Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry

Journal of Computational Chemistry

Volumn 34, Issue 6, 2013, Pages 492-504

  Bosson, Maël ^a   Grudinin, Sergei ^a   Redon, Stephane ^a  

^a UNIV GRENOBLE ALPES   (France)

Author keywords

adaptive; ASED MO; divide and conquer; interactive quantum chemistry; reduced basis

Indexed keywords

ACTIVE PARTS; ADAPTIVE; ASED-MO; ATOM SUPERPOSITION AND ELECTRON DELOCALIZATION MOLECULAR ORBITAL; COMPUTATIONAL RESOURCES; DIVIDE AND CONQUER; DIVIDE-AND-CONQUER APPROACH; DIVIDE-AND-CONQUER TECHNIQUE; INTERACTIVE RATES; LOCAL MINIMUMS; ON THE FLIES; REDUCED BASIS; STANDARD DESKTOP; TIME STEP; VIRTUAL PROTOTYPING;

MOLECULAR ORBITALS;

QUANTUM THEORY;

ALGORITHM; ARTICLE; CHEMICAL MODEL; QUANTUM THEORY;

ALGORITHMS; MODELS, CHEMICAL; QUANTUM THEORY;

EID: 84873425924     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23157     Document Type: Article

References (48)

1. C. J. Cramer, Essentials of Computational Chemistry: Theories and Models; Wiley: Hoboken, New Jersey, 2004.
2. R. S. Mulliken, Spectroscopy, Molecular Orbitals, and Chemical Bonding, Nobel Lecture, Elsevier: Amsterdam, 1966.
3. A. B. Anderson, Int. J. Quantum Chem. 1994, 49, 581.
4. M. Bosson, C. Richard, A. Plet, S. Grudinin, S. Redon, J. Comput. Chem. 2012, 18, 23.
5. S. L. Dixon, K. M. Merz, Jr., J. Chem. Phys. 1996, 104, 6643.
6. W. Pan, T. S. Lee, W. T. Yang, J. Comput. Chem. 1998, 19, 1101.
7. E. Breitmoser, A. G. Sunderland, A performance study of the PLAPACK and SCALAPACK eigensolvers on hpcx for the standard problem, Technical Report from the HPCx Consortium. Available at: http://www.hpcx.ac.uk/research/hpc/technical- reports/HPCxTR0406.pdf. Accessed on October 15, 2012.
8. P. Bientinesi, I. S. Dhillon, R. A. Van De Geijn, SIAM J. Sci. Comput. 2006, 27, 43.
9. H. Sutter, Dr. Dobb's J. 2005, 30, 202.
10. M. J. Rayson, P. R. Briddon, Comput. Phys. Commun. 2008, 178, 128.
11. M. D. Ermolaeva, A. van der Vaart, K. M. Merz, Jr., J. Phys. Chem. A 1999, 103, 1868.
12. W. Kohn, Phys. Rev. Lett. 1996, 76, 3168.
13. T.-S. Lee, W. Yang, Int. J. Quantum Chem. 1998, 69, 397.
14. P. R. Surján, D. Kohalmi, Z. Rolik, Á. Szabados, Chem. Phys. Lett. 2008, 450, 400.
15. J. J. P. Stewart, Int. J. Quantum Chem. 1996, 58, 133.
16. M. Bosson, S. Grudinin, X. Bouju, S. Redon, J. Comput. Phys. 2011, 231, 2581.
17. I. S. Ufimtsev, T. J. Martínez, J. Chem. Theory Comput. 2008, 4, 222.
18. M. Thottethodi, S. Chatterjee, A. R. Lebeck, In Proceedings of the 1998 ACM/IEEE Conference on Supercomputing (CDROM); IEEE Computer Society, Washington DC, 1998; pp. 1-14.
19. R. C. Whaley, A. Petitet, J. Dongarra, Parallel Comput. 2001, 27, 3.
20. E. Chan, E. S. Quintana-Orti, G. Quintana-Orti, R. Van De Geijn, In Proceedings of the Nineteenth Annual ACM Symposium on Parallel Algorithms and Architectures; ACM, New York, 2007; pp. 116-125.
21. V. Volkov, J. W. Demmel, In International Conference for High Performance Computing, Networking, Storage and Analysis, 2008, SC 2008; IEEE, Darestbury, 2008; pp. 1-11.
