overreact

⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.

Science Score: 67.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
Found 20 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary

Keywords

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

Last synced: 4 months ago · JSON representation ·

Repository

⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.

Basic Info

Host: GitHub
Owner: geem-lab
License: mit
Language: Python
Default Branch: main
Homepage: https://geem-lab.github.io/overreact-guide/
Size: 95.7 MB

Statistics

Stars: 56
Watchers: 2
Forks: 10
Open Issues: 18
Releases: 5

Topics

Created about 6 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Citation

README.md

---

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 -> 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:

console $ 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:

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 = {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}}, }

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.

Owner

Name: Molecular Electronic Structure Group
Login: geem-lab
Kind: organization
Location: Florianópolis, Brazil

Website: https://geem-ufsc.org/
Repositories: 10
Profile: https://github.com/geem-lab

⚛️📈 Molecular Electronic Structure Group

Citation (CITATION.bib)

@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}},
}

GitHub Events

Total

Issues event: 1
Watch event: 7
Delete event: 69
Issue comment event: 49
Push event: 67
Pull request review comment event: 1
Pull request review event: 9
Pull request event: 139
Fork event: 1
Create event: 67

Last Year

Issues event: 1
Watch event: 7
Delete event: 69
Issue comment event: 49
Push event: 67
Pull request review comment event: 1
Pull request review event: 9
Pull request event: 139
Fork event: 1
Create event: 67

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 480
Total Committers: 6
Avg Commits per committer: 80.0
Development Distribution Score (DDS): 0.54

Top Committers

Name	Email	Commits
dependabot[bot]	4**]@u**m	221
Felipe S. S. Schneider	s**e@p**r	147
Felipe S. S. Schneider	s**5@g**m	63
Felipe S. S. Schneider	s**e@p**r	26
Felipe S. S. Schneider	3**e@u**m	21
Letícia Maria Pequeno Madureira	l**0@g**m	2

Committer Domains (Top 20 + Academic)

posgrad.ufsc.br: 2

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 9
Total pull requests: 430
Average time to close issues: 12 months
Average time to close pull requests: 5 days
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 1.44
Average comments per pull request: 0.56
Merged pull requests: 293
Bot issues: 0
Bot pull requests: 416

Past Year

Issues: 1
Pull requests: 120
Average time to close issues: N/A
Average time to close pull requests: 10 days
Issue authors: 1
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.57
Merged pull requests: 38
Bot issues: 0
Bot pull requests: 118

View more stats

Top Authors

Issue Authors

schneiderfelipe (6)
Leticia-maria (3)
dependabot[bot] (2)

Pull Request Authors

dependabot[bot] (567)
schneiderfelipe (15)
m-rauen (2)
caprilesport (1)

Top Labels

Issue Labels

enhancement (4) bug (2) help wanted (2) good first issue (2) dependencies (2) python (2) gui (1) documentation (1)

Pull Request Labels

dependencies (567) python (557) github_actions (10)

Packages

Total packages: 2
Total downloads:
- pypi 17 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 8
Total maintainers: 1

proxy.golang.org: github.com/geem-lab/overreact

Documentation: https://pkg.go.dev/github.com/geem-lab/overreact#section-documentation
License: mit
Latest release: v1.2.0
published over 2 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

pypi.org: overreact

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

Homepage: https://geem-lab.github.io/overreact-guide/
Documentation: https://geem-lab.github.io/overreact-guide/
License: MIT
Latest release: 1.2.0
published over 2 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 17 Last month

Rankings

Dependent packages count: 10.0%

Stargazers count: 10.1%

Forks count: 13.3%

Average: 17.5%

Dependent repos count: 21.7%

Downloads: 32.3%

Maintainers (1)

schneiderfelipe

Last synced: 4 months ago

Dependencies

.github/workflows/codeql-analysis.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/python-package.yml actions

abatilo/actions-poetry v2 composite
actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite
psf/black stable composite

poetry.lock pypi

146 dependencies

pyproject.toml pypi

cclib ^1
jax ^0.4
jaxlib ^0.4
python >=3.8,<3.11
rich ^13
scipy ^1.10
thermo ^0.2