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The linked neighbour list (LNL) method for fast off-lattice Monte Carlo simulations of fluids. (English) Zbl 1333.82023
Summary: We present a new algorithm, called linked neighbour list (LNL), useful to substantially speed up off-lattice Monte Carlo simulations of fluids by avoiding the computation of the molecular energy before every attempted move. We introduce a few variants of the LNL method targeted to minimise memory footprint or augment memory coherence and cache utilisation. Additionally, we present a few algorithms which drastically accelerate neighbour finding. We test our methods on the simulation of a dense off-lattice Gay-Berne fluid subjected to periodic boundary conditions observing a speedup factor of about 2.5 with respect to a well-coded implementation based on a conventional link-cell. We provide several implementation details of the different key data structures and algorithms used in this work.
82C80 Numerical methods of time-dependent statistical mechanics (MSC2010)
82D15 Statistical mechanical studies of liquids
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[1] ()
[2] Allen, M.P.; Tildesley, R.M., Computer simulation of liquids, (1987), Clarendon Press Oxford · Zbl 0703.68099
[3] Frenkel, D.; Smith, B., Understanding molecular simulation: from algorithms to applications, (1996), Academic Press San Diego · Zbl 0889.65132
[4] Panagiotopoulos, A.Z., Mol. phys., 61, 813, (1987)
[5] Smit, B.; Karaborni, S.; Siepmann, J.I., J. chem. phys., 102, 2126, (1995)
[6] Pant, P.V.K.; Theodorou, D.N., Macromolecules, 28, 7224, (1995)
[7] Uhlherr, A.; Mavrantzas, V.G.; Doxastakis, M.; Theodorou, D.N., Macromolecules, 34, 8554, (2001)
[8] Baschnagel, J.; Binder, K.; Doruker, P.; Gusev, A.A.; Hahn, O.; Kremer, K.; Mattice, W.L.; Muller-Plathe, F.; Murat, M.; Paul, W.; Santos, S.; Suter, U.W.; Tries, V., Adv. polym. sci., 152, 41, (2000)
[9] Mavrantzas, V.G.; Boone, T.D.; Zervopoulou, E.; Theodorou, D.N., Macromolecules, 32, 5072, (1999)
[10] Metropolis, N., J. chem. phys., 21, 1087, (1953)
[11] Hockney, R.W.; Eastwood, J.W., Computer simulations using particles, (1981), McGraw-Hill New York · Zbl 0662.76002
[12] Verlet, L., Phys. chem., 46, 98, (1967)
[13] Sadus, R.J., Molecular simulation of fluids: theory, algorithms and object-orientation, (1999), Elsevier
[14] Heinz, T.N.; Hünenberger, P.H., A fast pairlist-construction algorithm for molecular simulations under period boundary conditions, J. comput. chem., 25, 1474, (2004)
[15] Yao, Z.; Wang, J.-S.; Liu, G.-R.; Cheng, M., Comput. phys. commun., 161, 27, (2004)
[16] Pütz, M.; Kolb, A., Comput. phys. commun., 113, 145, (1998)
[17] Mattson, W.; Rice, B.M., Comput. phys. commun., 119, 135, (1999)
[18] Gonnet, P., J. comput. chem., 28, 570, (2007)
[19] Zara, S.J.; Nicholson, D., Mol. simul., 5, 245, (1990)
[20] Gay, J.G.; Berne, B.J., J. chem. phys., 74, 3316, (1981)
[21] Berardi, R.; Fava, C.; Zannoni, C., Chem. phys. lett., 297, 462, (1995)
[22] (), 17-50
[23] J. Dongarra, A. Lumsdaine, X. Niu, R. Pozo, K. Remington, Sparse matrix libraries in C++ for high performance architectures, in: Proc. OON-SKI ’94
[24] Kotakemori, H.; Hasegawa, H.; Kajiyama, T.; Nukada, A.; Suda, R.; Nishida, A., Openmp shared memory parallel programming, (2008), Springer, pp. 153-163
[25] P.S. Lomdahl, D.M. Beazley, Multi-million particle molecular dynamics on MPPs, in: Second International Workshop, PARA95, Lyngby, Denmark, 1995
[26] J.C. Phillips, G. Zheng, S. Kumar, L.V. Kalé, NAMD: Biomolecular simulation on thousands of processors, in: Proc. SC ’02
[27] Grest, G.S.; Dünweg, B.; Kremer, K., Comput. phys. commun., 55, 269, (1989)
[28] T.C. Germann, K. Kadau, P.S. Lombdahl, 25 Tflop/s multibillion-atom molecular dynamics simulations and visualisation/analysis on BlueGene/L, in: Proc. SC ’05 · Zbl 1156.82329
[29] De Fabritiis, G., Comput. phys. commun., 176, 660, (2007)
[30] K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, D.E. Shaw, Scalable algorithms for molecular dynamics simulations on commodity clusters, in: Proc. SC ’08
[31] Rapaport, D.C., Comput. phys. commun., 174, 521, (2006)
[32] Anderson, J.A.; Lorenz, C.D.; Travesset, A., J. comput. phys., 227, 5342, (2008)
[33] Rapaport, D.C., Comput. phys. commun., 62, 271, (1991)
[34] Altmann, S.L., Rotations, quaternions and double groups, (1986), Dover Publications · Zbl 0683.20037
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