m-rauen / overreact Goto Github PK

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overreact is a library and a command-line tool for building and analyzing homogeneous microkinetic models from first-principles calculations:

In [1]: from overreact import api  # the api

In [2]: api.get_k("S -> E‡ -> S",  # your model
   ...:           {"S": "data/ethane/B97-3c/staggered.out",  # your data
   ...:            "E‡": "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.

overreact uses precise thermochemical partition funtions, tunneling corrections and data is parsed directly from computational chemistry output files thanks to cclib (see the list of its supported programs).

overreact is a Python package, so you can easily install it with pip:

$ pip install "overreact[cli,fast]"

See the installation guide for more details.

🚀 Where to go from here? Take a look at the short introduction. Or see below for more guidance.

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), 209–217. doi:10.1002/jcc.26861.

Here's the reference in BibTeX format:

@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         = {209–217},
  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}},
}

overreact is open-source, released under the permissive MIT license. See the LICENSE agreement.

This project was developed at the GEEM lab (Federal University of Santa Catarina, Brazil), and was partially funded by the Brazilian National Council for Scientific and Technological Development (CNPq), grant number 140485/2017-1.