M. Waroquier, J. Chem. Phys. JCPSA6 0021-9606 127, 164108 (2007). 10.1063/1.2789429
32. A. Ghysels, D. Van Neck, B. R. Brooks, V. Van Speybroeck, and M. Waroquier, J. Chem. Phys. JCPSA6 0021-9606 130, 084107 (2009). 10.1063/1.3071261
33. D. Kincaid and W. Cheney, Numerical Analysis (Brooks/Cole, Belmont, CA, 1991).
34. S. K. Burger, L. Yui, and P. W. Ayers, FORTRAN 90 code available at http://www.chemistry.mcmaster.ca/ayers/projects.html.
35. M. J. Frisch, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, GAUSSIAN03, Revision C.02, Gaussian Inc., Wallingford, CT, 2004.
36. GAUSSVIEW, version 3.0, Gaussian, Inc., Pittsburgh, PA, 2003.