22. A. K. Noor, J. M. Peters, In 20th Structures, Structural Dynamics, and Materials Conference, SIAM, Philadelphia: St. Louis, MO, 1979; pp. 116-126.
23. E. Cances, C. Le Bris, N. C. Nguyen, Y. Maday, A. T. Patera, G. S. H. Pau, In Proceedings of the Workshop for High Dimensional Partial Differential Equations in Science and Engineering, Montreal, 2007.
24. Y. Maday, U. Razafison, Comptes Rendus Math. 2008, 346, 243.
25. R. Hoffmann, J. Chem. Phys. 1963, 39, 1397.
26. F. Shimojo, R. K. Kalia, A. Nakano, P. Vashishta, Phys. Rev. B 2008, 77, 085103.
27. T. S. Lee, J. P. Lewis, W. Yang, Comput. Mater. Sci. 1998, 12, 259.
28. A. Van Der Vaart, D. Surez, K. M. Merz, J. Chem. Phys. 2000, 113, 10512.
29. W. Yang, T. S. Lee, J. Chem. Phys. 1995, 103, 5674.
30. M. Kobayashi, H. Nakai, In Linear-Scaling Techniques in Computational Chemistry and Physics, Vol. 97, Springer: Germary, 2011; p. 127.
31. R. Zalesny, M. G. Papadopoulos, P. G. Mezey, J. Leszczynski, Challenges and Advances in Computational Chemistry and Physics, Springer: Berlin, Vol. 13, 2011.
32. R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam, S. Crouzy, M. Vivaudou, S. Redon, Bioinformatics 2007, 23, i408.
33. G. W. Stewart, Linear Algebra Appl. 1979, 23, 69.
34. G. W. Stewart, J. Sun, Matrix Perturbation Theory, Vol. 175; Academic Press: San Diego, CA, 1990.
35. Intel, Math Kernel Library. Available at: www.intel.com/software/ products/mkl. Accessed on October 15, 2012.
36. J. O. Sofo, A. S. Chaudhari, G. D. Barber, Phys. Rev. B 2007, 75, 153401.
37. S. B. Legoas, P. A. S. Autreto, M. Z. S. Flores, D. S. Galvao, Arxiv preprint, 2009. arXiv:0903.0278.
38. SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems), NANO-D. Available at: http://nano-d.inrialpes.fr/ Accessed on October 15, 2012.
39. E. L. Briggs, D. J. Sullivan, J. Bernholc, Phys. Rev. B 1996, 54, 14362.
40. G. Kresse, J. Furthmüller, Comput. Mater. Sci. 1996, 6, 15.
41. L. Genovese, A. Neelov, S. Goedecker, T. Deutsch, S. A. Ghasemi, A. Willand, D. Caliste, O. Zilberberg, M. Rayson, A. Bergman, R. Schneider, J. Chem. Phys. 2008, 129, 014109.
42. S. Artemova, S. Redon, ARPS: Adaptively Restrained Particle Simulations, http://prl.aps.org/accepted/3b075Y70C611312666b2065803568b39c1d 67855b.
43. E. Agullo, J. Dongarra, R. Nath, S. Tomov, A fully empirical autotuned dense QR factorization for multicore architectures, Technical Report 242, LAPACK Working Note, 2011.
44. A. Buttari, J. Langou, J. Kurzak, J. Dongarra, Concurr. Comput. Pract. Exp. 2008, 20, 1573.
45. A. Buttari, J. Langou, J. Kurzak, J. Dongarra, Parallel Comput. 2009, 35, 38.
46. L. Liu, Z. Li, A. H. Sameh, In Proceedings of the 22nd Annual International Conference on Supercomputing; ACM, Washington DC, 2008; pp. 359-367.
47. G. H. Golub, C. F. Van Loan, Matrix Computations, Vol. 3; Johns Hopkins University Press, Baltimore, Maryland, 1996.
48. R. Chandra, Parallel Programming in OpenMP; Morgan Kaufmann, Burlington, Massachusetts, 2001.