COMPCHEM: Progress Towards GEMS a Grid Empowered Molecular Simulator and Beyond

Journal of Grid Computing

Volumn 8, Issue 4, 2010, Pages 571-586

  Laganà, Antonio ^a   Costantini, Alessandro ^a   Gervasi, Osvaldo ^a   Lago, Noelia Faginas ^a   Manuali, Carlo ^a   Rampino, Sergio ^a  

^a UNIVERSITY OF PERUGIA   (Italy)

Author keywords

EGEE; Grid; Molecular dynamics

Indexed keywords

AB INITIO; BUILDING BLOCKES; COMPUTATIONAL DEVELOPMENT; COMPUTING GRID; DYNAMICS EQUATION; EGEE; EXCHANGE PROCESS; GRID; MOLECULAR SIMULATORS; NUCLEAR MOTIONS; QUANTUM METHODS; STATISTICAL AVERAGING;

EQUATIONS OF MOTION; SIMULATORS;

MOLECULAR DYNAMICS;

EID: 78049337966     PISSN: 15707873     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10723-010-9164-x     Document Type: Article

References (60)

1. Laganà, A. (ed.): Supercomputer Algorithms for Reactivity, Dynamics and Kinetics of Small Molecules. Kluwer, Dordrecht. (1989). ISBN 0-7923-0226-5.
2. Hirst, D. M.: A Computational Approach to Chemistry. Blackwell Scientific Publications, Oxford (1990). ISBN 0-632-02431-3.
3. Schatz, G. C., Ratner, M. A.: Quantum Mechanics in Chemistry. Prentice Hall, Englewood Cliffs (1993). ISBN 0-13-075011-5.
4. Laganà, A., Riganelli, A. (eds.): Lecture Notes in Chemistry. Springer, Berlin (2000). ISBN 3-540-41202-6.
5. Laganà, A., Lendvay, G. (eds.): Theory of Chemical Reaction Dynamics. Kluwer, Dordrecht (2004). ISBN 1-4020-2165-6.
6. Laganà, A., Riganelli, A.: Computational Reaction and Molecular Dynamics: From Simple Systems and Rigorous Methods to Complex Systems and Approximate Methods. Lecture Notes in Chemistry, vol. 75, 1-10 (2000).
7. Gervasi, O., Crocchianti, S., Pacifici, L., Skouteris, D., Laganà, A.: Towards the Grid design of the dynamics engine of a molecular simulator. In: Lecture Series in Computer and Computational Science, vol. 7, pp. 1425-1428 (2006).
8. Gervasi, O., Manuali, C., Laganà, A., Costantini, A.: On the structuring of a molecular simulator as a Grid service. In: Chemistry and Material Science Applications on Grid Infrastructures. ICTP Lecture Notes, vol. 24, pp. 63-82 (2009). ISBN 92-95003-42-X.
9. Laganà, A., Riganelli, A., Gervasi, O.: On the structuring of the computational chemistry virtual organization COMPCHEM. Lect. Notes Comput. Sci. 3980, 665-674 (2006). http://compchem. unipg. it.
10. EGEE (Enabling Grids for E-Science in Europe): http://public. eu-egee. org.
11. Gervasi, O., Laganà, A.: SIMBEX: a portal for the a priori simulation of crossed beam experiments. Future Gener. Comput. Syst. 20(5), 703-716 (2004).
12. Newhouse, S.: http://web. eu-egi. eu/documents/other/egi-blueprint/.
13. Costantini, A.: Computational chemistry-requirements and experiences with use of MPI. In: EGEE, EGEE'09, Barcelona, September 09. http://indico. cern. ch/contributionDisplay. py?contribId=208& sessionId=19& confId=55893.
14. 3 Tropospheric in Middle Italy. http://indico. cern. ch/contributionDisplay. py?contribId=82& sessionId=137& confId=55893.
15. Chapman, S., Gelb, A., Bunker, D. L.: A + BC: A General Triatomic Classical Trajectory Program. Quantum Chemistry Program Exchange, QCPE 273, Indiana University (1975).
16. Polanyi, J. C., Schreiber, J. L.: The dynamics of bimolcular reactions in physical chemistry. An advanced treatise. In: Eyring, H., Jost, W., Henderson, D. (eds.) Kinetics of Gas Reactions, vol. VI, p. 383. Academic, New York (1974).
