v1.2.0

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

This is a feature release of overreact that, among other minor changes, improves integrator stability and parameter choices for the integrators overall. In particular, overreact now makes similar choices to scipy.integrate.solve_ivp, which should lead to fewer surprises. A big part of this was kindly contributed by @bmounssefjr.

⚠️ It was found out that the currently calculated analytical Jacobian leads to problems, which is most relevant when implicit integrators are employed. This affects LSODA, Radau and BDF. As such, the usage of analytical Jacobians has been disabled for this version until we find a fix for the bug. Even though it is a breaking chance per se, it is mild, as most of the change happened in places where user had previously no access. We hope to fix this issue soon. Previous and published results were not affected.

Update it using pip:

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

Overreact is licensed under the MIT license.

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

• Add basic issue templates by @schneiderfelipe in #378
• Enforce ruff rules by @schneiderfelipe in #392
• Improve integrator stability by @schneiderfelipe in #416
• Bump scipy to 1.10.1 by @dependabot in #371
• Bump markdown-it-py to 2.2.0 by @dependabot in #372
• Bump matplotlib to 3.7.1 by @dependabot in #385
• Bump flynt to 0.78 by @dependabot in #397
• Bump jaxlib to 0.4.7 by @dependabot in #402
• Bump black to 23.3.0 by @dependabot in #403
• Bump jax to 0.4.8 by @dependabot in #405
• Bump ipython to 8.12.0 by @dependabot in #404
• Bump debugpy to 1.6.7 by @dependabot in #410
• Bump mypy to 1.2.0 by @dependabot in #411
• Bump rich to 13.3.4 by @dependabot in #413
• chore(deps-dev): bump pytest to 7.3.1 by @dependabot in #414
• chore(deps): bump thermo to 0.2.24 by @dependabot in #420
• chore(deps-dev): bump pdoc to 13.1.1 by @dependabot in #419
• chore(deps-dev): bump types-setuptools to 67.7.0.0 by @dependabot in #418
• chore(deps-dev): bump ruff to 0.0.263 by @dependabot in #421

Full Changelog: v1.1.0...v1.2.0