A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation |
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Authors: | Aiichiro Nakano |
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Affiliation: | Collaboratory for Advanced Computing and Simulations, Department of Computer Science, Department of Physics & Astronomy, Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-0242, USA |
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Abstract: | A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molecular dynamics simulations for a sequence of atomic configurations (or states) to obtain a minimum energy path between initial and final local minimum-energy states. A directionally heated nudged elastic band method is introduced to search for thermally activated events without the knowledge of final states, which is then applied to an ensemble of bands in a path ensemble method for long-time simulation in the framework of the transition state theory. The resulting molecular kinetics (MK) simulation method is parallelized with a space-time-ensemble parallel nudged elastic band (STEP-NEB) algorithm, which employs spatial decomposition within each state, while temporal parallelism across the states within each band and band-ensemble parallelism are implemented using a hierarchy of communicator constructs in the Message Passing Interface library. The STEP-NEB algorithm exhibits good scalability with respect to spatial, temporal and ensemble decompositions on massively parallel computers. The MK simulation method is used to study low strain-rate deformation of amorphous silica. |
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Keywords: | 02.70.-c 02.70.Ns 82.20.Db |
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