Comparison of scalable fast methods for long-range interactions

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 88, Issue 6, 2013, Pages

  Arnold, Axel ^a   Fahrenberger, Florian ^a   Holm, Christian ^a   Lenz, Olaf ^a   Bolten, Matthias ^b   Dachsel, Holger ^c   Halver, Rene ^c   Kabadshow, Ivo ^c   Gähler, Franz ^d   Heber, Frederik ^e   Iseringhausen, Julian ^e   Hofmann, Michael ^f   Pippig, Michael ^f   Potts, Daniel ^f   Sutmann, Godehard ^c,g  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF WUPPERTAL   (Germany)

^c FORSCHUNGSZENTRUM JÜLICH   (Germany)

^d BIELEFELD UNIVERSITY   (Germany)

^e UNIVERSITY OF BONN   (Germany)

^f CHEMNITZ UNIVERSITY OF TECHNOLOGY   (Germany)

^g RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK SYSTEM; FAST METHODS; FAST MULTIPOLE METHOD; LONG RANGE INTERACTIONS; PARTICLE SYSTEMS; PERIODIC BOUNDARY CONDITIONS; SYSTEM SIZE; TYPICAL APPLICATION;

FAST FOURIER TRANSFORMS;

BENCHMARKING;

EID: 84887138812     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.88.063308     Document Type: Article

References (79)

