June 2019 Training reaction fixing hackathon

input/kinetics/families/1+2_Cycloaddition/training/reactions.py

@@ -149,18 +149,19 @@
     label = "CH2 + C2H2 <=> C3H4",
     degeneracy = 1.0,
     kinetics = Arrhenius(
-        A = (1.77e+15, 'cm^3/(mol*s)'),
+        A = (1.06e+15, 'cm^3/(mol*s)'),
         n = -0.662,
         Ea = (0.157737, 'kJ/mol'),
         T0 = (1, 'K'),
         Tmin = (200, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank = 5,
-    shortDesc = u"""Polino [carbene,acetylene]""",
+    shortDesc = u"""Polino et al. J. Phys. Chem. A 2013, 117, 12677−12692.""",
     longDesc = 
 u"""
-Converted to training reaction from rate rule: carbene;mb_tb_unsub
+Daniela Polino, Stephen J. Klippenstein, Lawrence B. Harding, and Yuri Georgievskii,Predictive Theory for the Addition and Insertion Kinetics of 1CH2
+Reacting with Unsaturated Hydrocarbons, J. Phys. Chem. A 2013, 117, 12677−12692.
 """,
 )
 

input/kinetics/families/Disproportionation/training/dictionary.txt

@@ -80,6 +80,13 @@ multiplicity 2
 3    H u0 p0 c0 {1,S}
 4 *4 H u0 p0 c0 {1,S}
 
+CH3_r1
+multiplicity 2
+1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
+
 H
 multiplicity 2
 1 *1 H u1 p0 c0

input/kinetics/families/Disproportionation/training/reactions.py

@@ -159,7 +159,7 @@
 
 entry(
     index = 5,
-    label = "CH3 + C2H5 <=> CH4 + C2H4",
+    label = "CH3_r1 + C2H5 <=> CH4 + C2H4",
     degeneracy = 3.0,
     kinetics = Arrhenius(
         A = (6.57e+14, 'cm^3/(mol*s)', '*|/', 1.1),
@@ -636,7 +636,7 @@
 
 entry(
     index = 20,
-    label = "CH3 + C3H7-2 <=> CH4 + C3H6-2",
+    label = "CH3_r1 + C3H7-2 <=> CH4 + C3H6-2",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (2.3e+13, 'cm^3/(mol*s)', '*|/', 1.7),
@@ -1151,7 +1151,7 @@
 
 entry(
     index = 37,
-    label = "CH3 + C4H9-2 <=> CH4 + C4H8-2",
+    label = "CH3_r1 + C4H9-2 <=> CH4 + C4H8-2",
     degeneracy = 1.0,
     kinetics = Arrhenius(
         A = (6.02e+12, 'cm^3/(mol*s)', '*|/', 2),
@@ -1457,7 +1457,7 @@
 
 entry(
     index = 46,
-    label = "CH3 + C3H5-2 <=> CH4 + C3H4",
+    label = "CH3_r1 + C3H5-2 <=> CH4 + C3H4",
     degeneracy = 1.0,
     kinetics = Arrhenius(
         A = (3.01e+12, 'cm^3/(mol*s)', '*|/', 3),
@@ -1814,7 +1814,7 @@
 
 entry(
     index = 57,
-    label = "CH3O + CH3 <=> CH4 + CH2O",
+    label = "CH3O + CH3_r1 <=> CH4 + CH2O",
     degeneracy = 1.0,
     kinetics = Arrhenius(
         A = (8.49e+13, 'cm^3/(mol*s)'),
@@ -2606,7 +2606,7 @@
 
 entry(
     index = 88,
-    label = "H2N2 + CH3 <=> CH4 + HN2",
+    label = "H2N2 + CH3_r1 <=> CH4 + HN2",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (3.2e+06, 'cm^3/(mol*s)'),
@@ -2738,7 +2738,7 @@
 
 entry(
     index = 94,
-    label = "H3N2 + CH3 <=> CH4 + H2N2-2",
+    label = "H3N2 + CH3_r1 <=> CH4 + H2N2-2",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (1.64e+06, 'cm^3/(mol*s)'),
@@ -2894,7 +2894,7 @@
 
 entry(
     index = 101,
-    label = "H2NO + CH3 <=> CH4 + HNO-2",
+    label = "H2NO + CH3_r1 <=> CH4 + HNO-2",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (3.2e+06, 'cm^3/(mol*s)'),
@@ -3050,7 +3050,7 @@
 
 entry(
     index = 108,
-    label = "H2NO-3 + CH3 <=> CH4 + HNO-3",
+    label = "H2NO-3 + CH3_r1 <=> CH4 + HNO-3",
     degeneracy = 1.0,
     kinetics = Arrhenius(
         A = (1.6e+06, 'cm^3/(mol*s)'),
@@ -3186,7 +3186,7 @@
 
 entry(
     index = 114,
-    label = "CH3 + CH2N <=> CH4 + CHN",
+    label = "CH3_r1 + CH2N <=> CH4 + CHN",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (1.62e+06, 'cm^3/(mol*s)'),
@@ -3362,7 +3362,7 @@
 
 entry(
     index = 122,
-    label = "CH2N-3 + CH3 <=> CH4 + CHN-2",
+    label = "CH2N-3 + CH3_r1 <=> CH4 + CHN-2",
     degeneracy = 1.0,
     kinetics = Arrhenius(
         A = (820000, 'cm^3/(mol*s)'),
@@ -3450,7 +3450,7 @@
 
 entry(
     index = 126,
-    label = "CH4N + CH3 <=> CH4 + CH3N-2",
+    label = "CH4N + CH3_r1 <=> CH4 + CH3N-2",
     degeneracy = 3.0,
     kinetics = Arrhenius(
         A = (7.2e+06, 'cm^3/(mol*s)'),
@@ -3538,7 +3538,7 @@
 
