Journal of Chemical Physics
Feedback | Help | Exit
The Journal of Chemical Physics
   
 
 
 
Previous Article
Theoretical study of CH4 photodissociation on the Pt(111) surface
The photodissociation of CH4/Pt(111) is studied by density functional theory and the state-averaged complete active space self-consistent field (SA-CASSCF) method using a cluster model Ptn (n=1,4,6,7,...
Next Article
Normal order and extended Wick theorem for a multiconfiguration reference wave function
A generalization of normal ordering and of Wick's theorem with respect to an arbitrary reference function as some generalized "physical vacuum" is formulated in a different (but essentially...

Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems containing thousands of atoms

J. Chem. Phys. 107, 425 (1997); doi:10.1063/1.474404

Issue Date: 8 July 1997

You are not logged in to this journal. Log in

Andrew D. Daniels, John M. Millam, and Gustavo E. Scuseria
Center for Nanoscale Science and Technology, Rice Quantum Institute, and Department of Chemistry, Rice University, Houston, Texas 77005-1892
Conventional semiempirical methods using diagonalization are not practical for calculations on molecular systems containing more than a few hundred atoms because of [script O](N3) time and [script O](N2) memory requirements, where N is the number of atoms. Currently, the time dominating step is diagonalization of the Fock matrix. This paper demonstrates how [script O](N3) diagonalization and [script O](N2) memory requirements are eliminated by using a conjugate gradient search for the density matrix with sparse matrix techniques. Our method makes high accuracy energy calculations on molecules containing thousands of atoms possible on the typical workstation. Benchmark examples are presented on polyglycine chains (20000 atoms), water clusters (up to 1800 atoms), and nucleic acids (up to 6304 atoms). ©1997 American Institute of Physics.
History: Received 13 January 1997; accepted 3 April 1997
Permalink: http://link.aip.org/link/?JCPSA6/107/425/1
BUY THIS ARTICLE   (US$28)
Download PDF (124 kB) View Cart

KEYWORDS and PACS

Keywords
PACS
  • 31.15.-p
    Electronic structure of atoms, molecules and their ions: theory Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations)
  • YEAR: 1996-97

