RMG v2.4.0 (?) Release Planning

[mliu49]

With the RMG-cat merge completed, I think we should have a new release soon. Potential target release date could be end of May. Please feel free to provide your own thoughts.

First, regarding the release number, I'm leaning towards 2.4.0. The RMG-cat merge is a major new feature, but it didn't introduce any backward compatibility issues, so I'm not sure if it would necessitate jumping to 3.0.0. Also, thinking ahead, it would be nice to transition to Python 3 and fix our variable naming inconsistencies for the 3.0.0 release, which would definitely involve breaking changes. Of course, this is also open for discussion.

Next, we need to identify any issues/PRs which we want to include in this release. Potential list:

• Update IPython notebooks and examples Update RMG's ipython notebooks #1541
• Multiprocessing Reaction generation using multiprocessing #1459
• Chemical identity comparison Chemical identity comparison for Molecules and Species #1329
• Uncertainty user experience fixes (PR coming soon)
• Database cleanup? @mjohnson541

Please use this issue thread to comment on the status of currently open PRs and whether or not they can/should be included in this release. RMG-database PRs can also be discussed here rather than creating a separate RMG-database issue.

[mliu49]

Another topic for discussion: Would we like to begin official support for Docker with this release?

For people not in the Green Group who may not know about this, we have been considering Docker as a way to offer a host-independent method of installing RMG. This can be especially useful for installing on HPC clusters which may already have support for Docker images. Somewhat surprisingly, there were already a couple of RMG images on Docker Hub. For testing, I've created a semi-official one which can be pulled: https://hub.docker.com/r/mliu49/rmg.

The main benefit would be offering a streamlined option for running RMG on a wider variety of systems, including non-ubuntu linux systems and windows, at the cost of adding another system which we would need to manage and support.

What this would entail:

• Finalize dockerfile for building RMG image
• Develop and document recommended workflow for using RMG via Docker
• Develop workflow for creating Docker images (ideally automated, but not strictly necessary)

[rwest]

Docker sounds like a decent idea, (though I'm not volunteering my own time to support it. I think @skrsna has done some docker stuff)

I think 2.4.0 is reasonable. Nice to have 3.0 be the Python 3 version.

May sounds like a good target

[alongd]

I think we should merge #1496 and ReactionMechanismGenerator/RMG-database#296
Might as well also do #1575, which is small
(all are rebased and should be good to go, #1575 still needs to be reviewed)

[goldmanm]

Is it worthwhile to get in commits necessary for the Arkane paper? Like @mjohnson541 's quantum hindered rotors, and my reorganizing the output of Arkane?

[alongd]

I agree, let's try to get it in

[mliu49]

RMG-Py v2.4.0 Release Notes (draft)

