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RMG-Py v2.2.0
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@mliu49 mliu49 released this 16 Jul 02:22
· 3519 commits to main since this release
2.2.0
1846c6c

  • New features:

    • New ring membership attribute added to atoms. Can be specified in group adjacency lists in order to enforce ring membership of atoms during subgraph matching.
    • Reactors now support specification of T, P, X ranges. Different conditions are sampled on each iteration to optimally capture the full parameter space.
    • New termination type! Termination rate ratio stops the simulation when the characteristic rate falls to the specified fraction of the maximum characteristic rate. Currently not recommended for systems with two-stage ignition.
    • New resonance transitions implemented for species with lone pairs (particularly N and S containing species). A filtration algorithm was also added to select only the most representative structures.
    • Formal support for trimolecular reaction families.
    • New isotopes module allows post-processing of RMG mechanisms to generate a mechanism with isotopic labeling.

  • Changes:

    • Library reactions can now be integrated into RMG pdep networks if the new elementary_high_p attribute is True
    • Library reactions may be duplicated by pdep reactions if the new allow_pdep_route attribute is True
    • Jupyter notebook for adding new training reactions has been revamped and is now located at ipython/kinetics_library_to_training.ipynb
    • Syntax for recommended families has changed to set notation instead of dictionaries, old style still compatible
    • Ranking system for database entries expanded to new 0-11 system from the old 0-5 system
    • Collision limit checking has been added for database entries

  • Cantherm:

    • Improved support for MolPro output files
    • Added iodine support
    • Automatically read spin multiplicity from quantum output
    • Automatically assign frequency scale factor for supported model chemistries
    • Plot calculated rates and thermo by default
    • New sensitivity analysis feature analyzes sensitivity of reaction rates to isomer/TS energies in pdep networks

  • Fixes:

    • Properly update charges when creating product templates in reaction families
    • Excessive duplicate reactions from different resonance structures has been fixed (bug introduced in 2.1.3)
    • Fixed rate calculation for MultiPdepArrhenius objects when member rates have different plists

  • A more formal deprecation process is now being trialed. Deprecation warnings have been added to functions to be removed in version 2.3.0:

    • All methods related to saving or reading RMG-Java databases and old-style adjacency lists
    • The group additivity method for kinetics estimation (unrelated to thermo group additivity)
    • The saveRestartPeriod option and the old method of saving restart files
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