v1.0alpha

[schneiderfelipe]

That is the first release of overreact, still alpha, but very functional. A manuscript about it is in preparation, but a Zenodo DOI will soon be available for citations.

overreact is licensed under the MIT license (#12).

You can read the documentation at https://geem-lab.github.io/overreact-docs/.

Some notable features

• Well-tested thermodynamics (Implement basic thermochemistry contributions #5, Support for calculating heat capacity #7, Ensure correct and (semi)automatic standard state corrections #17, Ensure good gas-phase thermochemistry #25, Ensure correct standard state corrections for solvated compounds #64, abb2417)
  • Automatic support of molecular symmetries (Detect reaction symmetry numbers #8, Automatically use reaction symmetry when necessary #62)
  • Automatic inversion of small imaginary frequencies, with a warning (Invert small imaginary frequencies #50)
  • Direct bias adjustment of computed free energies for fitting concentration profiles (Direct bias adjustment of computed free energies for fitting concentration profiles #13)
• Thoroughly tested (Run tests on macOS as well #45, Drop official support for PyPy #53, Create dependabot.yml #54, Do not test on macOS anymore, only on Ubuntu/Linux #57)
• Good command-line interface (Use Rich in the command-line interface #41, Use Rich library in the CLI #47, Use bias in the CLI and improve its verbose mode #66, Improve help page of the CLI #67, Simple refactoring #73)
  • Detailed description of results (Inform units in logging messages #36, Show some common units for reaction rate constants #37, Indicate the meaning of both rotational energies and entropies in the logs #38, Aways show (initial and) final concentrations in the output #51, Show initial and final concentrations in the output #56)
• Stable numerical integration of the reaction ODE system (Improve get_y #48, Solve a common error due to randomness #55, Improve numerical stability when integrating the ODE system #68, Improve numerical stability when integrating the ODE system #69)
  • Support for fixing concentration in chemical kinetic models (Support for fixing concentration in chemical kinetic models #14, Allow fixing concentrations of certain compounds #74)
• Good documentation (Create separate repository for documentation and improve it #49, Make documentation awesome 🎉 #83, Update docs & README.md #87)
• Semantic versioning (Inform we use semantic versioning #43)

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This discussion was created from the release v1.0alpha.