RMG-database release v3.2.0

.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

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

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
+""",
+)

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
+"""
+)