FMD：执行经典分子动力学模拟的并行库

IF 2.4 4区计算机科学 Q2 COMPUTER SCIENCE, SOFTWARE ENGINEERING

SoftwareX Pub Date : 2024-11-05 DOI:10.1016/j.softx.2024.101929

Arham Amouye Foumani

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引用次数: 0

摘要

本文介绍了基于 MPI 的并行库自由分子动力学（FMD）。本文介绍了利用 FMD 进行经典分子动力学（MD）模拟的典型程序的一般结构。本文主要介绍 FMD 的一个高级功能：计算分布式网格（又称 "turis"）上定义的物理场的能力。分布式网格的每个单元可由任意数量的 MPI 进程共享。分布式网格可用于将 MD 与连续模型相结合，或获取作为时间和空间函数的宏观量（如密度）。该库旨在为用户提供易于使用的界面，并为开发人员提供扩展代码所需的可重复使用工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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FMD: A parallel library for performing classical molecular dynamics simulations

In this paper, the MPI-based parallel library Free Molecular Dynamics (FMD) is introduced. The general structure of a typical program utilizing FMD to perform classical molecular dynamics (MD) simulation is described. Much of the paper is devoted to one of the advanced features of FMD: its ability to compute physical fields defined on distributed grids (a.k.a. “turies”). Each cell of a distributed grid may be shared among any number of MPI processes. Distributed grids can be used to combine MD with continuum models or to obtain macroscopic quantities, e.g. density, as functions of time and space. The library is designed to provide an easy to use interface for its users, as well as equip its developers with reusable tools required for expanding the code.

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来源期刊

SoftwareX COMPUTER SCIENCE, SOFTWARE ENGINEERING-

CiteScore

5.50

自引率

2.90%

发文量

184

审稿时长

9 weeks

期刊介绍： SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.