Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

Theoretical Chemistry Accounts

Volumn 117, Issue 4, 2007, Pages 541-553

  Mochizuki, Yuji ^a,b,c,d   Tanaka, Kiyoshi ^a,b,c   Yamashita, Katsumi ^e   Ishikawa, Takeshi ^c,d   Nakano, Tatsuya ^c,f   Amari, Shinji ^b   Segawa, Katsunori ^f   Murase, Tadashi ^e   Tokiwa, Hiroaki ^d   Sakurai, Minoru ^g  

^a UNIVERSITY OF TOKYO   (Japan)

^b INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d RIKKYO UNIVERSITY   (Japan)

^e NEC CORPORATION   (Japan)

^f NATIONAL INSTITUTE OF HEALTH SCIENCES   (Japan)

^g TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

CIS(D); Excited states; Fragment molecular orbital; Integral direct; MP2; Parallelism

Indexed keywords

EID: 33947513020     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-006-0181-6     Document Type: Article

References (62)

1. Blankenship RE (2002) Molecular mechanisms of photosynthesis. Blackwell, Oxford
2. Lanyi JK (1993) Biochim Biophys Acta 1183:241
3. Reichardt C (1994) Chem Rev 94:2319
4. Svensson M, Humbel S, Froese RJ, Matsubara T, Sieber S, Morokuma K (1996) J Phys Chem 100:19357
5. Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, New York
6. Kitaura K, Sawai T, Asada T, Nakano T, Uebayasi M (1999) Chem Phys Lett 312:319
7. Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M (1999) Chem Phys Lett 313:701
8. Nakano T, Kaminuma T, Sato T, Akiyama Y, Uebayasi M, Kitaura K (2000) Chem Phys Lett 318:614
9. Fedrov DG, Olson RM, Kitaura K, Gordon MS, Koseki S (2004) J Comp Chem 25:872
10. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, DupuisM, Montgomery JA(1993) J Comp Chem 14:1347, GAMESS, http://www.msg.ameslab.gov/GAMESS/
11. Fedorov DG, Kitaura K (2006) In: Starikov EB, Lewis JP, Tanaka S (eds) Modern methods for theoretical physical chemistry of biopolymers. Elsevier, Amsterdam, pp 3-38
12. Sekino H, Sengoku Y, Sugiki S, Kurita N (2003) Chem Phys Lett 378:589
13. Kendall RA, Apra E, Bernholdt DE, Bylaska EJ, Dupuis M, Fann GI, Harrison RJ, Ju J, Nichols JA, Nieplocha J, Straatsma TP, Windus TL, Wong AT (2000) Comp Phys Comm 128:260, NWCHEM, http://www.emsl.pnl.gov/docs/nwchem/nwchem.html
14. Nakano T, Kaminuma T, Sato T, Fukuzawa K, Akiyama Y, Uebayasi M, Kitaura K (2002) Chem Phys Lett 351:475, ABINIT-MP
15. Mochizuki Y, Nakano T, Koikegami S, Tanimori S, Abe Y, Nagashima U, Kitaura K (2004) Theor Chem Acc 112:442
16. Mochizuki Y, Koikegami S, Nakano T, Amari S, Kitaura K (2004) Chem Phys Lett 396:473
17. Mochizuki Y, Koikegami S, Amari S, Segawa K, Kitaura K, Nakano T (2005) Chem Phys Lett 406:283
18. Foresman JB, Head-Gordon M, Pople JA, Frisch MJ (1992) J Phys Chem 96:135
19. Fedorov DG, Kitaura K (2005) J Chem Phys 122:054108-1
20. Nakano T, Mochizuki Y, Fukuzawa K, Amari S, Tanaka S (2006) In: Starikov EB, Lewis JP, Tanaka S (eds) Modern methods for theoretical physical chemistry of biopolymers. Elsevier, Amsterdam, pp 39-52
21. Foresman JB, Frisch A (1996) Exploring chemistry with electrononic structure methods, 2nd edn. Gaussian, Pittsburgh
22. Kongsted J, Osted A, Pedersen TB, Mikkelsen KV, Christiansen O (2004) J Phys Chem A 108:8624
