{"id":38207512,"url":"https://github.com/geem-lab/overreact-guide","last_synced_at":"2026-01-17T00:38:42.153Z","repository":{"id":42714956,"uuid":"390766831","full_name":"geem-lab/overreact-guide","owner":"geem-lab","description":"⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data","archived":false,"fork":false,"pushed_at":"2023-01-04T22:50:51.000Z","size":4139,"stargazers_count":6,"open_issues_count":4,"forks_count":2,"subscribers_count":0,"default_branch":"main","last_synced_at":"2024-05-01T17:21:59.740Z","etag":null,"topics":["automation","chemical-kinetics","cli","computational-chemistry","computational-chemistry-logfiles","dsl","first-principles","guide","in-silico","library","microkinetics","modeling","overreact","python","qrrho","quantum-tunneling","reactions","rrho","thermochemistry","website"],"latest_commit_sha":null,"homepage":"https://geem-lab.github.io/overreact-guide","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"--- \u003c!-- prettier-ignore --\u003e\n\n\u003cdiv align=\"center\"\u003e\n\u003cp\u003e\n\u003ca href=\"https://pypi.org/project/overreact/\" \u003e\n\u003cimg src=\"https://img.shields.io/pypi/v/overreact\" alt=\"PyPI\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://pypi.org/project/overreact/\" \u003e\n\u003cimg src=\"https://img.shields.io/pypi/pyversions/overreact\" alt=\"Python Versions\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/geem-lab/overreact/actions/workflows/python-package.yml\" /\u003e\n\u003cimg src=\"https://github.com/geem-lab/overreact/actions/workflows/python-package.yml/badge.svg\" alt=\"CI\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://codecov.io/gh/geem-lab/overreact\" \u003e\n\u003cimg src=\"https://codecov.io/gh/geem-lab/overreact/branch/main/graph/badge.svg?token=4WAVXCRXY8\" alt=\"Coverage\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/geem-lab/overreact/blob/main/LICENSE\"\u003e\n\u003cimg src=\"https://img.shields.io/github/license/geem-lab/overreact\" alt=\"License\" /\u003e\n\u003c/a\u003e\n\u003c/p\u003e\n\u003cp\u003e\n\u003ca href=\"https://geem-lab.github.io/overreact-guide/\"\u003e\n\u003cimg src=\"https://img.shields.io/badge/user%20guide-available-blue\" alt=\"User guide\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/geem-lab/overreact/discussions\"\u003e\n\u003cimg src=\"https://img.shields.io/github/discussions/geem-lab/overreact\" alt=\"GitHub Discussions\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://github.com/geem-lab/overreact/issues\"\u003e\n\u003cimg src=\"https://img.shields.io/github/issues-raw/geem-lab/overreact\" alt=\"GitHub issues\" /\u003e\n\u003c/a\u003e\n\u003c/p\u003e\n\u003cp\u003e\n\u003ca href=\"https://pepy.tech/project/overreact\" \u003e\n\u003cimg src=\"https://pepy.tech/badge/overreact/month\" alt=\"downloads/month\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://pepy.tech/project/overreact\" \u003e\n\u003cimg src=\"https://pepy.tech/badge/overreact\" alt=\"total downloads\" /\u003e\n\u003c/a\u003e\n\u003c/p\u003e\n\u003cp\u003e\n\u003ca href=\"https://doi.org/10.1002/jcc.26861\" \u003e\n\u003cimg src=\"https://img.shields.io/badge/DOI-10.1002%2Fjcc.26861-blue\" alt=\"DOI\" /\u003e\n\u003c/a\u003e\n\u003ca href=\"https://doi.org/10.5281/zenodo.7504800\"\u003e\n\u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.7504800.svg\" alt=\"DOI\" /\u003e\n\u003c/a\u003e\n\u003c/p\u003e\n\u003cp\u003e\n\u003ca href=\"https://github.com/geem-lab/overreact#funding\" \u003e\n\u003cimg src=\"https://img.shields.io/badge/made%20in-Brazil-009c3b\" alt=\"Made in Brazil 🇧🇷\" /\u003e\n\u003c/a\u003e\n\u003c/p\u003e\n\u003c/div\u003e\n\n\u003cdiv align=\"center\"\u003e\n\u003cimg alt=\"overreact\" src=\"https://raw.githubusercontent.com/geem-lab/overreact-guide/master/logo.png\" /\u003e\n\u003c/div\u003e\n\n--- \u003c!-- prettier-ignore --\u003e\n\n**overreact** is a **library** and a **command-line tool** for building and\nanalyzing homogeneous **microkinetic models** from **first-principles\ncalculations**:\n\n```python\nIn [1]: from overreact import api  # the api\n\nIn [2]: api.get_k(\"S -\u003e E‡ -\u003e S\",  # your model\n   ...:           {\"S\": \"data/ethane/B97-3c/staggered.out\",  # your data\n   ...:            \"E‡\": \"data/ethane/B97-3c/eclipsed.out\"})\nOut[2]: array([8.16880917e+10])  # your results\n```\n\nThe user specifies a set of\nelementary reactions that are believed to be relevant for the overall chemical\nphenomena. **overreact** offers a hopefully complete but simple environment for\nhypothesis testing in first-principles chemical kinetics.\n\n\u003cdetails\u003e\n    \u003csummary style=\"cursor: pointer;\"\u003e\n        🤔 What is \u003cstrong\u003emicrokinetic modeling\u003c/strong\u003e?