Scalable and portable implementation of the fast multipole method on parallel computers

被引:38
作者
Ogata, S
Campbell, TJ
Kalia, RK
Nakano, A [1 ]
Vashishta, P
Vemparala, S
机构
[1] Univ So Calif, Collaboratory Adv Comp & Simulat, Dept Comp Sci,Dept Biomed Engn, Dept Mat Sci & Engn,Dept Phys & Astron, Los Angeles, CA 90089 USA
[2] Yamaguchi Univ, Dept Appl Sci, Ube, Yamaguchi 7558611, Japan
[3] Mississippi State Univ, Stennis Space Ctr, MS 39529 USA
[4] Louisiana State Univ, Dept Phys & Astron, Biol Computat & Visualizat Ctr, Concurrent Comp Lab Mat Simulat,Dept Comp Sci, Baton Rouge, LA 70801 USA
基金
美国国家航空航天局; 美国国家科学基金会;
关键词
fast multipole method; parallel computation; stress calculation; periodic boundary conditions; Coulomb interaction;
D O I
10.1016/S0010-4655(03)00246-7
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
A scalable and portable Fortran code is developed to calculate Coulomb interaction potentials of charged particles on parallel computers, based on the fast multipole method. The code has a unique feature to calculate microscopic stress tensors due to the Coulomb interactions, which is useful in constant-pressure simulations and local stress analyses. The code is applicable to various boundary conditions, including periodic boundary conditions in two and three dimensions, corresponding to slab and bulk systems, respectively. Numerical accuracy of the code is tested through comparison of its results with those obtained by the Ewald summation method and by direct calculations. Scalability tests show the parallel efficiency of 0.98 for 512 million charged particles on 512 IBM SP3 processors. The timing results on IBM SP3 are also compared with those on IBM SP4. (C) 2003 Published by Elsevier B.V.
引用
收藏
页码:445 / 461
页数:17
相关论文
共 22 条
[1]  
Allen M. P., 1987, Computer Simulation of Liquids
[2]   Dynamics of oxidation of aluminum nanoclusters using variable charge molecular-dynamics simulations on parallel computers [J].
Campbell, T ;
Kalia, RK ;
Nakano, A ;
Vashishta, P ;
Ogata, S ;
Rodgers, S .
PHYSICAL REVIEW LETTERS, 1999, 82 (24) :4866-4869
[3]   THE H = 0 TERM IN COULOMB SUMS BY THE EWALD TRANSFORMATION [J].
DEEM, MW ;
NEWSAM, JM ;
SINHA, SK .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (21) :8356-8359
[4]   ELECTROSTATIC LATTICE SUMS FOR SEMI-INFINITE LATTICES [J].
DELEEUW, SW ;
PERRAM, JW .
MOLECULAR PHYSICS, 1979, 37 (04) :1313-1322
[5]   SIMULATION OF ELECTROSTATIC SYSTEMS IN PERIODIC BOUNDARY-CONDITIONS .1. LATTICE SUMS AND DIELECTRIC-CONSTANTS [J].
DELEEUW, SW ;
PERRAM, JW ;
SMITH, ER .
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 1980, 373 (1752) :27-56
[6]   THE REDUCED CELL MULTIPOLE METHOD FOR COULOMB INTERACTIONS IN PERIODIC-SYSTEMS WITH MILLION-ATOM UNIT CELLS [J].
DING, HQ ;
KARASAWA, N ;
GODDARD, WA .
CHEMICAL PHYSICS LETTERS, 1992, 196 (1-2) :6-10
[7]  
GREENGARD L, 1987, RAPID EVOLUTION POTE
[8]  
GREENGARD L, 1985, J COMPUT PHYS, V60, P187
[9]  
Gropp W. D., 1994, Using MPI-Portable Parallel Programming with the Message -Parsing Interface
[10]   MOLECULAR-DYNAMICS COMPUTER-SIMULATION OF SURFACE PROPERTIES OF CRYSTALLINE POTASSIUM-CHLORIDE [J].
HEYES, DM ;
BARBER, M ;
CLARKE, JHR .
JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS II, 1977, 73 :1485-1496