--- <!-- prettier-ignore -->
<div align="center">
<p>
<a href="https://pypi.org/project/overreact/" >
<img src="https://img.shields.io/pypi/v/overreact" alt="PyPI" />
</a>
<a href="https://pypi.org/project/overreact/" >
<img src="https://img.shields.io/pypi/pyversions/overreact" alt="Python Versions" />
</a>
<a href="https://github.com/geem-lab/overreact/actions/workflows/python-package.yml" />
<img src="https://github.com/geem-lab/overreact/actions/workflows/python-package.yml/badge.svg" alt="CI" />
</a>
<a href="https://codecov.io/gh/geem-lab/overreact" >
<img src="https://codecov.io/gh/geem-lab/overreact/branch/main/graph/badge.svg?token=4WAVXCRXY8" alt="Coverage" />
</a>
<a href="https://github.com/geem-lab/overreact/blob/main/LICENSE">
<img src="https://img.shields.io/github/license/geem-lab/overreact" alt="License" />
</a>
</p>
<p>
<a href="https://geem-lab.github.io/overreact-guide/">
<img src="https://img.shields.io/badge/user%20guide-available-blue" alt="User guide" />
</a>
<a href="https://github.com/geem-lab/overreact/discussions">
<img src="https://img.shields.io/github/discussions/geem-lab/overreact" alt="GitHub Discussions" />
</a>
<a href="https://github.com/geem-lab/overreact/issues">
<img src="https://img.shields.io/github/issues-raw/geem-lab/overreact" alt="GitHub issues" />
</a>
</p>
<p>
<a href="https://pepy.tech/project/overreact" >
<img src="https://pepy.tech/badge/overreact/month" alt="downloads/month" />
</a>
<a href="https://pepy.tech/project/overreact" >
<img src="https://pepy.tech/badge/overreact" alt="total downloads" />
</a>
</p>
<p>
<a href="https://doi.org/10.1002/jcc.26861" >
<img src="https://img.shields.io/badge/DOI-10.1002%2Fjcc.26861-blue" alt="DOI" />
</a>
<a href="https://doi.org/10.5281/zenodo.7504800">
<img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7504800.svg" alt="DOI" />
</a>
</p>
<p>
<a href="https://github.com/geem-lab/overreact#funding" >
<img src="https://img.shields.io/badge/made%20in-Brazil-009c3b" alt="Made in Brazil š§š·" />
</a>
</p>
</div>
<div align="center">
<img alt="overreact" src="https://raw.githubusercontent.com/geem-lab/overreact-guide/master/logo.png" />
</div>
--- <!-- prettier-ignore -->
**overreact** is a **library** and a **command-line tool** for building and
analyzing homogeneous **microkinetic models** from **first-principles
calculations**:
```python
In [1]: from overreact import api # the api
In [2]: api.get_k("S -> Eā” -> S", # your model
...: {"S": "data/ethane/B97-3c/staggered.out", # your data
...: "Eā”": "data/ethane/B97-3c/eclipsed.out"})
Out[2]: array([8.16880917e+10]) # your results
```
The user specifies a set of
elementary reactions that are believed to be relevant for the overall chemical
phenomena. **overreact** offers a hopefully complete but simple environment for
hypothesis testing in first-principles chemical kinetics.
<details>
<summary style="cursor: pointer;">
š¤ What is <strong>microkinetic modeling</strong>?
</summary>
<p>
<strong>Microkinetic modeling</strong> is a technique used to predict the outcome
of complex chemical reactions.
It can be used
to investigate the catalytic transformations
of molecules.
<strong>overreact</strong> makes it easy to create
and analyze microkinetic models built
from computational chemistry data.
</p>
</details>
<br/>
<details>
<summary style="cursor: pointer;">
š§ What do you mean by <strong>first-principles calculations</strong>?
</summary>
<p>
We use the term <strong>first-principles calculations</strong> to refer to
calculations performed using quantum chemical modern methods such as
<a href="https://en.wikipedia.org/wiki/Hartree%E2%80%93Fock_method">Wavefunction</a>
and
<a href="https://en.wikipedia.org/wiki/Density_functional_theory">Density Functional</a>
theories.