17. Storchi, L., Tarantelli, F., Laganà, A.: Computing molecular energy surfaces on a Grid. Lect. Notes Comput. Sci. 3980, 675-683 (2006).
18. Verdicchio, M.: Thesis of the Euromaster in Theoretical Chemistry and Computational Modelling, Perugia (2009).
19. Gordon, M. S., Schmidt, M. W.: Advances in electronic structure theory: GAMESS a decade later. In: Dykstra, C. E., Frenking, G., Kim, K. S., Scuseria, G. E. (eds.) Theory and Applications of Computational Chemistry: The First Forty Years, pp. 1167-1189. Elsevier, Amsterdam (2005).
20. DALTON: A Molecular Electronic Structure Program, Release 2.0 (2005). See http://daltonprogram. org.
21. Werner, H. J., Knowles, P. J.: MOLPRO: A Package of Ab Initio Programs, Version 2002. 6. http://www. molpro. net/.
22. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, Jr., J. A., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C. Iyengar, S. S. Tomasi, J. Cossi, M. Rega, Millam, N. J., Klene, M. Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R. E., Stratmann, O., Yazyev, A. J., Austin, R., Cammi, C., Pomelli, J. W., Ochterski, R., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, O., Foresman, J. B., Ortiz, J. V., Cioslowski, J., Fox, D. J.: Gaussian 09, Revision A. 1. Gaussian, Wallingford (2009).
23. Arteconi, L., Laganà, A., Pacifici, L.: A web based application to fit potential energy functionals to ab initio values. Lect. Notes Comput. Sci. 3980, 694-700 (2006).
24. Angeli, C., Bendazzoli, G. L., Borini, S., Cimiraglia, R., Emeerson, A., Evangelisti, S., Maynau, D., Monari, A., Rossi, E., Sanchez-Marin, J., Szalay, P. G., Tajti, A.: The problem of interoperability: a common data format for quantum chemistry codes. Int. J. Quant. Chem. 107, 2082-2091 (2007).
25. Schatz, G. C.: Potential energy surfaces. Lect. Notes Chem. 75, 15-32 (2000).
26. Murrell, J. N., Carter, S., Farantos, S. C., Huxley, P., Varandas, A. J. C.: Molecular Potential Energy Functions. Wiley, London (1984).
27. Garcia, E., Laganà, A.: Diatomic potential functions for triatomic scattering. Mol. Phys. 56, 621-627 (1985).
28. Garcia, E., Laganà, A.: A new bond order functional form for triatomic molecules: a fit of the BeFH potential energy. Mol. Phys. 56, 629-639 (1985).
29. Aguado, A., Tablero, C., Paniagua, M.: Global fit of ab initio potential energy surfaces I: triatomic systems. Comput. Phys. Commun. 108, 259-266 (1998).
30. Laganà, A.: A rotating bond order formulation of the atom diatom potential energy surface. J. Chem. Phys. 95, 2216-2217 (1991).
31. Laganà, A., Ochoa de Aspuru, G., Garcia, E.: The largest angle generalization of the rotating bond order potential: three different atom reactions. J. Chem. Phys. 108, 3886-3896 (1998).
32. Rodriguez, A., Garcia, E., Hernandez, M. L., Laganà, A.: A LAGROBO strategy to fit potential energy surfaces: the OH + HCl reaction. Chem. Phys. Lett. 360, 304-312 (2002).
33. 1g) system on a LEPS surface: inelastic and reactive probabilities. Mol. Phys. 102(21-22), 2237-2248 (2004).
34. Pack, R. T.: Space-fixed vs body-fixed axes in atom-diatomic molecule scattering. Sudden approximations. J. Chem. Phys. 60, 633-700 (1974).
35. McGuire, P. M., Kouri, D.: Quantum mechanical close coupling approach to molecular collisions: jz-conserving coupled states approximation. J. Chem. Phys. 60 2488-2503 (1974).
