{"title":"zacrotools:一个Python库,用于动态蒙特卡罗模拟的自动准备,分析和可视化。","authors":"Hector Prats*, ","doi":"10.1021/acs.jpca.5c02802","DOIUrl":null,"url":null,"abstract":"<p >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.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"129 29","pages":"6608–6614"},"PeriodicalIF":2.8000,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302213/pdf/","citationCount":"0","resultStr":"{\"title\":\"ZacrosTools: A Python Library for Automated Preparation, Analysis, and Visualization of Kinetic Monte Carlo Simulations with Zacros\",\"authors\":\"Hector Prats*, \",\"doi\":\"10.1021/acs.jpca.5c02802\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p >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.</p>\",\"PeriodicalId\":59,\"journal\":{\"name\":\"The Journal of Physical Chemistry A\",\"volume\":\"129 29\",\"pages\":\"6608–6614\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2025-07-14\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302213/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"The Journal of Physical Chemistry A\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://pubs.acs.org/doi/10.1021/acs.jpca.5c02802\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Journal of Physical Chemistry A","FirstCategoryId":"1","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acs.jpca.5c02802","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
ZacrosTools: A Python Library for Automated Preparation, Analysis, and Visualization of Kinetic Monte Carlo Simulations with Zacros
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.
期刊介绍:
The Journal of Physical Chemistry A is devoted to reporting new and original experimental and theoretical basic research of interest to physical chemists, biophysical chemists, and chemical physicists.