For instance, the three-line example code above calculates the rate of methyl rotation in ethane (at
<a href="https://doi.org/10.1063/1.5012601">B97-3c</a>).
(Rather surprisingly, the error found is less than 2%
<a href="http://dx.doi.org/10.1126/science.1132178">when compared to available experimental results</a>.)
</p>
</details>
<br/>
**overreact** uses **precise thermochemical partition funtions**, **tunneling
corrections** and data is **parsed directly** from computational chemistry
output files thanks to [`cclib`](https://cclib.github.io/) (see the
[list of its supported programs](https://cclib.github.io/#summary)).
## Installation
**overreact** is a Python package, so you can easily install it with
[`pip`](https://pypi.org/project/pip/):
```console
$ pip install "overreact[cli,fast]"
```
See the
[installation guide](https://geem-lab.github.io/overreact-guide/install.html)
for more details.
> **š** **Where to go from here?** Take a look at the
> [short introduction](https://geem-lab.github.io/overreact-guide/tutorial.html).
> Or see
> [below](https://geem-lab.github.io/overreact-guide/intro.html#where-to-go-next)
> for more guidance.
## Citing **overreact**
If you use **overreact** in your research, please cite:
> Schneider, F. S. S.; Caramori, G. F.
> _**Overreact**, an in Silico Lab: Automative Quantum Chemical Microkinetic Simulations for Complex Chemical Reactions_.
> Journal of Computational Chemistry **2022**, 44 (3), 209ā217.
> [doi:10.1002/jcc.26861](https://doi.org/10.1002/jcc.26861).
Here's the reference in [BibTeX](http://www.bibtex.org/) format:
```bibtex
@article{overreact_paper2022,
title = {Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions},
author = {Schneider, Felipe S. S. and Caramori, Giovanni F.},
year = {2022},
month = {Apr},
journal = {Journal of Computational Chemistry},
publisher = {Wiley},
volume = {44},
number = {3},
pages = {209ā217},
doi = {10.1002/jcc.26861},
issn = {1096-987x},
url = {http://dx.doi.org/10.1002/jcc.26861},
}
@software{overreact_software2021,
title = {geem-lab/overreact: v1.2.0 \vert{} Zenodo},
author = {Felipe S. S. Schneider and Let\'{\i}cia M. P. Madureira and Giovanni F. Caramori},
year = {2023},
month = {Jan},
publisher = {Zenodo},
doi = {10.5281/zenodo.7504800},
url = {https://doi.org/10.5281/zenodo.7504800},
version = {v1.2.0},
howpublished = {\url{https://github.com/geem-lab/overreact}},
}
```
## License
**overreact** is open-source, released under the permissive **MIT license**. See
[the LICENSE agreement](https://github.com/geem-lab/overreact/blob/main/LICENSE).
## Funding
This project was developed at the [GEEM lab](https://geem-ufsc.org/)
([Federal University of Santa Catarina](https://en.ufsc.br/), Brazil), and was
partially funded by the
[Brazilian National Council for Scientific and Technological Development (CNPq)](https://cnpq.br/),
grant number 140485/2017-1.
