A parallel distributed data CPHF algorithm for analytic hessians

Journal of Computational Chemistry

Volumn 28, Issue 10, 2007, Pages 1685-1694

  Alexeev, Yuri ^a   Schmidt, Michael W ^b   Windus, Theresa L ^a   Gordon, Mark S ^b  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

CPHF; DDI; Hessians; Parallel

Indexed keywords

ANALYTIC HESSIANS; COUPLED PERTURBED HARTREE-FOCK (CPHF) ALGORITHMS; DISTRIBUTED DATA ANALYTIC HESSIAN ALGORITHM;

COMPUTATIONAL METHODS; PERTURBATION TECHNIQUES; POTENTIAL ENERGY SURFACES; PROGRAM PROCESSORS; RESOURCE ALLOCATION;

PARALLEL ALGORITHMS;

EID: 34547272485     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20633     Document Type: Article

References (46)

1. Moller, C.; Plesset, M. S. Phys Rev 1934, 46, 618.
2. Crawford, T. D.; Schaefer, H. F. Rev Comput Chem 1996, 14, 33.
3. Ivanic, J.; Ruedenberg, K. Theor Chem Acc 2001, 106, 339.
4. Schmidt, M. W.; Gordon, M. S. Annu Rev Phys Chem 1998, 49, 233.
5. Gwinn, W. D. J Chem Phys 1971, 55, 477.
6. (a) Pulay, P. Mol Phys 1969, 17, 197.
7. (b) McIver, J. W.; Komornicki, A. J Am Chem Soc 1972, 94, 2625.
8. Yamaguchi, Y.; Osamura, Y.; Goddard, J. D.; Schaefer, H. F. A New Dimension to Quantum Chemistry; Oxford University Press: New York, 1994.
9. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J Comput Chem 1993, 14, 1347.
10. Horn, H.; Weiss, H.; Haser, M.; Ehrig, M.; Ahlrichs, R. J Comput Chem 1991, 9, 1058.
11. Stevens, R. M.; Pitzer, R. M.; Lipscomb, W. N. J Chem Phys 1963, 38, 550.
12. Gerratt, J.; Mills, I. M. J Chem Phys 1968, 49, 1719.
13. Pople, J. A.; Krishnan, R.; Schlegel, H. B.; Binkley, J. S. Int J Quantum Chem 1979, S13, 225.
14. King, H. F.; Komornicki, A. In Geometrical Derivatives of Energy Surfaces and Molecular Properties; Jorgenser, P.; Simons, J., Eds.; D. Reidel; Dordrecht, The Netherlands, 1986; p. 207.
15. Osamura, Y.; Yamaguchi, Y.; Fox, D. J.; Vincent, M. A.; Schaefer, H. F. J Mol Struct 1983, 103, 183.
16. Pulay, P. J Chem Phys 1983, 78, 5043.
17. Frisch, M. J.; Head-Gordon M.; Pople, J. A. Chem Phys 1990, 141, 189.
18. Windus, T. L.; Schmidt, M. W.; Gordon, M. S. Chem Phys Lett 1993, 216, 375.
19. Marquez, A. M.; Oviedo, J.; Sanz, J. F.; Dupuis, M. J Comput Chem 1997, 18, 159.
20. Sosa, C. P.; Ochterski, J.; Carpenter, J.; Frisch, M. J. J Comput Chem 1998, 19, 1053.
21. Baker, J.; Wolinski, K.; Malagoli, M.; Pulay, P. Mol Phys 2004, 102, 2475.
22. Korambath, P. P.; Kong, J.; Furlani, T. R.; Head-Gordon, M. Mol Phys 2002, 100, 1755.
23. (a) Wormer, P. E. S.; Visser, F.; Paldus, J. J Comput Phys 1982, 48, 23.
24. (b) Greenbaum, A.; Seager, M. SLAP-Sparse Linear Algebra Package 2.0.
25. (a) Schmidt, M. W.; Fletcher, G. D.; Bode, B. M.; Gordon, M. S. Comput Phys Commun 2000, 128, 190.
