Parallel molecular dynamics simulations for short-ranged many-body potentials

C. F. Cornwell; L. T. Wille

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Parallel molecular dynamics simulations for short-ranged many-body potentials

机译：短距离多体电势的并行分子动力学模拟

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摘要

A new method is described that permits the efficient execution of parallel molecular dynamics simulations for irregular problems with several thousands of atoms on Single-Instruction Multiple-Data computers. The approach is based on a data-parallel atomic decomposition scheme and has overall time-complexity O(N), where N is the size of the system. The method has been implemented on a MasPar MP-1 computer and was found to obey theoretical timing estimates. The methodology has wide applicability and can be ported to other architectures in a straightforward manner.

机译：描述了一种新方法，该方法可以在单指令多数据计算机上有效执行具有数千个原子的不规则问题的并行分子动力学模拟。该方法基于数据并行原子分解方案，并具有整体时间复杂度O（N），其中N是系统的大小。该方法已在MasPar MP-1计算机上实现，并且发现该方法符合理论时序估计。该方法具有广泛的适用性，并且可以以直接的方式移植到其他架构。

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《Computer physics communications》 |2000年第2期|共15页
作者
C. F. Cornwell; L. T. Wille;
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正文语种 eng
中图分类计算机的应用;
关键词
molecular dynamics; parallel computing; many-body potentials; clusters; nanotubes;

机译：分子动力学;并行计算;多体势;簇;纳米管;

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专利

1. Parallel molecular dynamics simulations for short-ranged many-body potentials [J] . C. F. Cornwell, L. T. Wille Computer physics communications . 2000,第1a2期

机译：短距离多体电势的并行分子动力学模拟
2. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water [J] . George S. Fanourgakis, Vinod Tipparaju, Jarek Nieplocha, Theoretical Chemistry Accounts . 2007,第1期

机译：具有多体，灵活，可极化的经验电势的分子动力学模拟的有效并行化方案：在水中的应用
3. Domain-Decomposition Parallelization for Molecular Dynamics Algorithm with Short-Ranged Potentials on Epiphany Architecture [J] . V. Nikolskii, V. Stegailov Lobachevskii journal of mathematics . 2018,第9期

机译：跨越界面施工的分子动力学算法的域分解并行化
4. Efficient parallelization of molecular dynamics simulations with short-ranged forces [C] . Ralf Meyer High Performance Computing Symposium . 2014

机译：具有短途力量的分子动力学模拟的高效平行化
5. Dynamic load balancing of many-body molecular dynamics simulations in grid environments. [D] . Venkata, Sumanth Jannyavula. 2007

机译：网格环境中多体分子动力学模拟的动态负载平衡。
6. The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations [O] . Urban Boršnik, Benjamin T. Miller, Bernard R. Brooks, -1

机译：用于并行分子动力学模拟的分布式对角线分解方法
7. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water [O] . George S. Fanourgakis, Vinod Tipparaju, Jarek Nieplocha, 2006

机译：具有多体，灵活，可极化的经验电势的分子动力学模拟的有效并行化方案：在水中的应用

Parallel molecular dynamics simulations for short-ranged many-body potentials

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