Modified force decomposition algorithms for calculating three-body interactions via molecular dynamics
JH Li and ZW Zhou and RJ Sadus, COMPUTER PHYSICS COMMUNICATIONS, 175, 683-691 (2006).
A force decomposition (FD) method previously used for two-body interactions is extended to three-body interactions. Three modified force decomposition strategies, namely cyclic decomposition (CD), balanced cyclic decomposition (BD) and precise decomposition (PD) are proposed. They are based on the decomposition of the three-body force matrix and the precise estimation of triplets involved in each row of the force matrix. The proposed decomposition algorithms are implemented using MPI and tested in molecular dynamics (MD) simulations. Their performance is studied in terms of load balance, speedup and parallel efficiency. A theoretical analysis of the effective triplets is performed, which can be used to predict the balance status. Both the theoretical analysis and molecular dynamics simulation demonstrate that the traditional force decomposition (FD) has a poor balance status resulting in lower speedup and efficiency compared with our strategies. The improved overall performance achieved with the modified force decomposition strategies can be directly attributed to the improved load balance. The modified decomposition strategies are particularly effective for many-body interactions in small to middle sized hornogeneous problems, where the effectiveness of existing parallel strategies is restricted by severe imbalance or a relatively large cut- off. (c) 2006 Elsevier B.V. All rights reserved.
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