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>
ReactionMechanismGenerator · Aug 8, 2023 · b7ff163 · b7ff163
2 parents 1017fbb + e87df88
commit b7ff163
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diff --git a/.github/workflows/CI.yml b/.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

diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,9 @@
 #
 ################################################################################
 
+# MacOS Files
+.DS_Store
+
 # Eclipse project files
 .project
 .pydevproject

diff --git a/families/images/1,2_XY_interchange.png b/families/images/1,2_XY_interchange.png
diff --git a/families/images/1,3_sigmatropic_rearrangement.png b/families/images/1,3_sigmatropic_rearrangement.png
diff --git a/families/images/2+2_cycloaddition.png b/families/images/2+2_cycloaddition.png
diff --git a/families/images/2+2_cycloaddition_CCO.png b/families/images/2+2_cycloaddition_CCO.png
diff --git a/families/images/2+2_cycloaddition_CO.png b/families/images/2+2_cycloaddition_CO.png
diff --git a/families/images/2+2_cycloaddition_CS.png b/families/images/2+2_cycloaddition_CS.png
diff --git a/families/images/2+2_cycloaddition_Cd.png b/families/images/2+2_cycloaddition_Cd.png
diff --git a/families/images/Br_Abstraction.png b/families/images/Br_Abstraction.png
diff --git a/families/images/Cl_Abstraction.png b/families/images/Cl_Abstraction.png
diff --git a/families/images/Disproportionation-Y.png b/families/images/Disproportionation-Y.png
diff --git a/families/images/F_Abstraction.png b/families/images/F_Abstraction.png
diff --git a/families/images/Ketoenol.png b/families/images/Ketoenol.png
diff --git a/families/images/Surface_Abstraction_Beta.png b/families/images/Surface_Abstraction_Beta.png
diff --git a/families/images/Surface_Abstraction_Beta_double_vdW.png b/families/images/Surface_Abstraction_Beta_double_vdW.png
diff --git a/families/images/Surface_Adsorption_Dissociative_Double.png b/families/images/Surface_Adsorption_Dissociative_Double.png
diff --git a/families/images/XY_Addition_MultipleBond.png b/families/images/XY_Addition_MultipleBond.png
diff --git a/families/images/XY_elimination_hydroxyl.png b/families/images/XY_elimination_hydroxyl.png
diff --git a/families/images/halocarbene_recombination.png b/families/images/halocarbene_recombination.png
diff --git a/families/images/halocarbene_recombination_double.png b/families/images/halocarbene_recombination_double.png
diff --git a/families/images/intra_halogen_migration.png b/families/images/intra_halogen_migration.png
diff --git a/families/images/ketoenol.png b/families/images/ketoenol.png
diff --git a/families/rmg_reaction_families.pdf b/families/rmg_reaction_families.pdf
diff --git a/input/FilterArrheniusFits.yml b/input/FilterArrheniusFits.yml
@@ -854,7 +854,7 @@ bimol:
       class: ScalarQuantity
       value: 1.2857274295511825
   intra_substitutionS_isomerization: null
-  ketoenol: null
+  1,3_sigmatropic_rearrangement: null
   lone_electron_pair_bond: null
 class: FilterLimitFits
 unimol:
@@ -2025,7 +2025,7 @@ unimol:
     n:
       class: ScalarQuantity
       value: 1.7166803824148895
-  ketoenol:
+  1,3_sigmatropic_rearrangement:
     A:
       class: ScalarQuantity
       units: s^-1

diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py
@@ -440,3 +440,87 @@
 Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1492)
 """,
 )
+
+entry(
+    label = "C2_triplebond",
+    species =
+"""
+1 C u0 p1 c-1 {2,T}
+2 C u0 p0 c+1 {1,T}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+https://pubs.acs.org/doi/pdf/10.1021/ct400867h discusses complex wavefunction for C2
+and that it cannot be assigned definitive bond order. We are forbidding the C2 triple bond
+becuase we do not have good thermo for `Ctc` (C u0 p0 c+1 {1,T}) atomtype
+""",
+)
+
+entry(
+    label = "CO2X2",
+    species =
+"""
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 X u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+We assume that CO2 binds only via physisorption to the surface
+""",
+)
+
+entry(
+    label = "CO2X3",
+    species =
+"""
+1 O u0 p2 c0 {3,S} {6,S}
+2 O u0 p2 c0 {3,S} {5,S}
+3 C u0 p0 c0 {1,S} {2,S} {4,D}
+4 X u0 p0 c0 {3,D}
+5 X u0 p0 c0 {2,S}
+6 X u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+We assume that CO2 binds only via physisorption to the surface
+""",
+)
+
+
+entry(
+    label = "O2X2",
+    species =
+"""
+1 O u0 p2 c0 {2,S} {3,S}
+2 O u0 p2 c0 {1,S} {4,S}
+3 X u0 p0 c0 {1,S}
+4 X u0 p0 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+O2 dissociates upon adsorption
+""",
+)
+
+entry(
+    label = "OCX2",
+    species =
+"""
+1 O u0 p2 c0 {2,S} {3,S}
+2 C u0 p0 c0 {1,S} {4,T}
+3 X u0 p0 c0 {1,S}
+4 X u0 p0 c0 {2,T}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+CO binds in a monodentate configuration
+""",
+)
diff --git a/input/kinetics/families/1,2_XY_interchange/groups.py b/input/kinetics/families/1,2_XY_interchange/groups.py
@@ -0,0 +1,193 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "1,2_XY_interchange/groups"
+shortDesc = u""
+longDesc = u"""
+
+X1-R2-R3-Y4    ->    Y4-R2-R3-X1
+
+Y = F,Cl,Br,I
+X = F,Cl,Br,I,O
+"""
+
+template(reactants=["XY"], products=["YX"], ownReverse=True)
+
+reversible = True
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['FORM_BOND', '*2', 1, '*4'],
+])
+
+entry(
+    index = 0,
+    label = "XY",
+    group = "OR{YY,OY}",
+    kinetics = None,
+)
+
+entry(
+    index = 1,
+    label = "YY",
+    group =
+"""
+1 *1 Val7   u0 {2,S}
+2 *2 Cs     u0 {1,S} {3,S}
+3 *3 Cs     u0 {2,S} {4,S}
+4 *4 Val7   u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "FF",
+    group =
+"""
+1 *1 F1s   u0 {2,S}
+2 *2 Cs    u0 {1,S} {3,S}
+3 *3 Cs    u0 {2,S} {4,S}
+4 *4 F1s   u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 3,
+    label = "ClCl",
+    group =
+"""
+1 *1 Cl1s  u0 {2,S}
+2 *2 Cs    u0 {1,S} {3,S}
+3 *3 Cs    u0 {2,S} {4,S}
+4 *4 Cl1s  u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 4,
+    label = "BrBr",
+    group =
+"""
+1 *1 Br1s  u0 {2,S}
+2 *2 Cs    u0 {1,S} {3,S}
+3 *3 Cs    u0 {2,S} {4,S}
+4 *4 Br1s  u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 5,
+    label = "FCl",
+    group =
+"""
+1 *1 F1s  u0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S}
+3 *3 Cs   u0 {2,S} {4,S}
+4 *4 Cl1s u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 6,
+    label = "FBr",
+    group =
+"""
+1 *1 F1s   u0 {2,S}
+2 *2 Cs  u0 {1,S} {3,S}
+3 *3 Cs  u0 {2,S} {4,S}
+4 *4 Br1s  u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 7,
+    label = "ClBr",
+    group =
+"""
+1 *1 Cl1s  u0 {2,S}
+2 *2 Cs    u0 {1,S} {3,S}
+3 *3 Cs    u0 {2,S} {4,S}
+4 *4 Br1s  u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 8,
+    label = "OY",
+    group =
+"""
+1 *1 O2s    u0 {2,S}
+2 *2 Cs     u0 {1,S} {3,S}
+3 *3 Cs     u0 {2,S} {4,S}
+4 *4 Val7   u0 {3,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 9,
+    label = "OF",
+    group =
+"""
+1 *1 O2s  u0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S}
+3 *3 Cs   u0 {2,S} {4,S}
+4 *4 F1s  u0 {3,S}
+""",
+    kinetics = None,
+)
+
+
+entry(
+    index = 10,
+    label = "OCl",
+    group =
+"""
+1 *1 O2s  u0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S}
+3 *3 Cs   u0 {2,S} {4,S}
+4 *4 Cl1s u0 {3,S}
+""",
+    kinetics = None,
+)
+
+
+entry(
+    index = 11,
+    label = "OBr",
+    group =
+"""
+1 *1 O2s  u0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S}
+3 *3 Cs   u0 {2,S} {4,S}
+4 *4 Br1s u0 {3,S}
+""",
+    kinetics = None,
+)
+
+
+tree(
+"""
+L1: XY
+    L2: YY
+        L3: FF
+        L3: ClCl
+        L3: BrBr
+        L3: FCl
+        L3: FBr
+        L3: ClBr
+    L2: OY
+        L3: OF
+        L3: OBr
+        L3: OCl
+"""
+)