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RMG-Py v2.4.0
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@mliu49 mliu49 released this 14 Jun 22:32
· 2212 commits to stable since this release
2.4.0
caebd48
  • Heterogeneous catalysis!
    • RMG-cat fork has been merged #1573
      • Introduce SurfaceReactor
      • Thermo estimation for adsorbed species
      • Surface reaction generation and kinetics estimation
    • Introduce Van der Waals bonds (order 0) and quadruple bonds (order 4) #1542
  • Arkane
    • Automatically detect rotor symmetry #1526
    • Introduce new YAML files for storing and loading species statmech data #1402, #1551
    • Don't create species dictionary file if there are no structures #1528
    • Improvements to network explorer tool #1545
    • Improved class inheritance for quantum log file classes #1571
    • Automatic determination of optical isomers and symmetry using symmetry package #1571
    • Parse CCSD(T) energies from Molpro output #1592
    • Automatically determine molecule linearity #1601
    • Determine frequency scaling factor based on geom/freq method rather than sp method #1612
    • Improve logging related to energy barriers #1575
    • Ensure that translational mode is calculated for atoms #1620
  • Miscellaneous features
    • New enumerate_bonds method of Molecule to generate dictionary of bond types #1525
    • Introduce RMGObject parent class to support YAML dumping and loading #1402, #1540
    • Add support for fluorine atomtypes #1543
    • Introduce ArrheniusBM class for Blower-Masel kinetics #1461
    • Allow defining and using co-solvents for solvent libraries #1558
    • Introduce strict option to perform isomorphism between species/molecules while ignoring electrons and bond orders #1329
    • Molecule and Species objects can be instantiated by providing SMILES or InChI argument directly, and the identifiers can be accessed via the SMILES and InChI attributes #1329
    • Parallelization has been completely refactored using Python multiprocessing module in replacement of scoop, currently supports parallel reaction generation and QMTP #1459
    • Improvements to usability of uncertainty analysis functionality #1593
  • Bug fixes
    • Various fixes for supporting mono-atomic molecules in Arkane #1513, #1521
    • Ensure keras_backend is set consistently #1535
    • Fix handling of disconnected graphs in VF2 isomorphism algorithm #1538
    • Ignore hydrogen bonds when converting to RDKit molecule #1552
    • Other miscellaneous bugs #1546, #1556, #1593, #1600, #1622
  • Backward incompatible changes
    • Hydrogen bonds are now order 0.1 (instead of 0) #1542
  • New dependencies
    • pyyaml (required) #1402
    • scikit-learn (required) #1461
    • textgenrnn (optional) #1573
  • Other
    • Windows binaries are no longer officially supported. The new recommended way to use RMG on Windows computers is via a virtual machine or through the Linux subsystem. See documentation for updated installation instructions. #1531, #1534
    • Documentation updates #1544, #1567
    • Logging/exception improvements #1538, #1562
    • PEP-8 improvements #1566, #1592, #1596
    • Solver output files (png/csv) now report moles instead of mole fractions #1542
    • Replace global RMGDatabase object if the database is reloaded #1565
    • Print ML generated quote upon completion of RMG jobs #1573
    • Infrastructure for automatically generated reaction rate trees #1461
    • Testing related changes #1597, #1599
    • Updates to example Jupyter notebooks #1541, #1593
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