• Heterogeneous catalysis!
  • RMG-cat fork has been merged RMG-NLP #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) Non-cat changes to master from cat branch, 2  #1542
• Arkane
  • Automatically detect rotor symmetry Determine the rotor symmetry number from the potential scan #1526
  • Introduce new YAML files for storing and loading species statmech data Save and parse Arkane species with all statmech properties using YAML format #1402, Load and dump TS YAML files in Arkane #1551
  • Don't create species dictionary file if there are no structures Minor: Modified saving proceedure of species_dictionary.txt in Arkane #1528
  • Improvements to network explorer tool Network Explorer Part 2 #1545
  • Improved class inheritance for quantum log file classes Auto optical isomer ex symmetry arkane #1571
  • Automatic determination of optical isomers and symmetry using symmetry package Auto optical isomer ex symmetry arkane #1571
  • Parse CCSD(T) energies from Molpro output Parse CCSD(T) energies (no F12) in Molpro #1592
  • Automatically determine molecule linearity Determine a species linearity from xyz #1601
  • Determine frequency scaling factor based on geom/freq method rather than sp method Derive the frequency scaling factor in Arkane from the frequency level #1612
  • Improve logging related to energy barriers Improve error/warning messages concerning energy barriers in Arkane #1575
  • Ensure that translational mode is calculated for atoms Calculate the translational mode if doesn't exist #1620
• Miscellaneous features
  • New enumerate_bonds method of Molecule to generate dictionary of bond types Enable enumeration of bond types present in a molecule #1525
  • Introduce RMGObject parent class to support YAML dumping and loading Save and parse Arkane species with all statmech properties using YAML format #1402, BugFix: Empty list as val in RMGObject.as_dict() and .make_object() #1540
  • Add support for fluorine atomtypes Adding Fluorine as a new element in RMG #1543
  • Introduce ArrheniusBM class for Blower-Masel kinetics Automatic Tree Generation Part 3 #1461
  • Allow defining and using co-solvents for solvent libraries Allow cosolvents to be defined in a solvent library #1558
  • Introduce strict option to perform isomorphism between species/molecules while ignoring electrons and bond orders Chemical identity comparison for Molecules and Species #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 Chemical identity comparison for Molecules and Species #1329
  • Parallelization has been completely refactored using Python multiprocessing module in replacement of scoop, currently supports parallel reaction generation and QMTP Reaction generation using multiprocessing #1459
  • Improvements to usability of uncertainty analysis functionality Uncertainty fixes and user experience improvement #1593
• Bug fixes
  • Various fixes for supporting mono-atomic molecules in Arkane Allow hasStatMech to assess atomic molecules #1513, Processing monoatomic species in Arkane/molpro #1521
  • Ensure keras_backend is set consistently Set KERAS_BACKEND=theano before importing DDE #1535
  • Fix handling of disconnected graphs in VF2 isomorphism algorithm Non-cat changes to master from cat branch, 1 #1538
  • Ignore hydrogen bonds when converting to RDKit molecule Allow RDKit to ignore hydrogen bonds #1552
  • Other miscellaneous bugs Move variable initiation to avoid undefined variable error #1546, Properly remove forbidden species from edge #1556, Uncertainty fixes and user experience improvement #1593, Fix resonance structure generation and filtration bugs #1600, In training notebook, save once per family instead of per reaction #1622
• Backward incompatible changes
  • Hydrogen bonds are now order 0.1 (instead of 0) Non-cat changes to master from cat branch, 2  #1542
• New dependencies
  • pyyaml (required) Save and parse Arkane species with all statmech properties using YAML format #1402
  • scikit-learn (required) Automatic Tree Generation Part 3 #1461
  • textgenrnn (optional) RMG-NLP #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. VM Windows Install #1531, Update the RMG Installation Documentation #1534
  • Documentation updates Consolidate Arkane documentation input file #1544, Documentation fixes and additions - installation related #1567
  • Logging/exception improvements Non-cat changes to master from cat branch, 1 #1538, Enhanced error message of Arkane GaussianLog loadGeometry #1562
  • PEP-8 improvements Corrected raise Error as e syntax #1566, Parse CCSD(T) energies (no F12) in Molpro #1592, Improved coding style in Arkane #1596
  • Solver output files (png/csv) now report moles instead of mole fractions Non-cat changes to master from cat branch, 2  #1542
  • Replace global RMGDatabase object if the database is reloaded Initialize the global RMGDatabase object upon calling it #1565
  • Print ML generated quote upon completion of RMG jobs RMG-NLP #1573
  • Infrastructure for automatically generated reaction rate trees Automatic Tree Generation Part 3 #1461
  • Testing related changes Modify test-database make target to not capture stdout and log #1597, Tests: Added a Molpro negative frequency test to Arkane #1599
  • Updates to example Jupyter notebooks Update RMG's ipython notebooks #1541, Uncertainty fixes and user experience improvement #1593

RMG-database v2.4.0 Release Notes (draft)

(note that the tags here are odd because this issue is in the RMG-Py repo; the final release notes will be in the RMG-database repo so they will be normal)

