A DOMAIN DECOMPOSITION PARALLEL-PROCESSING ALGORITHM FOR MOLECULAR-DYNAMICS SIMULATIONS OF POLYMERS

被引：30
作者：
BROWN, D
CLARKE, JHR
OKUDA, M
YAMAZAKI, T
机构：
[1] UNIV MANCHESTER,INST SCI & TECHNOL,DEPT CHEM,MANCHESTER M60 1QD,LANCS,ENGLAND
[2] FUJITSU LTD,MIHAMA KU,CHIBA 261,JAPAN
来源：
COMPUTER PHYSICS COMMUNICATIONS | 1994年 / 83卷 / 01期
关键词：
D O I：
10.1016/0010-4655(94)90030-2
中图分类号：
TP39 [计算机的应用];
学科分类号：
081203 ; 0835 ;
摘要：
We describe in this paper a domain decomposition molecular dynamics algorithm for use on distributed memory parallel computers which is capable of handling systems containing rigid bond constraints and three- and four-body potentials as well as non-bonded potentials. The algorithm has been successfully implemented on the Fujitsu 1024 processor element AP1000 machine. The performance has been compared with and benchmarked against the alternative cloning method of parallel processing [D. Brown, J.H.R. Clarke, M. Okuda and T. Yamazaki, J. Chem. Phys., 100 (1994) 1684] and results obtained using other scalar and vector machines. Two parallel versions of the SHAKE algorithm, which solves the bond length constraints problem, have been compared with regard to optimising the performance of this procedure.
引用
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页码：1 / 13
页数：13
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