“Checker board” Periodic boundary conditions in molecular dynamics codes

作     者：Dzwinel, Witold Kitowski, Jacek Mosci Ski, Jacek 

作者机构：Institute of Computer Science PL-30-059 Cracow AGH al. Mickiewicza 30 Poland 

出 版 物：《Molecular Simulation》 (Mol. Simul.)

年 卷 期：1991年第7卷第3-4期

页      面：171-179页

学科分类：0710[理学-生物学] 0810[工学-信息与通信工程] 1205[管理学-图书情报与档案管理] 071010[理学-生物化学与分子生物学] 07[理学] 0817[工学-化学工程与技术] 0805[工学-材料科学与工程（可授工学、理学学位）] 0703[理学-化学] 0701[理学-数学] 0811[工学-控制科学与工程] 0702[理学-物理学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

主　　题：computational algorithms Lennard-Jones potentials link-cell method Molecular dynamics periodic boundary conditions 

摘      要：Checker board periodic boundary conditions for molecular simulation are proposed. They represent a simple geometric transformation of the well known periodic boundary conditions formulae for variety of periodic and regular computational boxes (e.g. the truncated octahedron, rhombic dodecahedron, hexagonal prism, etc.) into a shifted parallelepiped periodic grid. As a result, the choice of an optional computational box shape is equivalent to the proper choice of the basic parallelepiped sides lengths. The checker board periodic boundary conditions have been applied in a molecular dynamics (MD) code based on the link-cell method (using Lennard-Jones interactions). Simulation efficiency is approximately the same as for the classical cubic periodic boundary transformations. © 1991, Taylor & Francis Group, LLC. All rights reserved.