overreact 1.2.0

Description:

overreact 1.2.0

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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.