RMG-database 'v3.2.0' release.

RMG-Database Version 3.2.0
==========================
Date: August 2, 2023

- Thermochemistry
    - Identified and fitted thermo for missing groups using the following libraries:
        'Klippenstein_Glarborg2016', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo',
        'primaryThermoLibrary', 'primaryNS', 'NitrogenCurran', 'NOx2018', 'FFCM1(-)',
        'SulfurLibrary', 'SulfurGlarborgH2S', 'SABIC_aromatics'
    - Added more solutes and solvents to the solvent library
    - Updated GAV method for solvation thermo to use more groups
    - Added the following new halogen thermo libraries:
        - CHOF_G4
        - CHOCl_G4
        - CHOBr_G4
        - CHOFCl_G4
        - CHOClBr_G4
        - CHOFBr_G4
        - CHOFClBr_G4
        - Chlorination
        - halogens
        - 2-BTP
        - 2-BTP_G4
    - Added new halogens group entries for group.py, radical.py nonring.py, and longDistanceInteraction_noncyclic.py
    - Added the following species to the primaryThermoLibrary: F, HF, F2, Br, HBr, Br2, NO, NO2, CO, OCCCO
    - Updated halogen group entries with molecule symmetry number correction
    - Added corrections for overestimation of triplet and multidentate adsorbates
    - Added CO2, COOH, and HCOO to the Pt(111) thermo database
    - Added halogens statmech library
    - Added F/Cl/Br-benzene group additivity values
    - Added "heavy halogen interaction" long distance thermo group
    - Added thermo library with 1D rotor scans for species in ketoenol, retroene, and 1,3 sigmatropic rearrangement training reactions
    - Added more Pt(111) thermo data
    - Added correction to S6ddd thermo group

- Kinetics
    - Added coverage-dependent kinetics for surface reactions
    - Added new halogens kinetics families and libraries
    - Added the following new families:
        - 1,3 sigmatropic rearrangement
        - Intra halogen migration family
        - Surface_Abstraction_Beta
        - Surface_Abstraction_Beta_double_vdW
        - Surface_Adsorption_Dissociative_Double
        - Surface_Dissociation_to_Bidentate
        - XY_elimination_hydroxy
    - Autogenerated the following family trees:
        - 1,3_Insertion_CO2
        - 1,3_NH3_elimination
        - 1,3_sigmatropic_rearrangement
        - 2+2_cycloaddition
        - Bimolec_Hydroperoxide_Decomposition
        - Birad_recombination
        - CO Disproportionation
        - Cyclopentadiene_scission
        - Diels alder addition
        - Disproportionation
        - Ketoenol
        - Peroxyl Disproportionation
        - Retroene
        - Substitution_O
    - Added new rates and refit the following family trees:
        - 1,3_Insertion CO2
        - 1,3 sigmatropic rate tree
        - Diels Alder Addition
        - Intra_R_Add_Endo/Exocyclic
        - retroene
        - ketoenol
        - aromatic_H_abstraction (new rates from Hou et al.)
        - Surface_Adsorption_Bidentate
        - Surface_Adsorption_Double
        - Surface_Adsorption_Single
        - Surface_Adsorption_vdW
        - Surface_Bidentate_Dissociation
        - Surface_Dissociation
        - Surface_Dissociation_Beta
        - Surface_vdW_to_Bidentate
    - Added PrimaryH2O2 library with rates by Konnov
    - Updated reactions for PrimaryNitrogenLibrary
    - Added surface library reactions for ammonia
    - Merged all 2+2_cycloaddition families in to one 2+2_cycloaddition family
    - Generate Intra R Add Endo/Exocyclic rate trees from the ring opening direction to help distinguish between endo/exo
    - Added training reactions and groups related to PAH formation
    - Save additional DFT settings information for metal binding energy calculations
    - Added corrections to primaryH2O2 library
    - Added corrections to Klippenstein_Glarborg2016 library related to singlet/triplet carbene reactions and other incorrectly imported reactions

- Transport
    - Added NIST transport library for fluorines
    - Added new halogen transport groups
    - Added Nitrogen groups to transport

- QM Corrections
    - Added frequency scaling factors AEC and BAC for wB97X-D3/def2-TZVP and B97-D3/def2-mSVP
    - Added notebooks demonstrating how to update AEC and BAC
    - Updated AECs for CCSD(T)-F12/cc-pVXZ-F12 st X = D, T
    - Added frequency factors for b2plypd3/def2tzvp, b2plypd3/aug-cc-pvtz, b2plypd3/cc-pvtz
    - Updated BAC using correct frequency scaling factor for:
        - wB97X-D3/def2-TZVP
        - B97-D3/def2-mSVP
        - CCSD(T)-F12/cc-pVTZ-F12//wB97X-D3/def2-TZVP
        - CCSD(T)-F12/cc-pVDZ-F12//wB97X-D3/def2-TZVP

- Bugfixes
    - Fixed the number of unpaired radicals in surface vdW families
    - Fixed typos in training reactions field names
    - Fixed enthalpy errors in adsorption corrections for O-containing species on Pt(111)
    - Fixed some errors in surface training reaction rates
    - Fixed some minor errors in the solvent library
    - Fixed typos in coverage dependent kinetics parameters
    - Used forbidden group to fix error where unsymmetric head node leads to Undeterminable Kinetics Error
    - Removed duplicates in XY_addition_multiplebond
    - Fixed typo in R_Recombination training reaction units
    - Fixed incorrectly imported species H2CCC and C3H2 in the CurranPentane library
    - Fixed master to main in trigger script
    - Added the missing reactant and product number in the intra_R_Add families
    - Fixed Intra_R_Add_Endocyclic/Exocyclic families by generating from the ring opening direction and enumerating backbones

- Miscellaneous
    - Updated Github Actions workflow for better handling of dual RMG-Py and RMG-database pull requests
    - Added the Blowers-Masel tree generation notebook
    - Added [C-]#[C+] to forbidden structures
    - Added thermally forbidden 2pi + 2pi cycloaddition to forbidden structures
    - Changed Github Actions to run on main branch instead of master
    - Updated 2+2_cycloaddition reaction family images

Co-authored-by: Sevy Harris <harris.se@northeastern.edu>
Co-authored-by: Richard West <r.west@northeastern.edu>

Author: rwest

.github/workflows/CI.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 5
     env: # update this if needed to match a pull request on the RMG-database
-      RMG_PY_BRANCH: master
+      RMG_PY_BRANCH: main
     defaults:
       run:
         shell: bash -l {0}
@@ -42,7 +42,7 @@ jobs:
           cd ../RMG-Py
           make
       - name: Trigger RMG-tests
-        if: ${{ github.event_name == 'push' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/stable' }} # only push events to branches other than master and stable
+        if: ${{ github.event_name == 'push' && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/stable' }} # only push events to branches other than main and stable
         env:
           GH_TOKEN: ${{ secrets.RMG_DEV_TOKEN }}
         run: ./trigger-rmg-tests.sh

.gitignore

@@ -4,6 +4,9 @@
 #
 ################################################################################
 
+# MacOS Files
+.DS_Store
+
 # Eclipse project files
 .project
 .pydevproject