• Heterogeneous catalysis!
  • RMG-cat fork has been merged RMG-Cat!! RMG-database#309
  • New kinetics families
    • Surface_Adsorption_Single
    • Surface_Adsorption_vdW
    • Surface_Adsorption_Dissociative
    • Surface_Dissociation
    • Surface_Abstraction
    • Surface_Adsorption_Double
    • Surface_Dissociation_vdW
    • Surface_Adsorption_Bidentate
    • Surface_Bidentate_Dissociation
    • Surface_Recombination (deprecated, use Surface_Dissociation instead)
  • New thermo group types
    • adsorptionNi
    • adsorptionPt
  • New thermo libraries
    • surfaceThermoNi
    • surfaceThermoPt
• New kinetics families
  • 1,2_NH3_elimination Hydrazine pyrolysis RMG-database#326
  • 1,3_NH3_elimination Hydrazine pyrolysis RMG-database#326
• New kinetics libraries
  • HydrazinePDep Hydrazine pyrolysis RMG-database#326
• New transport libraries
  • OneDMinN2 Hydrazine pyrolysis RMG-database#326
• Kinetics training reaction additions
  • 1,2_shiftC Aromatics 2018 dec RMG-database#306
  • Intra_R_Add_Endocyclic Aromatics 2018 dec RMG-database#306, New Groups Lai 03162018 RMG-database#258
  • Intra_R_Add_Exocyclic Aromatics 2018 dec RMG-database#306, New Groups Lai 03162018 RMG-database#258, Add Intra_R_Add_Exocyclic training reactions from Wang et al. 2015 RMG-database#331
  • Intra_ene_reaction Aromatics 2018 dec RMG-database#306
  • R_Addition_COm Aromatics 2018 dec RMG-database#306
  • R_Addition_MultipleBond Aromatics 2018 dec RMG-database#306, New Groups Lai 03162018 RMG-database#258
  • R_Recombination Aromatics 2018 dec RMG-database#306, Hydrazine pyrolysis RMG-database#326
  • Intra_H_migration Aromatics 2018 dec RMG-database#306
  • H_Abstraction Hydrazine pyrolysis RMG-database#326
• Kinetics library additions
  • primaryNitrogenLibrary Hydrazine pyrolysis RMG-database#326
  • Lai_Hexylbenzene New Groups Lai 03162018 RMG-database#258
• Thermo library additions
  • CBS_QB3_1dHR, thermo_DFT_CCSDTF12_BAC Added AIBN and its decomposition products to thermo libraries RMG-database#319
  • primaryNS Hydrazine pyrolysis RMG-database#326
  • Lai_Hexylbenzene New Groups Lai 03162018 RMG-database#258
• Thermo group additions
  • ring, polycyclic, radical New Groups Lai 03162018 RMG-database#258
• Changes
  • [adjlist] kinetics/libraries/Klippenstein_Glarborg2016 fix bond order mistake in Klippenstein_Glarborg2016 RMG-database#308
  • [labels] thermo/libraries/CBS_QB3_1dHR, Narayanaswamy Aromatics 2018 dec RMG-database#306
  • [units] kinetics/libraries/Sulfur/GlarborgMarhsall, Nitrogen_Dean_and_Bozzelli, primaryNitrogenLibrary, primarySulfurLibrary Correct some units in reaction libraries. RMG-database#311
  • [units] R_Addition_MultipleBond/training, R_Recombination/training Correct A factor units in training depositories RMG-database#312
  • [adjlist] kinetics/libraries/GRI-Mech3.0-N Corrected NH structure in GRI libraries RMG-database#313
  • [adjlist] thermo/libraries/GRI-Mech3.0-N, GRI-Mech3.0 Corrected NH structure in GRI libraries RMG-database#313
  • [rates] Disproportionation/training, R_Addition_MultipleBond/training Hydrazine pyrolysis RMG-database#326
  • [labels] kinetics/libraries/NOx2018 Hydrazine pyrolysis RMG-database#326
  • [labels, attributes] kinetics/libraries/Nitrogen_Dean_and_Bozelli Hydrazine pyrolysis RMG-database#326
  • [labels] kinetics/librariesNitrogen_Glarbog_Gimenez_et_al, Nitrogen_Glarborg_Zhang_et_al Hydrazine pyrolysis RMG-database#326
  • [labels, adjlist] thermo/libraries/BurcatNS Hydrazine pyrolysis RMG-database#326
  • [labels] thermo/libraries/NOx2018, NitrogenCurran Hydrazine pyrolysis RMG-database#326
  • [labels] transport/libraries/NOx2018 Hydrazine pyrolysis RMG-database#326
  • [adjlist] Intra_R_Add_Endocyclic/training Change Intra_R_Add_Endo training rxns to benzene bonds RMG-database#332
  • [value] thermo/groups/ring/12dioxetane The thermo parameters of ring(12dioxetane) fitted with CBS-QB3 calculation results RMG-database#327
  • [adjlist] thermo/libraries/GRI-Mech3.0 Corrected the adjlist (and multiplicity) of N2O in GRI_Mech RMG-database#336
  • [value] thermo/libraries/primaryThermoLibrary Update entropy of triplet oxygen atom RMG-database#338

[mliu49]

Please feel free to edit the draft release notes above. I would also appreciate it if everyone could help keep this up to date as we merge more PRs before the release.

[mliu49]

Release is done!