Parallel Molecular Dynamics with Irregular Domain Decomposition

被引：7

作者：

Bisson, Mauro ^{[1
]}

Bernaschi, Massimo ^{[2
]}

Melchionna, Simone ^{[3
,4
]}

机构：

[1] Univ Roma La Sapienza, Dept Comp Sci, Rome, Italy

[2] CNR, Ist Applicaz Calcolo, Rome, Italy

[3] Ecole Polytech Fed Lausanne, Inst Mat Sci & Engn, CH-1015 Lausanne, Switzerland

[4] CNR, IPCF, Rome, Italy

来源：

COMMUNICATIONS IN COMPUTATIONAL PHYSICS | 2011年 / 10卷 / 04期

关键词：

Molecular dynamics; irregular domain decomposition; parallel algorithms; hemodynamics; SCALE;

D O I：

10.4208/cicp.140810.021210a

中图分类号：

O4 [物理学];

学科分类号：

0702 ;

摘要：

The spatial domain of Molecular Dynamics simulations is usually a regular box that be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

引用

页码：1071 / 1088

页数：18

共 9 条

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