Parallel Molecular Dynamics with Irregular Domain Decomposition

作     者：Mauro Bisson Massimo Bernaschi Simone Melchionna 

作者机构：Department of Computer ScienceUniversity of Rome"Sapienza"Italy Istituto Applicazioni CalcoloConsiglio Nazionale delle RicercheRomeItaly Institute of Material Sciences and Engineering´Ecole Polytechnique F´ed´erale de LausanneSwitzerland CNR-IPCFIstituto Processi Chimico-FisiciConsiglio Nazionale delle RicercheRomeItaly 

出 版 物：《Communications in Computational Physics》 (计算物理通讯（英文）)

年 卷 期：2011年第10卷第9期

页      面：1071-1088页

核心收录：

学科分类：07[理学] 0701[理学-数学] 070101[理学-基础数学] 

主　　题：Molecular dynamics irregular domain decomposition parallel algorithms hemodynamics 

摘      要：The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel *** 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 *** those cases,the geometry of the domain becomes an additional input parameter that directly influences the outcome of the *** 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.