23. Kongsted J, Osted A, Mikkelsen KV, Åstrand P.-O., Christiansen O (2004) J Chem Phys 121:8435
24. Hirata S, Valiev M, Dupuis M, Xantheas SS, Sugiki S, Sekino H (2005) Mole Phys 103:2255
25. Meyer TE (1985) Biochim Biophys Acta 806:175
26. Imamoto Y, Kataoka M, Tokunaga F (1996) Biochem 35:14047
27. Head-Gordon M, Rico RJ, Oumi M, Lee TJ (1994) Chem Phys Lett 219:21
28. Szabo A, Ostlund NS (1982) Modern quantum chemistry. MacMillan, New York
29. Burke K, Werschnik J, Gross EKU (2005) J Chem Phys 123:062206, references therein
30. Dreuw A,Weisman JL, Head-Gordon M (2003) J Chem Phys 119:2943
31. Odelius M, Kirchner B, Hutter J (2004) J Phys Chem A 108:2044
32. Casida ME (2005) J Chem Phys 122:054111
33. Oumi M, Maurice D, Lee TJ, Head-Gordon M (1997) Chem Phys Lett 279:151
34. Head-Gordon M, Lee TJ (1997) In: Bartlett RJ (ed) Recent advances in coupled cluster methods.World Scientific, Singapore, pp 221.253
35. Head-Gordon M, Oumi M, Maurice D (1999) Mole Phys 96:593
36. Hirata S (2005) J Chem Phys 122:094105-1
37. Hirata S (2003) J Phys Chem A 107:9887
38. Pople JA, Head-Gordon M, Raghavachari K (1987) J Chem Phys 87:5968
39. Tanaka K (1972) Dr. Thesis, Department of Chemistry, Faculty of Science, Hokkaido University
40. Tanaka K (1974) Intern J Quant Chem 13:981
41. Pauncz R (2000) The construction of spin eigenfunctions. Kluwer, New York
42. Dykstra CE, Davidson ER (2000) Intern J Quant Chem 78:226
43. Head-Gordon M, Pople JA, Frisch MJ (1988) Chem Phys Lett 153:503
44. Message Passing Interface (MPI), http://www.mpi-forum.org/
45. Basic linear algebra subroutines (BLAS), http://www.netlib. org/blas/
46. Martin ME, Sánchez ML, Olivares del Valle FJ, Aguilar MA (2000) J Chem Phys 113:6308
47. Roos BO,Taylor PR, Siegbahn PEM (1980) Chem Phys 48:157
48. Kawashima K, Dupuis M, Hirao K (2002) J Chem Phys 117:248
49. Dupuis M, Kawashima Y, Hirao K (2002) J Chem Phys 117:1256
50. Koch H, JØrgensen P (1990) J Chem Phys 93:3333
51. Stanton JF, Bartlett RJ (1993) J Chem Phys 98:7029
52. Robin MB (1985) Higher excited states of polyatomic molecules. Academic, New York
53. Gaussian 03 Revision B 0.4, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, BaroneV, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, 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 JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PM W, Johnson B, Chen W, Wong MW, Gonzalez C, (2003) Pople JA, Gaussian, Pittsburgh, http://www.gaussian.com/
54. Yoda M, Houjou H, Inoue Y, Sakurai M (2001) J Phys Chem B 105:9887
55. Protein Data Bank (PDB), http://www.rcsb.org/
56. Andersson K, Malmqvist PA, Roos BO, Sadlej AJ, Wolinski K (1990) 94:5483
57. Molina V,Merchan M(2001) Proc Natl Acad Sci USA 98:4299
58. Kawaguchi K, Yamato T (2006) Chem Phys Lett 430:386
59. Matsuura A, Sato H, Houjou H, Saito S, Hayashi H, Sakurai M (2006) J Comp Chem 27:1623
60. Nielsen IB, Boyé-Péronne S, El Ghazaly MOA, Kristensen MB, Nielsen SB, Andersen LH (2005) Biophys J 89:2597
61. Kowalski K, Piecuch P (2001) J Chem Phys 115:2966
62. Piecuch P, Kucharski SA, Kowalski K, Musial M(2002) Comp Phys Comm 149:71