\n    \u003c/summary\u003e\n    \u003cp\u003e\n        \u003cstrong\u003eMicrokinetic modeling\u003c/strong\u003e is a technique used to predict the outcome\n        of complex chemical reactions.\n        It can be used\n        to investigate the catalytic transformations\n        of molecules.\n        \u003cstrong\u003eoverreact\u003c/strong\u003e makes it easy to create\n        and analyze microkinetic models built\n        from computational chemistry data.\n    \u003c/p\u003e\n\u003c/details\u003e\n\n\u003cbr/\u003e\n\n\u003cdetails\u003e\n    \u003csummary style=\"cursor: pointer;\"\u003e\n        🧐 What do you mean by \u003cstrong\u003efirst-principles calculations\u003c/strong\u003e?\n    \u003c/summary\u003e\n    \u003cp\u003e\n        We use the term \u003cstrong\u003efirst-principles calculations\u003c/strong\u003e to refer to\n        calculations performed using quantum chemical modern methods such as\n        \u003ca href=\"https://en.wikipedia.org/wiki/Hartree%E2%80%93Fock_method\"\u003eWavefunction\u003c/a\u003e\n        and\n        \u003ca href=\"https://en.wikipedia.org/wiki/Density_functional_theory\"\u003eDensity Functional\u003c/a\u003e\n        theories.\n        For instance, the three-line example code above calculates the rate of methyl rotation in ethane (at\n        \u003ca href=\"https://doi.org/10.1063/1.5012601\"\u003eB97-3c\u003c/a\u003e).\n        (Rather surprisingly, the error found is less than 2%\n        \u003ca href=\"http://dx.doi.org/10.1126/science.1132178\"\u003ewhen compared to available experimental results\u003c/a\u003e.)\n    \u003c/p\u003e\n\u003c/details\u003e\n\n\u003cbr/\u003e\n\n**overreact** uses **precise thermochemical partition funtions**, **tunneling\ncorrections** and data is **parsed directly** from computational chemistry\noutput files thanks to [`cclib`](https://cclib.github.io/) (see the\n[list of its supported programs](https://cclib.github.io/#summary)).\n\n## Installation\n\n**overreact** is a Python package, so you can easily install it with\n[`pip`](https://pypi.org/project/pip/):\n\n```console\n$ pip install \"overreact[cli,fast]\"\n```\n\nSee the\n[installation guide](https://geem-lab.github.io/overreact-guide/install.html)\nfor more details.\n\n\u003e **🚀** **Where to go from here?** Take a look at the\n\u003e [short introduction](https://geem-lab.github.io/overreact-guide/tutorial.html).\n\u003e Or see\n\u003e [below](https://geem-lab.github.io/overreact-guide/intro.html#where-to-go-next)\n\u003e for more guidance.\n\n## Citing **overreact**\n\nIf you use **overreact** in your research, please cite:\n\n\u003e Schneider, F. S. S.; Caramori, G. F.\n\u003e _**Overreact**, an in Silico Lab: Automative Quantum Chemical Microkinetic Simulations for Complex Chemical Reactions_.\n\u003e Journal of Computational Chemistry **2022**, 44 (3), 209–217.\n\u003e [doi:10.1002/jcc.26861](https://doi.org/10.1002/jcc.26861).\n\nHere's the reference in [BibTeX](http://www.bibtex.org/) format:\n\n```bibtex\n@article{overreact_paper2022,\n  title         = {Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions},\n  author        = {Schneider, Felipe S. S. and Caramori, Giovanni F.},\n  year          = {2022},\n  month         = {Apr},\n  journal       = {Journal of Computational Chemistry},\n  publisher     = {Wiley},\n  volume        = {44},\n  number        = {3},\n  pages         = {209–217},\n  doi           = {10.1002/jcc.26861},\n  issn          = {1096-987x},\n  url           = {http://dx.doi.org/10.1002/jcc.26861},\n}\n@software{overreact_software2021,\n  title         = {geem-lab/overreact: v1.1.0 \\vert{} Zenodo},\n  author        = {Felipe S. S. Schneider and Let\\'{\\i}cia M. P. Madureira and  Giovanni F. Caramori},\n  year          = {2023},\n  month         = {Jan},\n  publisher     = {Zenodo},\n  doi           = {10.5281/zenodo.7504800},\n  url           = {https://doi.org/10.5281/zenodo.7504800},\n  version       = {v1.1.0},\n  howpublished  = {\\url{https://github.com/geem-lab/overreact}},\n}\n```\n\n## License\n\n**overreact** is open-source, released under the permissive **MIT license**. See\n[the LICENSE agreement](https://github.com/geem-lab/overreact/blob/main/LICENSE).\n\n## Funding\n\nThis project was developed at the [GEEM lab](https://geem-ufsc.org/)\n([Federal University of Santa Catarina](https://en.ufsc.br/), Brazil), and was\npartially funded by the\n[Brazilian National Council for Scientific and Technological Development (CNPq)](https://cnpq.br/),\ngrant number 140485/2017-1.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeem-lab%2Foverreact-guide","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgeem-lab%2Foverreact-guide","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeem-lab%2Foverreact-guide/lists"}