Merge pull request #228 from ReactionMechanismGenerator/Non_R_Add_Aro…

…matic_Training Aromatic Training Reactions for Non-R-Addition Families
ReactionMechanismGenerator · May 8, 2018 · 143445f · 143445f
2 parents e6f5af1 + 1a3e5d7
commit 143445f
Show file tree

Hide file tree

Showing 36 changed files with 9,747 additions and 66 deletions.
diff --git a/families/rmg_reaction_families.cdx b/families/rmg_reaction_families.cdx
diff --git a/families/rmg_reaction_families.pdf b/families/rmg_reaction_families.pdf
diff --git a/input/kinetics/families/1,2_shiftC/groups.py b/input/kinetics/families/1,2_shiftC/groups.py
@@ -0,0 +1,384 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "1,2_shiftC/groups"
+shortDesc = u""
+longDesc = u"""
+1,2-methyl shift from a Carbon to another Carbon.
+Could possibly be generalized to include  1,2-methyl shift from an Oxygen to Carbon and vice versa.
+1,2-methyl shift from Sulfur to Carbon has separate family (1,2_shiftS).
+"""
+
+template(reactants=["cCCJ"], products=["cCCJ"], ownReverse=True)
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*1', 1, '*3'],
+    ['GAIN_RADICAL', '*2', '1'],
+    ['LOSE_RADICAL', '*3', '1'],
+])
+
+boundaryAtoms = ["*1", "*3"]
+
+entry(
+    index = 1,
+    label = "cCCJ",
+    group = 
+"""
+1 *1 C   u0 c0 {2,S}
+2 *2 C   u0 {1,S} {3,S}
+3 *3 C   u1 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "CJ",
+    group = 
+"""
+1 *3 C   u1
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 3,
+    label = "cCsCJ",
+    group =
+"""
+1 *1 C  u0 c0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S}
+3 *3 C   u1 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 4,
+    label = "cCs(-HH)CJ",
+    group =
+"""
+1 *1 C  u0 c0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S} {7,S} {8,S}
+3 *3 C   u1 {2,S}
+7    H   u0 {2,S}
+8    H   u0 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 5,
+    label = "cCs(-HR!H)CJ",
+    group =
+"""
+1 *1 C  u0 c0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S} {7,S} {8,S}
+3 *3 C   u1 {2,S}
+7    H   u0 {2,S}
+8    R!H   u0 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 6,
+    label = "cCs(-R!HR!H)CJ",
+    group =
+"""
+1 *1 C  u0 c0 {2,S}
+2 *2 Cs   u0 {1,S} {3,S} {7,S} {8,S}
+3 *3 C   u1 {2,S}
+7    R!H   u0 {2,S}
+8    R!H   u0 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 7,
+    label = "cCdCJ",
+    group =
+"""
+1 *1 C  u0 c0 {2,S}
+2 *2 Cd   u0 {1,S} {3,S}
+3 *3 C   u1 {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 8,
+    label = "CdsJ",
+    group = 
+"""
+1 *3 Cd u1 {2,D}
+2    C  u0 {1,D}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 9,
+    label = "CsJ",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    R  u0 {1,S}
+3    R  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 10,
+    label = "CsJ-HH",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    H  u0 {1,S}
+3    H  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 11,
+    label = "CsJ-CsH",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    Cs u0 {1,S}
+3    H  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 12,
+    label = "CsJ-CsCs",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    Cs u0 {1,S}
+3    Cs u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 13,
+    label = "CsJ-SsH",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    S2s u0 {1,S}
+3    H  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 14,
+    label = "CsJ-SsSs",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    S2s u0 {1,S}
+3    S2s u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 15,
+    label = "CsJ-CsSs",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    Cs u0 {1,S}
+3    S2s u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 16,
+    label = "CsJ-OneDe",
+    group = 
+"""
+1 *3 Cs               u1 {2,S} {3,S}
+2    R                u0 {1,S}
+3    [Cd,Ct,Cb,CO,CS] u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 17,
+    label = "CsJ-OneDeH",
+    group = 
+"""
+1 *3 Cs               u1 {2,S} {3,S}
+2    H                u0 {1,S}
+3    [Cd,Ct,Cb,CO,CS] u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 18,
+    label = "CsJ-CdH",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    H  u0 {1,S}
+3    Cd u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 19,
+    label = "CsJ-OneDeCs",
+    group = 
+"""
+1 *3 Cs            u1 {2,S} {3,S}
+2    Cs            u0 {1,S}
+3    [Cd,Ct,Cb,CO,CS] u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 20,
+    label = "CsJ-CdCs",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    Cs u0 {1,S}
+3    Cd u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 21,
+    label = "CsJ-OneDeSs",
+    group = 
+"""
+1 *3 Cs            u1 {2,S} {3,S}
+2    S2s            u0 {1,S}
+3    [Cd,Ct,Cb,CO] u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 22,
+    label = "CsJ-CdSs",
+    group = 
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    S2s u0 {1,S}
+3    Cd u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 23,
+    label = "CsJ-TwoDe",
+    group =
+"""
+1 *3 Cs               u1 {2,S} {3,S}
+2    [Cd,Ct,Cb,CO,CS] u0 {1,S}
+3    [Cd,Ct,Cb,CO,CS] u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 24,
+    label = "CsJ-CdCd",
+    group =
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    Cd u0 {1,S}
+3    Cd u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 25,
+    label = "CsJ-(CdCdCd)H",
+    group =
+"""
+1 *3 Cs u1 {2,S} {3,S}
+2    H  u0 {1,S}
+3    Cd u0 {1,S} {4,D}
+4    Cd u0 {5,S} {3,D}
+5    Cd u0 {4,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 26,
+    label = "C",
+    group =
+"""
+1 *1 C  u0 c0
+
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 27,
+    label = "CH3",
+    group =
+"""
+1 *1 C  u0 c0 {4,S} {5,S} {6,S}
+4    H   u0 {1,S}
+5    H   u0 {1,S}
+6    H   u0 {1,S}
+""",
+    kinetics = None,
+)
+
+
+tree(
+"""
+L1: cCCJ
+    L2: cCsCJ
+        L3: cCs(-HH)CJ
+        L3: cCs(-HR!H)CJ
+        L3: cCs(-R!HR!H)CJ
+    L2: cCdCJ
+L1: CJ
+    L2: CdsJ
+    L2: CsJ
+        L3: CsJ-HH
+        L3: CsJ-CsH
+        L3: CsJ-CsCs
+        L3: CsJ-SsH
+        L3: CsJ-SsSs
+        L3: CsJ-CsSs
+        L3: CsJ-TwoDe
+            L4: CsJ-CdCd
+        L3: CsJ-OneDe
+            L4: CsJ-OneDeH
+                L5: CsJ-(CdCdCd)H
+                L5: CsJ-CdH
+            L4: CsJ-OneDeCs
+                L5: CsJ-CdCs
+            L4: CsJ-OneDeSs
+                L5: CsJ-CdSs
+L1: C
+    L2: CH3
+"""
+)
+
diff --git a/input/kinetics/families/1,2_shiftC/rules.py b/input/kinetics/families/1,2_shiftC/rules.py
@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "1,2_shiftC/rules"
+shortDesc = u""
+longDesc = u"""
+
+"""
+