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"description": "--- <!-- prettier-ignore -->\n\n<div align=\"center\">\n<p>\n<a href=\"https://pypi.org/project/overreact/\" >\n<img src=\"https://img.shields.io/pypi/v/overreact\" alt=\"PyPI\" />\n</a>\n<a href=\"https://pypi.org/project/overreact/\" >\n<img src=\"https://img.shields.io/pypi/pyversions/overreact\" alt=\"Python Versions\" />\n</a>\n<a href=\"https://github.com/geem-lab/overreact/actions/workflows/python-package.yml\" />\n<img src=\"https://github.com/geem-lab/overreact/actions/workflows/python-package.yml/badge.svg\" alt=\"CI\" />\n</a>\n<a href=\"https://codecov.io/gh/geem-lab/overreact\" >\n<img src=\"https://codecov.io/gh/geem-lab/overreact/branch/main/graph/badge.svg?token=4WAVXCRXY8\" alt=\"Coverage\" />\n</a>\n<a href=\"https://github.com/geem-lab/overreact/blob/main/LICENSE\">\n<img src=\"https://img.shields.io/github/license/geem-lab/overreact\" alt=\"License\" />\n</a>\n</p>\n<p>\n<a href=\"https://geem-lab.github.io/overreact-guide/\">\n<img src=\"https://img.shields.io/badge/user%20guide-available-blue\" alt=\"User guide\" />\n</a>\n<a href=\"https://github.com/geem-lab/overreact/discussions\">\n<img src=\"https://img.shields.io/github/discussions/geem-lab/overreact\" alt=\"GitHub Discussions\" />\n</a>\n<a href=\"https://github.com/geem-lab/overreact/issues\">\n<img src=\"https://img.shields.io/github/issues-raw/geem-lab/overreact\" alt=\"GitHub issues\" />\n</a>\n</p>\n<p>\n<a href=\"https://pepy.tech/project/overreact\" >\n<img src=\"https://pepy.tech/badge/overreact/month\" alt=\"downloads/month\" />\n</a>\n<a href=\"https://pepy.tech/project/overreact\" >\n<img src=\"https://pepy.tech/badge/overreact\" alt=\"total downloads\" />\n</a>\n</p>\n<p>\n<a href=\"https://doi.org/10.1002/jcc.26861\" >\n<img src=\"https://img.shields.io/badge/DOI-10.1002%2Fjcc.26861-blue\" alt=\"DOI\" />\n</a>\n<a href=\"https://doi.org/10.5281/zenodo.7504800\">\n<img src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.7504800.svg\" alt=\"DOI\" />\n</a>\n</p>\n<p>\n<a href=\"https://github.com/geem-lab/overreact#funding\" >\n<img src=\"https://img.shields.io/badge/made%20in-Brazil-009c3b\" alt=\"Made in Brazil \ud83c\udde7\ud83c\uddf7\" />\n</a>\n</p>\n</div>\n\n<div align=\"center\">\n<img alt=\"overreact\" src=\"https://raw.githubusercontent.com/geem-lab/overreact-guide/master/logo.png\" />\n</div>\n\n--- <!-- prettier-ignore -->\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 -> E\u2021 -> S\", # your model\n ...: {\"S\": \"data/ethane/B97-3c/staggered.out\", # your data\n ...: \"E\u2021\": \"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<details>\n <summary style=\"cursor: pointer;\">\n \ud83e\udd14 What is <strong>microkinetic modeling</strong>?\n </summary>\n <p>\n <strong>Microkinetic modeling</strong> 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 <strong>overreact</strong> makes it easy to create\n and analyze microkinetic models built\n from computational chemistry data.\n </p>\n</details>\n\n<br/>\n\n<details>\n <summary style=\"cursor: pointer;\">\n \ud83e\uddd0 What do you mean by <strong>first-principles calculations</strong>?\n </summary>\n <p>\n We use the term <strong>first-principles calculations</strong> to refer to\n calculations performed using quantum chemical modern methods such as\n <a href=\"https://en.wikipedia.org/wiki/Hartree%E2%80%93Fock_method\">Wavefunction</a>\n and\n <a href=\"https://en.wikipedia.org/wiki/Density_functional_theory\">Density Functional</a>\n theories.\n For instance, the three-line example code above calculates the rate of methyl rotation in ethane (at\n <a href=\"https://doi.org/10.1063/1.5012601\">B97-3c</a>).\n (Rather surprisingly, the error found is less than 2%\n <a href=\"http://dx.doi.org/10.1126/science.1132178\">when compared to available experimental results</a>.)\n </p>\n</details>\n\n<br/>\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> **\ud83d\ude80** **Where to go from here?** Take a look at the\n> [short introduction](https://geem-lab.github.io/overreact-guide/tutorial.html).\n> Or see\n> [below](https://geem-lab.github.io/overreact-guide/intro.html#where-to-go-next)\n> for more guidance.\n\n## Citing **overreact**\n\nIf you use **overreact** in your research, please cite:\n\n> Schneider, F. 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