Parallel algorithms for molecular dynamics with induction forces |
| |
| Authors: | Jianhui Li Zhongwu Zhou Richard J Sadus |
| |
| Affiliation: | 1. Center for Atmosphere Ocean Science, Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, United States;2. Center for Prototype Climate Modelling, NYU-Abu Dhabi, United Arab Emirates;1. Faculty of Agro Based Industry, Universiti Malaysia Kelantan, 17600 Jeli, Kelantan, Malaysia;2. School of Mathematical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia;3. Department of Mathematics, Babe?-Bolyai University, R-400084 Cluj-Napoca, Romania;1. Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, PR China;2. Xi’an Flight Automatic Control Research Institute, Xi’an 710065, PR China;1. School of Chemical Engineering, Fuzhou University, Fuzhou 350116, China;2. Department of Mechanical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan;3. School of Civil Engineering and Architecture, Wuhan Polytechnic University, Wuhan, Hubei 430023, China |
| |
| Abstract: | We examine parallel algorithms for molecular dynamics simulations involving long-range induction interactions. The algorithms are tested by performing molecular dynamics simulations of water with an intermolecular potential that explicitly includes contributions from pair, three-body and induction interactions. Both cyclic and balanced force decomposition methods are implemented to decompose the parallelizable components of induction, pair and three-body interactions using a message passing interface. We report that more than 90% of the induction calculation, and 98% of the total calculation can be effectively parallelized. A reasonably good speedup of 15.7 times and an efficiency of 49.1% are obtained on 32 processors with the balance force decomposition algorithm. |
| |
| Keywords: | |
| 本文献已被 ScienceDirect 等数据库收录！ |
|
