zbMATH — the first resource for mathematics

A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements. (English) Zbl 1321.82005
Griebel, Michael (ed.), Singular phenomena and scaling in mathematical models. Cham: Springer (ISBN 978-3-319-00785-4/hbk; 978-3-319-00786-1/ebook). 327-346 (2014).
Summary: It is the ultimate goal of concurrent multiscale methods to provide computational tools that allow to simulation physical processes with the accuracy of micro-scale and the computational speed of macro-scale models. As a matter of fact, the efficient and scalable implementation of concurrent multiscale methods on clusters and supercomputers is a complicated endeavor. In this article we present the parallel multiscale simulation tool Maci which has been designed for efficient coupling between molecular dynamics and finite element codes. We propose a specification for a thin yet versatile interface for the coupling of molecular dynamics and finite element codes in a modular fashion. Further we discuss the parallelization strategy pursued in Maci, in particular, focusing on the parallel assembly of transfer operators and their efficient execution.
For the entire collection see [Zbl 1278.00016].

82-08 Computational methods (statistical mechanics) (MSC2010)
82C80 Numerical methods of time-dependent statistical mechanics (MSC2010)
65M60 Finite element, Rayleigh-Ritz and Galerkin methods for initial value and initial-boundary value problems involving PDEs
Full Text: DOI
[1] Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Oxford Science, Oxford (1987) · Zbl 0703.68099
[2] Anciaux, G., Coulaud, O., Roman, J.: High performance multiscale simulation or crack propagation. In: Proceedings of the 2006 International Conference Workshops on Parallel Processing, Columbus, pp. 473-480. IEEE Computer Society (2006)
[3] Armstrong, R., Gannon, D., Geist, A., Keahey, K., Kohn, S., McInnes, L., Parker, S., Smolinski, B.: Toward a common component architecture for high-performance scientific computing. In: Proceedings of the Eighth International Symposium on High Performance Distributed Computing, Redondo Beach, pp. 115-124 (1999)
[4] Balay, S., Brown, J., Buschelman, K., Gropp, W., Kaushik, D., Knepley, M., McInnes, L., Smith, B., Zhang, H.: Petsc web page.
[5] Bastian, P., Birken, K., Johannsen, K., Lang, S., Neuss, N., Rentz-Reichert, H., Wieners, C.: UG - a flexible software toolbox for solving partial differential equations. Comput. Vis. Sci. 1, 27-40 (1997) · Zbl 0970.65129 · doi:10.1007/s007910050003
[6] Beazley, D.M.: Swig: an easy to use tool for integrating scripting languages with C and C++. In: Proceedings of the 4th Conference on USENIX Tcl/Tk Workshop, USENIX Association, TCLTK’96, Berkeley, vol. 4, pp. 15-15 (1996)
[7] Bowers, K.J., Chow, E., Xu, H., Dror, R.O., Eastwood, M.P., et al.: Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, pp. 84-88 (2006)
[8] Broughton, J.Q., Abraham, F.F., Bernstein, N., Kaxiras, E.: Concurrent coupling of length scales: methodology and application. Phys. Rev. B 60, 2391-2403 (1999) · doi:10.1103/PhysRevB.60.2391
[9] Davis, T.A.: Algorithm 832: UMFPACK, an unsymmetric-pattern multifrontal method. ACM Trans. Math. Softw. 30, 196-199 (2004) · Zbl 1072.65037 · doi:10.1145/992200.992206
[10] Fackeldey, K., Krause, R.: Multiscale coupling in function space - weak coupling between molecular dynamics and continuum mechanics. Int. J. Numer. Method Eng. 79(12), 1517-1535 (2009) · Zbl 1176.74179 · doi:10.1002/nme.2626
[11] Fackeldey, K., Krause, D., Krause, R.: Numerical validation of a constraints-based multiscale method for solids. In: Meshfree Methods for Partial Differential Equations V. Lecture Notes in Computational Science and Engineering, vol. 79, pp. 141-154. Springer, Berlin (2011) · Zbl 1432.74012
[12] Fackeldey, K., Krause, D., Krause, R., Lenzen, C.: Coupling molecular dynamics and continua with weak constraints. Multiscale Model. Simul. 9(4), 1459-1494 (2011) · Zbl 1244.82004 · doi:10.1137/100782097
[13] Fasshauer, G.E.: Meshfree Approximation Methods with · Zbl 1123.65001
[14] Forum MPI: MPI: a message-passing interface standard, version 2.2 (2009)
[15] Global Array:
[16] Griebel, M., Knapek, S., Zumbusch, G.: Numerical Simulation in Molecular Dynamics. Springer, Berlin/Heidelberg (2007) · Zbl 1131.76001
[17] Heroux, M.A., Bartlett, R.A., Howle, V.E., Hoekstra, R.J., et al.: An overview of the Trilinos project. ACM Trans. Math. Softw. 31(3), 397-423 · Zbl 1136.65354
[18] Krause, D., Krause, R.: Parallel scale-transfer in multiscale MD-FE coupling using remote memory access. In: Workshop Proceedings of the IEEE 7th International Conference on E-Science, e-Science 2011, Stockholm, pp. 66-73, 5-8 Dec 2011
[19] Lammps:
[20] Ma, J., Lu, H., Wang, B., Hornung, R., Wissink, A., Komanduri, R.: Multiscale simulations using generalized interpolation material point (GIMP) method and molecular dynamics (MD). Comput. Model. Eng. Sci. 14, 101-118 (2006) · Zbl 1357.74083
[21] Mapper Project:
[22] Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., KalĂ©, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comput. Chem. 26(16), 1781-1802 (2005) · Zbl 05429657 · doi:10.1002/jcc.20289
[23] Plimpton, S.J.: Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117, 1-19 (1995) · Zbl 0830.65120 · doi:10.1006/jcph.1995.1039
[24] Schweitzer, M.A.: A Parallel Multilevel Partition of Unity Method for Elliptic Partial Differential Equations. Lecture Notes in Computational Science and Engineering, vol. 29. Springer, Berlin (2003) · Zbl 1016.65099
[25] Smolinski, B.A., Kohn, S.R., Elliott, N., Dykman, N.: Language interoperability for high-performance parallel scientific components. In: Proceedings of the Third International Symposium on Computing in Object-Oriented Parallel Environments, ISCOPE’99, San Francisco, pp 61-71. Springer (1999)
[26] Streitz, F.H., Glosli, J.N., Patel, M.V., Chan, B., Yates, R.K., et al.: 100+ TFlop solidification simulations on BlueGene/L. In: Proceedings of the ACM/IEEE Conference on Supercomputing (SC05), Seattle (2005)
[27] Wagner, G.J., Liu, W.K.: Coupling of atomistic and continuum simulations using a bridging scale decomposition. J. Comput. Phys. 190, 249-274 (2003) · Zbl 1169.74635 · doi:10.1016/S0021-9991(03)00273-0
[28] Xiao, S., Ni, J., Wang, S.: The bridging domain multiscale method and its high performance computing implementation. J. Comput. Theor. Nanosci. 5, 1-10 (2008) · doi:10.1166/jctn.2008.001a
[29] Xiao, S.P., Belytschko, T.: A bridging domain method for coupling continua with molecular dynamics. Comput. Method Appl. Eng. 193, 1645-1669 (2004) · Zbl 1079.74509 · doi:10.1016/j.cma.2003.12.053
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.