1. P. H. Hünenberger and J. A. McCammon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.477873 110, 1856 (1999).
2. P. P. Ewald, Ann. Phys. ANPYA2 0003-3804 10.1002/andp.19213690304 369, 253 (1921).
3. D. Fincham, Mol. Simul. MOSIEA 0892-7022 10.1080/08927029408022180 13, 1 (1994).
4. J. W. Perram, H. G. Petersen, and S. W. de Leeuw, Mol. Phys. 10.1080/00268978800101471 65, 875 (1988).
5. J. Lekner, Physica A 0378-4371 10.1016/0378-4371(91)90226-3 176, 485 (1991).
6. R. Sperb, Mol. Simul. 0892-7022 10.1080/08927029408021982 13, 189 (1994).
7. F. Dehez, M. Martins-Costa, D. Rinaldi, and C. Millot, J. Chem. Phys. 0021-9606 10.1063/1.1931667 122, 234503 (2005). (Pubitemid 41100422)
8. A. J. C. Ladd, Mol. Phys. MOPHAM 0026-8976 10.1080/00268977800101701 36, 463 (1978).
9. R. Sperb, Mol. Simul. 0892-7022 10.1080/08927029808024176 20, 179 (1998).
10. R. Sperb, Mol. Simul. 0892-7022 10.1080/08927029908022096 22, 199 (1999).
11. A. Arnold and C. Holm, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/S0010-4655(02)00586-6 148, 327 (2002).
12. A. Arnold and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2052647 123, 144103 (2005). (Pubitemid 41476699)
13. A. Grzybowski, E. GwóÅdå, and A. Bródka, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.61.6706 61, 6706 (2000).
14. M. Porto, J. Phys. A: Math. Gen. JPHAC5 0305-4470 10.1088/0305-4470/33/ 35/309 33, 6211 (2000).
15. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Taylor & Francis, Bristol, PA, 1988).
16. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464397 98, 10089 (1993).
17. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.470117 103, 8577 (1995).
18. M. Deserno and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.477414 109, 7678 (1998). (Pubitemid 128678339)
19. V. Ballenegger, J. J. Cerdà, and C. Holm, J. Chem. Theory Comput. 1549-9618 10.1021/ct2001792 8, 936 (2012).
20. M. Deserno and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.477415 109, 7694 (1998). (Pubitemid 128678340)
21. J. E. Barnes and P. Hut, Nature (London) NATUAS 0028-0836 10.1038/324446a0 324, 446 (1986).
22. L. Greengard and V. Rokhlin, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(87)90140-9 73, 325 (1987).
23. K. N. Kudin and G. E. Scuseria, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1771634 121, 2886 (2004).
24. A. C. Maggs and V. Rossetto, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.88.196402 88, 196402 (2002).
25. I. Pasichnyk and B. Dünweg, J. Phys.: Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/16/38/017 16, 3999 (2004).
26. A. Arnold and C. Holm, in Advanced Computer Simulation Approaches for Soft Matter Sciences, edited by, C. Holm, and, K. Kremer, Advances in Polymer Sciences Vol. II (Springer, Berlin, 2005), pp. 59-109.
27. G. A. Cisneros, V. Babin, and C. Sagui, Biomolecular Simulations (Springer, Berlin, 2013), pp. 243-270.
28. D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic Press, San Diego, 2002).
29. C. Sagui and T. A. Darden, in Simulation and Theory of Electrostatic Interactions in Solution, edited by, L. R. Pratt, and, G. Hummer, (AIP, Melville, NY, 1999), pp. 104-113.
30. G. Sutmann, P. Gibbon, and T. Lippert (eds.), Fast Methods for Long Range Interactions in Complex Systems (IAS, Jülich, 2009).
31. A. Y. Toukmaji and J. A. Board, Jr., Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(96)00016-1 95, 73 (1996).
32. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 1549-9618 10.1021/ct700301q 4, 435 (2008).
33. S. J. Plimpton, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1995.1039 117, 1 (1995).
34. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, and K. Schulten, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20289 26, 1781 (2005). (Pubitemid 43078511)
35. ESPRESSO - Extensible Simulation Package for Research on Soft Matter, http://espressomd.org
36. SCAFACOS - Scalable Fast Coloumb Solvers, http://www.scafacos.de
37. B. Luty, M. Davis, I. Tironi, and W. van Gunsteren, Mol. Simul. MOSIEA 0892-7022 10.1080/08927029408022004 14, 11 (1994).
38. A. Y. Toukmaji and J. A. Board, Jr., Comput. Phys. Commun. 0010-4655 10.1016/0010-4655(96)00016-1 95, 73 (1996).
39. E. L. Pollock and J. Glosli, Comput. Phys. Commun. 0010-4655 10.1016/0010-4655(96)00043-4 95, 93 (1996).
40. K. Esselink, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(95) 00003-X 87, 375 (1995).
41. S. W. de Leeuw, J. W. Perram, and E. R. Smith, Proc. R. Soc. London Ser. A 1364-5021 10.1098/rspa.1980.0136 373, 57 (1980).
