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https://github.com/geem-lab/overreact

āš›ļøšŸ“ˆ Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.
https://github.com/geem-lab/overreact

automation chemical-kinetics cli computational-chemistry computational-chemistry-logfiles dsl first-principles in-silico library microkinetics modeling overreact python qrrho quantum-tunneling reactions rrho thermochemistry

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āš›ļøšŸ“ˆ Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.

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Made in Brazil šŸ‡§šŸ‡·










overreact




--- 



**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.



    

        šŸ¤” What is microkinetic modeling?

    

    


        Microkinetic modeling is a technique used to predict the outcome

        of complex chemical reactions.

        It can be used

        to investigate the catalytic transformations

        of molecules.

        overreact makes it easy to create

        and analyze microkinetic models built

        from computational chemistry data.

    







    

        šŸ§ What do you mean by first-principles calculations?

    

    


        We use the term first-principles calculations to refer to

        calculations performed using quantum chemical modern methods such as

        Wavefunction

        and

        Density Functional

        theories.

        For instance, the three-line example code above calculates the rate of methyl rotation in ethane (at

        B97-3c).

        (Rather surprisingly, the error found is less than 2%

        when compared to available experimental results.)

    







**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.



> **šŸš€** **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), 209ā€“217.

> [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         = {209ā€“217},

  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.7865357},

  url           = {https://doi.org/10.5281/zenodo.7865357},

  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.