36. Balint-Kurti, G. G.: Time dependent quantum approaches to chemical reactivity. Lect. Notes Chem. 75, 74-87 (2000).
37. 2 reaction. Theor. Chem. Acc. (in press).
38. Tsai, Y. R., Cheng, L. T., Osher, S., Zhao, H. K.: Fast sweeping algorithms for a cLass of Hamilton-Jacobi equations. SIAM J. Numer. Anal. 41, 673-694 (2003).
39. Skouteris, D., Castillo, J. F., Manolopulos, D. E.: ABC: a quantum reactive scatering program. Comput. Phys. Commun. 133, 128-135 (2000).
40. 2 and Cl + HCl. Chem. Phys. Lett. 150, 92-98 (1998).
41. Casavecchia, P., Balucani, N., Volpi, G. G.: The chemical dynamics and kinetics of small radicals. In: Lin, K., Wagner, A. F. (eds.) Adv. Ser. Phys. Chem., vol. 6, chapter 9. World Scientific, Singapore (1995).
42. Lee, Y. T.: In: Scoles, G. (ed.) Atomic and Molecular Beam Method. Oxford University Press, New York (1987).
43. Siska, P. E.: Iterative unfolding of intensity data, with application to molecular beam scattering. J. Chem. Phys. 59, 6052 (1973).
44. Skouteris, D., De Fazio, D., Cavalli, S., Aquilanti, V.: Quantum stereodynamics for the two product channels of the F + HD reaction from the complete scattering matrix in the stereodirected representation. J. Phys. Chem. A 113, 14807-14812 (2009).
45. Saracibar, A., Sanchez, C., Garcia, E., Laganà, A., Skouteris, D.: Grid computing in time dependent quantum reactive dynamics. Lect. Notes Comput. Sci. 5072, 1065-1080 (2008).
46. Bellucci, D., Tasso, S., Laganà, A.: Parallel model for a discrete variable wavepacket propagation. Lect. Notes Comput. Sci. 2658, 341-349 (2003).
47. Gregori, S., Tasso, S., Laganà, A.: Fine grain parallelization of a discrete variable wavepacket calculation using ASSIST-CL. Lect. Notes Comput. Sci. 3044, 437-444 (2004).
48. Kacsuk, P., Sipos, G.: Multi-Grid, Multi-user workflows in the P-GRADE portal. Journal of Grid Computing 3(3-4), 221-238 (2005).
49. Kacsuk, P., Dózsa, G., Kovács, J., Lovas, R., Podhorszki, N. Z., Balaton Gombás, G.: P-GRADE: a Grid programming environment. Journal of Grid Computing 1. 171-197 (2003).
50. Kacsuk, P., Farkas, Z., Herman, G.: Workflow-level parameter study support for production Grids. Lect. Notes in Comput. Sci. 4707, 872-885 (2007).
51. Skouteris, D., Costantini, A., Laganà, A., Sipos, G., Balaski, A., Kacsuk, P.: Implementation of the ABC quantum mechanical reactive scattering program on the EGEE Grid platform. Lect. Notes Comput. Sci. 5072, 1108-1120 (2008).
52. Multi-Grid installation of P-GRADE portal: http://portal. p-grade. hu/multi-Grid.
53. Kacsuk, P., Sipos, G.: Multi-Grid, Multi-user workflows in the P-GRADE Grid portal. Journal of Grid Computing 3, 221-238 (2006).
54. 2reaction calculated on two potential energy surfaces. Lect. Notes Comput. Sci. 5072, 1081-1093 (2008).
55. 2 reaction: quantum detailed probabilities and thermal rate coefficients. Theor. Chem. Acc. 123, 249-256 (2009).
56. Manolopulos, D. E.: An improved log derivative method for inelastic scattering. J. Chem. Phys. 85, 6425-6429 (1986).
57. Pack, R. T., Parker, G. A.: Quantum scattering in the three dimentions using hyperspherical (APH) coordinates. Theory. J. Chem. Phys. 87, 3888-3921 (1987).
58. Manuali, C., Laganà, A., Rampino, S.: GRIF: a Grid Framework for a web service approach to reactive scattering. Comp. Phys. Commun. 181, 1179-1185 (2010).
59. www. cineca. it.
60. www. cnaf. infn. it.