42. E. R. Smith, Proc. R. Soc. London, Ser. A 1364-5021 10.1098/rspa.1981. 0064 375, 475 (1981).
43. M. Neumann, Mol. Phys. MOPHAM 0026-8976 10.1080/00268978300102721 50, 841 (1983).
44. M. Griebel, S. Knapek, and G. Zumbusch, Numerical Simulation in Molecular Dynamics - Numerics, Algorithms, Parallelization, Applications, 1st ed. (Springer-Verlag, Heidelberg, 2007).
45. W. Spotz and G. Carey, Numer. Methods Partial Differ. Equations 0749-159X 10.1002/(SICI)1098-2426(199603)12:2<235::AID-NUM6>3.0.CO;2-R 12, 235 (1996).
46. G. Sutmann and B. Steffen, J. Comput. Appl. Math. JCAMDI 0377-0427 10.1016/j.cam.2005.03.041 187, 142 (2006). (Pubitemid 41586510)
47. U. Trottenberg, C. W. Oosterlee, and A. Schuller, Multigrid (Academic Press, San Diego, 2000).
48. S. W. de Leeuw, J. W. Perram, and E. R. Smith, Proc. R. Soc. London Ser. A 1364-5021 10.1098/rspa.1980.0135 373, 27 (1980).
49. J. W. Perram, H. G. Petersen, and S. W. De Leeuw, Mol. Phys. MOPHAM 0026-8976 10.1080/00268978800101471 65, 875 (1988).
50. M. Pippig and D. Potts, SIAM J. Sci. Comput. 1064-8275 10.1137/120888478 35, C411 (2013).
51. F. Weik, Master's thesis, Universität Stuttgart, 2011.
52. V. Ballenegger, J. J. Cerdà, O. Lenz, and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2816570 128, 034109 (2008).
53. J. J. Cerdà, V. Ballenegger, O. Lenz, and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3000389 129, 234104 (2008).
54. A. Neelov and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3430521 132, 234103 (2010).
55. H. Q. Ding, R. D. Ferraro, and D. B. Gennery, A Portable 3D FFT Package for Distributed-Memory Parallel Architectures (SIAM, Philadelphia, 1995), pp. 70-71.
56. J. Keiner, S. Kunis, and D. Potts, ACM Trans. Math. Software 0098-3500 10.1145/1555386.1555388 36, 1 (2009).
57. D. Potts, G. Steidl, and M. Tasche, in Modern Sampling Theory: Mathematics and Applications, edited by, J. J. Benedetto, and, P. J. S. G. Ferreira, (Birkhäuser, Boston, 2001), pp. 247-270.
58. D. Potts and G. Steidl, SIAM J. Sci. Comput. SJOCE3 1064-8275 10.1137/S1064827502400984 24, 2013 (2003).
59. D. Potts, G. Steidl, and A. Nieslony, Numer. Math. NUMMA7 0029-599X 10.1007/s00211-004-0538-5 98, 329 (2004). (Pubitemid 39216472)
60. F. Hedman and A. Laaksonen, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.04.106 425, 142 (2006). (Pubitemid 43866661)
61. M. Pippig and D. Potts, in Fast Methods for Long-Range Interactions in Complex Systems, edited by, G. Sutmann, P. Gibbon, and, T. Lippert, IAS-Series (Forschungszentrum, Jülich, 2011), pp. 131-158.
62. M. Pippig, PNFFT, PNFFT, Parallel Nonequispaced FFT subroutine library, http://www.tu-chemnitz.de/~mpip/software.
63. M. Pippig, SIAM J. Sci. Comput. SJOCE3 1064-8275 10.1137/120885887 35, C213 (2013).
64. M. Pippig, PFFT, Parallel FFT subroutine library, http://www.tu-chemnitz. de/~mpip/software.
65. A. Arnold and M. Pippig (unpublished).
66. L. Greengard and V. Rokhlin, Acta Numer. 0962-4929 10.1017/ S0962492900002725 6, 229 (1997).
67. C. A. White and M. Head-Gordon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.468354 101, 6593 (1994).
68. H. Dachsel, M. Hofmann, and G. Rünger, Proceedings of the 13th International Euro-Par Conference, 4641 LNCS (Springer, Berlin, 2007), pp. 695-704.
69. C. A. White and M. Head-Gordon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.472369 105, 5061 (1996).
70. H. Dachsel, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3358272 132, 119901 (2010).
71. F. Fahrenberger and C. Holm, arXiv: 1309.7859.
72. B. W. H. van Beest, G. J. Kramer, and R. A. van Santen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.64.1955 64, 1955 (1990).
73. JUQUEEN web site, http://www.fz-juelich.de/ias/jsc/juqueen
74. JUGENE - Jülich Blue Gene/P, http://www.fz-juelich.de/ias/jsc/EN/ Expertise/Supercomputers/JUGENE/JUGENE-node.html
75. JUROPA - Jülich Research on Petaflop Architectures, http://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JUROPA/JUROPA-node. html
76. M. Bolten, F. Fahrenberger, F. Gähler, R. Halver, F. Heber, M. Hofmann, I. Kabadshow, O. Lenz, and M. Pippig, scafacos Manual, http://www.scafacos.de.
77. M. Bolten, Multigrid Methods for Structured Grids and Their Application in Particle Simulation (Bergische Universität Wuppertal, Wuppertal, 2008).
78. E. Hairer, C. Lubich, and G. Wanner, Geometric Numerical Integration. Structure-Preserving Algorithms for Ordinary Differential Equations (Springer, Heidelberg, 2002).
79. J. Stadler, R. Mikulla, and H. R. Trebin, Int. J. Mod. Phys. C IJMPEO 0129-1831 10.1142/S0129183197000990 8, 1131 (1997).