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Add release notes for version 2.4.0
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‎documentation/source/users/rmg/releaseNotes.rst‎

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RMG-Py Version 2.3....
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======================
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(pre-release development version)
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- Miscellaneous changes:
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- Output files in 'solver' directory now show species amounts (numbers of moles) not mole fractions.
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RMG-Py Version 2.4.0
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====================
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Date: June 14, 2019
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- Heterogeneous catalysis!
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- RMG-cat fork has been merged #1573
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- Introduce SurfaceReactor
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- Thermo estimation for adsorbed species
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- Surface reaction generation and kinetics estimation
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- Introduce Van der Waals bonds (order 0) and quadruple bonds (order 4) #1542
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- Arkane
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- Automatically detect rotor symmetry #1526
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- Introduce new YAML files for storing and loading species statmech data #1402, #1551
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- Don't create species dictionary file if there are no structures #1528
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- Improvements to network explorer tool #1545
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- Improved class inheritance for quantum log file classes #1571
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- Automatic determination of optical isomers and symmetry using ``symmetry`` package #1571
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- Parse CCSD(T) energies from Molpro output #1592
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- Automatically determine molecule linearity #1601
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- Determine frequency scaling factor based on geom/freq method rather than sp method #1612
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- Improve logging related to energy barriers #1575
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- Ensure that translational mode is calculated for atoms #1620
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- Miscellaneous features
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- New ``enumerate_bonds`` method of Molecule to generate dictionary of bond types #1525
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- Introduce ``RMGObject`` parent class to support YAML dumping and loading #1402, #1540
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- Add support for fluorine atomtypes #1543
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- Introduce ``ArrheniusBM`` class for Blower-Masel kinetics #1461
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- Allow defining and using co-solvents for solvent libraries #1558
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- Introduce ``strict`` option to perform isomorphism between species/molecules while ignoring electrons and bond orders #1329
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- 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
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- Parallelization has been completely refactored using Python multiprocessing module in replacement of scoop, currently supports parallel reaction generation and QMTP #1459
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- Improvements to usability of uncertainty analysis functionality #1593
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- Bug fixes
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- Various fixes for supporting mono-atomic molecules in Arkane #1513, #1521
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- Ensure ``keras_backend`` is set consistently #1535
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- Fix handling of disconnected graphs in VF2 isomorphism algorithm #1538
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- Ignore hydrogen bonds when converting to RDKit molecule #1552
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- Other miscellaneous bugs #1546, #1556, #1593, #1600, #1622
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- Backward incompatible changes
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- Hydrogen bonds are now order 0.1 (instead of 0) #1542
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- New dependencies
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- pyyaml (required) #1402
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- scikit-learn (required) #1461
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- textgenrnn (optional) #1573
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- Other
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- 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
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- Documentation updates #1544, #1567
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- Logging/exception improvements #1538, #1562
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- PEP-8 improvements #1566, #1592, #1596
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- Solver output files (png/csv) now report moles instead of mole fractions #1542
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- Replace global RMGDatabase object if the database is reloaded #1565
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- Print ML generated quote upon completion of RMG jobs #1573
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- Infrastructure for automatically generated reaction rate trees #1461
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- Testing related changes #1597, #1599
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- Updates to example Jupyter notebooks #1541, #1593
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RMG-database Version 2.4.0
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==========================
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Date: June 14, 2019
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- Heterogeneous catalysis!
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- RMG-cat fork has been merged #309
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- New kinetics families
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- Surface_Adsorption_Single
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- Surface_Adsorption_vdW
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- Surface_Adsorption_Dissociative
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- Surface_Dissociation
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- Surface_Abstraction
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- Surface_Adsorption_Double
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- Surface_Dissociation_vdW
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- Surface_Adsorption_Bidentate
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- Surface_Bidentate_Dissociation
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- Surface_Recombination (deprecated, use Surface_Dissociation instead)
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- New thermo group types
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- adsorptionNi
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- adsorptionPt
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- New thermo libraries
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- surfaceThermoNi
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- surfaceThermoPt
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- New kinetics families
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- 1,2_NH3_elimination #326
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- 1,3_NH3_elimination #326
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- New kinetics libraries
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- HydrazinePDep #326
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- New transport libraries
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- OneDMinN2 #326
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- Kinetics training reaction additions
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- 1,2_shiftC #306
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- Intra_R_Add_Endocyclic #306, #258
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- Intra_R_Add_Exocyclic #306, #258, #331
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- Intra_ene_reaction #306
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- R_Addition_COm #306
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- R_Addition_MultipleBond #306, #258
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- R_Recombination #306, #326
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- Intra_H_migration #306
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- H_Abstraction #326
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- Kinetics library additions
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- primaryNitrogenLibrary #326
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- Lai_Hexylbenzene #258
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- Thermo library additions
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- CBS_QB3_1dHR, thermo_DFT_CCSDTF12_BAC #319
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- primaryNS #326
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- Lai_Hexylbenzene #258
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- Thermo group additions
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- ring, polycyclic, radical #258
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- Changes
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- [adjlist] kinetics/libraries/Klippenstein_Glarborg2016 #308
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- [labels] thermo/libraries/CBS_QB3_1dHR, Narayanaswamy #306
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- [units] kinetics/libraries/Sulfur/GlarborgMarhsall, Nitrogen_Dean_and_Bozzelli, primaryNitrogenLibrary, primarySulfurLibrary #311
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- [units] R_Addition_MultipleBond/training, R_Recombination/training #312
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- [adjlist] kinetics/libraries/GRI-Mech3.0-N #313
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- [adjlist] thermo/libraries/GRI-Mech3.0-N, GRI-Mech3.0 #313
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- [rates] Disproportionation/training, R_Addition_MultipleBond/training #326
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- [labels] kinetics/libraries/NOx2018 #326
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- [labels, attributes] kinetics/libraries/Nitrogen_Dean_and_Bozelli #326
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- [labels] kinetics/librariesNitrogen_Glarbog_Gimenez_et_al, Nitrogen_Glarborg_Zhang_et_al #326
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- [labels, adjlist] thermo/libraries/BurcatNS #326
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- [labels] thermo/libraries/NOx2018, NitrogenCurran #326
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- [labels] transport/libraries/NOx2018 #326
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- [adjlist] Intra_R_Add_Endocyclic/training #332
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- [value] thermo/groups/ring/12dioxetane #327
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- [adjlist] thermo/libraries/GRI-Mech3.0 #336
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- [value] thermo/libraries/primaryThermoLibrary #338
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RMG-Py Version 2.3.0

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