overreact 1.2.0

⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data

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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.

🤔 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.

🧐 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 (see the list of its supported programs).

Installation

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.

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), 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.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.

Funding

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.