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SEAMM：用于原子和分子建模的模拟环境。

SEAMM: A Simulation Environment for Atomistic and Molecular Modeling.

作者信息

Saxe Paul, Nash Jessica, Mostafanejad Mohammad, Marin-Rimoldi Eliseo, Hafiz Hasnain, Hector Louis G, Crawford T Daniel

机构信息

Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

Molecular Sciences Software Institute, Blacksburg, Virginia 24060, United States.

出版信息

J Phys Chem A. 2025 Jul 31;129(30):6973-6993. doi: 10.1021/acs.jpca.5c03164. Epub 2025 Jul 18.

DOI:10.1021/acs.jpca.5c03164
PMID:40679150
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12319917/
Abstract

The simulation environment for atomistic and molecular modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations. The graphical interface reduces the entry barrier for the use of new simulation tools, facilitating the interoperability of a wide range of simulation tools available to solve complex scientific and engineering problems in computational molecular science. Workflows are represented graphically by user-friendly flowcharts, which are shareable and reproducible. When a flowchart is executed within the SEAMM environment, all results, as well as metadata describing the workflow and codes used, are saved in a datastore that can be viewed using a browser-based dashboard, which allows collaborators to view the results and use the flowcharts to extend the results. SEAMM is a powerful productivity and collaboration tool that enables interoperability between simulation codes and ensures reproducibility and transparency in scientific research. We illustrate the flexibility and productivity of SEAMM with three examples: a simple molecular dynamics calculation to provide an overview; exploring the rearrangement of methylisocyanide to acetonitrile using a wide range of quantum codes and force fields; and using SEAMM for industrial research on battery materials with simulations of the diffusivity and ionic conductivity of electrolytes and the density, thermal expansion, and thermal conductivity of cathode materials as a function of lithiation.

摘要

原子和分子模拟的仿真环境（SEAMM）是一个用Python编写的开源软件包，它提供了一个图形界面，用于设置、执行和分析分子及材料模拟。该图形界面降低了使用新模拟工具的入门门槛，促进了各种模拟工具的互操作性，可用于解决计算分子科学中的复杂科学和工程问题。工作流程由用户友好的流程图以图形方式表示，这些流程图是可共享和可重现的。当在SEAMM环境中执行流程图时，所有结果以及描述工作流程和所用代码的元数据都会保存在一个数据存储中，可以使用基于浏览器的仪表板进行查看，这使得合作者能够查看结果并使用流程图来扩展结果。SEAMM是一个强大的生产力和协作工具，能够实现模拟代码之间的互操作性，并确保科学研究的可重复性和透明度。我们用三个例子来说明SEAMM的灵活性和生产力：一个简单的分子动力学计算以提供概述；使用多种量子代码和力场探索甲基异氰化物向乙腈的重排；以及将SEAMM用于电池材料的工业研究，模拟电解质的扩散率和离子电导率以及阴极材料的密度、热膨胀和热导率与锂化的关系。

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