26. (b) Olson, R. M.; Schmidt, M. W.; Gordon, M. S.; Rendell A. P. Proceedings of Supercomputing 2003, IEEE Computer Society, http://www.sc- conference.org/ sc2003/tech_papers.php.
27. (c) Fedorov, D. G.; Olson, R. M.; Kitaura, K.; Gordon, M. S.; Koseki S. J Comput Chem 2004, 25, 872.
28. Alexeev, Y.; Kendall, R. A.; Gordon, M. S. Comput Phys Commun 2002, 143, 69.
29. Sterling, T. L.; Becker, D. J.; Savarese, D. F. How to Build a Beowulf - A Guide to the Implementation and Applications of PC Clusters; MIT Press: Cambridge, 1999.
30. Each node of this IBM p640 cluster contains four 375 MHz Power 3-II processors, 16 GB of RAM memory, and two 1 gigabit/sec Ethernet cards. For more details, see http://www.scl.ameslab.gov/ Projects/pCluster (Accessed August 2006).
31. II/Elan-4 interconnect. For more details, see http:// mscf.emsl.pnl.gov/hardware/summary_mpp2.shtml (Accessed August 2006)
32. Snir, M.; Otto, S.; Huss-Lederman, S.; Walker, D., Dongarra, J. MPI - The Complete Reference, Vol. 1: The MPI Core; MIT Press: Cambridge, 1998.
33. (a) Harrison, R. J. Theor Chim Acta 1993, 84, 363.
34. (b) Nieplocha, J.; Harrison, R. J.; Littlefield, R. J. Proceedings of Supercomputing 1994, IEEE Computer Society Press, Washington, 1994; p. 340.
35. Gropp, W.; Huss-Lederman, S.; Lumsdaine, A.; Lusk, E.; Nitzburg, B.; Saphir, W.; Snir, M. MPI - The Complete Reference, Vol. 2: The MPI Extensions; MIT Press: Cambridge, 1998.
36. Dupuis, M.; King, H. F. Int J Quantum Chem 1977, 11, 613.
37. Pople, J. A.; Hehre, W. J. J Comput Phys 1978, 27, 161.
38. Rys, J.; Dupuis, M., King, H. F. J Comput Chem 1983, 4, 154.
39. Harrison, R. J.; Kendall, R. A.; Littlefield, R. J.; Foster, I. T.; Tilson, J. L.; Wagner, A. F.; Shepard, R. L. J Comput Chem 1996, 17, 109.
40. Harrison, R. J.; Guest, M. F.; Kendall, R. A.; Bernholdt, D. E.; Wong, A. T.; Stave, M.; Anchell, J. L.; Hess, A. C.; Littlefield, R. J.; Fann, G. L.; Neiplocha, J.; Thomas, G. S.; Elwood, D.; Tilson, J. L.; Shepard, R. L.; Wagner, A. F.; Foster, I. T.; Lusk, E.; Stevens, R. J Comput Chem 1996, 17, 124.
41. Kolb, A.; Busby, S.; Buc, H.; Garges, S.; Adhya, S. Annu Rev Biochem 1993, 62, 749.
42. Each node of this cluster contains one 667 MHz EV67 AXP "alpha" processor, 1 GB of RAM memory, and a 1.28 gigabit/sec Myrinet card. For more details, see http://www.scl.ameslab.gov/Projects/ Infemo/Inferno.html (Accessed May 19, 2006).
43. Each node of this cluster contains two 1.8 GHz Athlon MP2200 processors, 2 GB of RAM memory, and a 2 gigabit/sec Myrinet card. For more details, see http://www.scl.ameslab.gov/Projects/SCI_cluster/SCI_cluster.html (Accessed May 19, 2006).
44. White, E. H.; Capra, F.; McElroy, W. D. J Am Chem Soc 1961, 83, 2402.
45. Gould, S. J.; Minott, D. A. J Org Chem 1992, 57, 5214.
46. DeMong, D. E.; Williams, R. M. J Am Chem Soc 2003, 125, 8561.