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ZacrosTools:一个用于使用Zacros自动准备、分析和可视化动力学蒙特卡洛模拟的Python库。

ZacrosTools: A Python Library for Automated Preparation, Analysis, and Visualization of Kinetic Monte Carlo Simulations with Zacros.

作者信息

Prats Hector

机构信息

Institute of Materials Chemistry, Technische Universität Wien, 1060 Vienna, Austria.

Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.

出版信息

J Phys Chem A. 2025 Jul 24;129(29):6608-6614. doi: 10.1021/acs.jpca.5c02802. Epub 2025 Jul 14.

Abstract

This paper presents ZacrosTools, a free and open-source Python library designed to simplify and automate the preparation and analysis of kinetic Monte Carlo (KMC) simulations with the widely used Zacros package. ZacrosTools provides a user-friendly and robust interface for building KMC models, automating the generation of Zacros input files, extracting and processing simulation data, and visualizing results through multiple plotting functionalities. The library benefits new users by simplifying model preparation and helping them avoid common mistakes while also being suitable to advanced users who wish to fine-tune complex KMC models and conduct comprehensive analyses. ZacrosTools is extensively documented with numerous examples available on ReadTheDocs and is publicly accessible on GitHub under the MIT license. Furthermore, it integrates continuous integration via GitHub Actions to facilitate seamless contributions from the user community.

摘要

本文介绍了ZacrosTools,这是一个免费的开源Python库,旨在简化并自动化使用广泛应用的Zacros软件包进行的动力学蒙特卡罗(KMC)模拟的准备和分析工作。ZacrosTools为构建KMC模型提供了一个用户友好且强大的界面,可自动生成Zacros输入文件,提取和处理模拟数据,并通过多种绘图功能可视化结果。该库通过简化模型准备工作并帮助新用户避免常见错误,使新用户受益,同时也适用于希望微调复杂KMC模型并进行全面分析的高级用户。ZacrosTools有大量文档记录,在ReadTheDocs上有众多示例,并且在GitHub上根据MIT许可公开可用。此外,它通过GitHub Actions集成了持续集成,以促进用户社区的无缝贡献。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a48/12302213/b3ce079eef61/jp5c02802_0001.jpg

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