Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory

被引：56
|
作者：
Shimojo, F
Kalia, RK
Nakano, A [1 ]
Vashishta, P
机构：
[1] Univ So Calif, Dept Mat Sci & Engn, Dept Phys & Astron, Dept Comp Sci, Los Angeles, CA 90089 USA
[2] Kumamoto Univ, Dept Phys, Kumamoto 8608555, Japan
来源：
COMPUTER PHYSICS COMMUNICATIONS | 2005年 / 167卷 / 03期
基金：
美国国家科学基金会;
关键词：
parallel computing; molecular dynamics; density functional theory; linear scaling algorithm;
D O I：
10.1016/j.cpc.2005.01.005
中图分类号：
TP39 [计算机的应用];
学科分类号：
081203 ; 0835 ;
摘要：
A linear-scaling algorithm has been developed to perform large-scale molecular-dynamics (MD) simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory. A divide-arid-conquer algorithm is used to compute the electronic structure, where non-additive contribution to the kinetic energy is included with an embedded cluster scheme. Electronic wave functions are represented on a real-space grid, which is augmented with coarse multigrids to accelerate the convergence of iterative solutions and adaptive fine grids around atoms to accurately calculate ionic pseudopotentials. Spatial decomposition is employed to implement the hierarchical-grid algorithm on massively parallel computers. A converged solution to the electronic-structure problem is obtained for a 32,768-atom amorphous CdSe system on 512 IBM POWER4 processors. The total energy is well conserved during MD simulations of liquid Rb, showing the applicability of this algorithm to first principles MD simulations. The parallel efficiency is 0.985 on 128 Intel Xeon processors for a 65,536-atom CdSe system. (c) 2005 Elsevier B.V. All rights reserved.
引用
收藏
页码：151 / 164
页数：14
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