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (42)
View in Separate Window/Tab
For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. D. Bakowies and W. Thiel, J. Am. Chem. Soc. 113, 3704 (1991).
  2. D. Bakowies, M. Bühl, and W. Thiel, J. Am. Chem. Soc. 117, 10 113 (1995).
  3. J. P. Stewart, Int. J. Quantum Chem. 58, 133 (1996).
  4. T.-S. Lee, D. M. York, and W. Yang, J. Chem. Phys. 105, 2744 (1996).
  5. S. L. Dixon and K. M. Merz, Jr., J. Chem. Phys. 104, 6643 (1996).
  6. X. P. Li, R. W. Nunes, and D. Vanderbilt, Phys. Rev. B 47, 10 891 (1993);
    7. R. W. Nunes and D. Vanderbilt, ibid. 50, 17 611 (1994).
  7. S.-Y. Qiu, C. Z. Wang, K. M. Ho, and C. T. Chan, J. Phys. Condensed. Matter 6, 9153 (1994).
  8. C. H. Xu and G. E. Scuseria, Chem. Phys. Lett. 262, 219 (1996).
  9. J. M. Millam and G. E. Scuseria, J. Chem. Phys. (in press).
  10. C. A. White, B. G. Johnson, P. M. W. Gill, and M. Head-Gordon, Chem. Phys. Lett. 230, 8 (1994).
  11. M. C. Strain, G. E. Scuseria, and M. J. Frisch, Science 271, 51 (1996).
  12. M. J. S. Dewar and W. Thiel, J. Am. Chem. Soc. 99, 4499 (1977).
  13. A. D. Becke, J. Chem. Phys. 88, 2547 (1988).
  14. R. E. Stratmann, G. E. Scuseria, and M. J. Frisch, Chem. Phys. Lett. 257, 213 (1996).
  15. L. P. Davis, R. M. Guidry, J. R. Williams, M. J. S. Dewar, and H. S. Rzepa, J. Comp. Chem. 2, 433 (1981).
  16. M. J. S. Dewar, M. L. McKee, and H. S. Rzepa, J. Am. Chem. Soc. 100, 3607 (1978).
  17. M. J. S. Dewar, E. G. Zoebisch, E. F. Hearly, and J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).
  18. M. J. S. Dewar and C. H. Reynolds, J. Comp. Chem. 2, 140 (1986).
  19. M. J. S. Dewar and W. Thiel, J. Am. Chem. Soc. 99, 4899 (1977).
  20. M. J. S. Dewar and H. S. Rzepa, J. Am. Chem. Soc. 100, 777 (1978).
  21. M. J. S. Dewar and M. L. McKee, J. Comp. Chem. 4, 84 (1978).
  22. M. J. S. Dewar and E. F. Healy, J. Comp. Chem. 4, 542 (1983).
  23. M. J. S. Dewar, G. L. Grady, and J. J. P. Stewart, J. Am. Chem. Soc. 106, 6771 (1984).
  24. M. S. Dewaret al., Organometallics 4, 1964 (1985).
  25. J. J. P. Stewart, J. Comp. Chem. 10, 209 (1989).
  26. J. J. P. Stewart, J. Comp. Chem. 10, 221 (1989).
  27. R. C. Bingham, M. Dewar, and Lo, J. Am. Chem. Soc. 97, 1285, 1294, 1302, 1307 (1975).
  28. R. McWeeny, Rev. Mod. Phys. 32, 335 (1960).
  29. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and W. P. Flannery, Numerical Recipes in Fortran, 2nd ed. (Cambridge University Press, Cambridge, 1992).
  30. S. Pissanetsky, Sparse Matrix Technology (Academic, London, 1984).
  31. The polyglycine chains are similar to those described in Refs. 4, 37, and 38. Coordinates for these molecules are available from us.
  32. The water clusters up to 150 water molecules are those used in Ref. 39. We obtained the coordinates from the authors of Ref. 39. Coordinates for the 300 and 600 water molecule cluster are available from us.
  33. GAUSSIAN 95, Development Version, Revision D.4, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, M. C. Strain, J. C. Burant, R. E. Stratmann, G. A. Petersson, J. A. Montgomery, V. G. Zakrzewski, T. Keith, K. Raghavachari, M. A. Al-Laham, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, C. Gonzalez, M. Head-Gordon, P. M. W. Gill, B. G. Johnson, and J. A. Pople, Gaussian, Inc., Pittsburgh Pennsylvania, 1996.
  34. J. Almöf, K. Faergi, Jr., and K. Korsell, J. Comp. Chem. 3, 385 (1982).
  35. P. Pulay, J. Comp. Chem. 3, 556 (1982).
  36. The 368 atom RNA molecule is from Ref. 40. The 651 atom DNA molecule is from Ref. 41 with sodium atoms added to balance the charge. The 1576 atom RNA molecule is from Ref. 42. Hydrogens were added with Xplor. All larger RNA molecules were made from replicating the 1576 atom RNA molecule.
  37. W. Yang, Phys. Rev. Lett. 66, 1438 (1991).
  38. W. Yang, J. Mol. Struct. (Theochem) 255, 461 (1992).
  39. E. Schwegler and M. Challacombe, J. Chem. Phys. 105, 2726 (1996).
  40. J. Hutter, P. Carloni, and M. Parrinello, J. Am. Chem. Soc. 118, 8710 (1996).
  41. J. D. Baleja, R. T. Pon, and B. D. Sykes, Biochemistry 29, 4828 (1990).
  42. S. E. Lietzke, V. E. Carperos, and C. E. Kundrot, Acta Crystallogr. Sect. D 52, 687 (1996).

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.


Copyright © American Institute of Physics