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@schneiderfelipe schneiderfelipe released this 04 Jan 22:24
· 283 commits to main since this release
v1.1.0
74e9211

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

overreact

This is a feature release of overreact that improves output, automatic choice of most parameters and adds support for Python 3.10.

Update it using pip:

$ pip install -U 'overreact[cli,fast]'

Overreact is licensed under the MIT license.

ℹ️ By the way, our manuscript has been featured in the latest issue of the Journal of Computational Chemistry! 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},
}

What's Changed

Highlights

It just works®:
overreact is easier than ever. We fine-tuned the choice of many parameters, so that your simulations run smoothly right from the start. It is now smart enough to guess for how long to simulate (bde5bec, 3c842a7), which solver to use (928b48d), how fast should an equilibrium be (3a516bd, 1d2cbc8, 645578c), how to handle edge cases when correcting for quantum tunneling (0e5ad84), which species actually make sense to plot when generating a kinetic profile (2de3dbd), how large show the first time step be in a simulation (8eafc35, a4cd60d, ae55264), and more.

Adjust energies per species:
You can now use the extra_energy_term flag to adjust the energy of a single species (777155c).

User-interface and output:
The output has been enhanced and is clearer than ever (13fd9ae, 4f2c0d4, dec2297), which now shows the progress of the calculation as it is being performed (2d4d894). Error messages and warnings have been improved as well (92c7cb0).

Documentation and resources:
We greatly improved consistency between the documentation, API and command-line help (f0bc3b9, d828d37, 0ae4727, 1a2d030, c6daa55). In fact, we now have two sets of documentations: the user guide, focused on the use of the command-line application, and the Python API documentation (b1c7456, 4ecacfc, ea298d0, 8ca1c7f, b6c8886, da22151, 8eb5f06, 0212376). We now have an improved README.md file (79ba5f2, df90408, c2b62ed, 0be2ad8, 64da6b9, #149), as well as a great CONTRIBUTING.md thanks to @Leticia-maria (fcccbd1, f1ce7c0, #133). Thanks, Letícia!

Code quality and API:
The user-facing API is now almost completely type-hinted (37cca8d, 819773c). There might be some rough edges yet, so feel free to open an issue if you see something. Lots of housekeeping has been taken place as well, mostly to keep the code base modern, performant, and easy to use (f47206b, ea27d5b, 2f6a176, fb99f6c, 7622789, f60a705). We now target Python versions 3.8-3.10 (bc67e7d, c089244), and use Ruff and Black to keep the code base as tidy as possible (cddc09d, a0f1be3, 14dde86).

Pull requests

Here are the list of relevant pull requests since last version.

New Contributors

Full Changelog: v1.0.2...v1.1.0

Contributors

dependabot and Leticia-maria
Assets 2
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