 entry(
     index = 130,
-    label = "CH3 + CH4N-2 <=> CH4 + CH3N-3",
+    label = "CH3_r1 + CH4N-2 <=> CH4 + CH3N-3",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (3.2e+06, 'cm^3/(mol*s)'),
@@ -3607,7 +3607,7 @@
 
 entry(
     index = 133,
-    label = "CH3 + CH2NO <=> CH4 + CHNO",
+    label = "CH3_r1 + CH2NO <=> CH4 + CHNO",
     degeneracy = 2.0,
     kinetics = Arrhenius(
         A = (3.2e+06, 'cm^3/(mol*s)'),

input/kinetics/families/H_Abstraction/groups.py

@@ -21,14 +21,19 @@
 entry(
     index = 0,
     label = "X_H_or_Xrad_H_Xbirad_H_Xtrirad_H",
-    group = "OR{Xtrirad_H, Xbirad_H, Xrad_H, X_H}",
+    group = """
+1 *1 R u[0,1,2,3] {2,S}
+2 *2 H u0 {1,S}
+""",
     kinetics = None,
 )
 
 entry(
     index = 1,
     label = "Y_rad_birad_trirad_quadrad",
-    group = "OR{Y_rad, Y_1centerbirad, Y_1centertrirad, Y_1centerquadrad}",
+    group = """
+1 *3 R u[1,2,3,4]
+""",
     kinetics = None,
 )
 

input/kinetics/families/H_Abstraction/training/dictionary.txt

@@ -251,20 +251,6 @@ CH3N-2
 4    H u0 p0 c0 {2,S}
 5    H u0 p0 c0 {1,S}
 
-CH3_p1
-multiplicity 2
-1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
-2    H u0 p0 c0 {1,S}
-3    H u0 p0 c0 {1,S}
-4    H u0 p0 c0 {1,S}
-
-CH3_r3
-multiplicity 2
-1 *3 C u1 p0 c0 {2,S} {3,S} {4,S}
-2    H u0 p0 c0 {1,S}
-3    H u0 p0 c0 {1,S}
-4    H u0 p0 c0 {1,S}
-
 C5H11
 multiplicity 2
 1     C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
@@ -1164,14 +1150,21 @@ H3NO-2
 4    H u0 p0 c0 {2,S}
 5 *2 H u0 p0 c0 {1,S}
 
-CH4b
+CH4
+1    C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
+5    H u0 p0 c0 {1,S}
+
+CH4_r12
 1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
 2 *2 H u0 p0 c0 {1,S}
 3    H u0 p0 c0 {1,S}
 4    H u0 p0 c0 {1,S}
 5    H u0 p0 c0 {1,S}
 
-CH4p
+CH4_p23
 1 *3 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
 2 *2 H u0 p0 c0 {1,S}
 3    H u0 p0 c0 {1,S}
@@ -1285,13 +1278,6 @@ multiplicity 2
 4 H u0 p0 c0 {1,S}
 5 H u0 p0 c0 {2,S}
 
-CH4
-1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
-2 H u0 p0 c0 {1,S}
-3 H u0 p0 c0 {1,S}
-4 H u0 p0 c0 {1,S}
-5 H u0 p0 c0 {1,S}
-
 C3H7O2
 multiplicity 2
 1     O u0 p2 c0 {2,S} {3,S}
@@ -2075,11 +2061,16 @@ H2S
 2 *2 H u0 p0 c0 {1,S}
 3    H u0 p0 c0 {1,S}
 
-H2O
+H2O_r12
 1 *1 O u0 p2 c0 {2,S} {3,S}
 2 *2 H u0 p0 c0 {1,S}
 3    H u0 p0 c0 {1,S}
 
+H2O_p23
+1 *3 O u0 p2 c0 {2,S} {3,S}
+2 *2 H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+
 C4H10b
 1  *1 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
 2     C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
@@ -2413,6 +2404,14 @@ multiplicity 2
 5    H u0 p0 c0 {3,S}
 6    H u0 p0 c0 {2,S}
 
+H3N2
+multiplicity 2
+1 N u0 p1 c0 {2,S} {4,S} {5,S}
+2 *3 N u1 p1 c0 {1,S} {3,S}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {1,S}
+
 C6H6-2
 1  *1 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
 2     C u0 p0 c0 {1,S} {8,S} {9,S} {10,S}
@@ -2594,6 +2593,27 @@ C4H8-8
 11    H u0 p0 c0 {4,S}
 12    H u0 p0 c0 {4,S}
 
+CH3_r12
+multiplicity 2
+1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4 *2 H u0 p0 c0 {1,S}
+
+CH3_r3
+multiplicity 2
+1 *3 C u1 p0 c0 {2,S} {3,S} {4,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
+
+CH3_p1
+multiplicity 2
+1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
+
 CH3_p23
 multiplicity 2
 1 *3 C u1 p0 c0 {2,S} {3,S} {4,S}
@@ -3243,12 +3263,6 @@ NH3_p23
 3    H u0 p0 c0 {1,S}
 4    H u0 p0 c0 {1,S}
 
-NH3_r
-1 *1 N u0 p1 c0 {2,S} {3,S} {4,S}
-2 *2 H u0 p0 c0 {1,S}
-3    H u0 p0 c0 {1,S}
-4    H u0 p0 c0 {1,S}
-
 N2H2(T)_r3
 multiplicity 3
 1 *3 N u1 p1 c0 {2,S} {3,S}
@@ -3332,13 +3346,6 @@ multiplicity 3
 3    H u0 p0 c0 {1,S}
 4    H u0 p0 c0 {1,S}
 
-H2NN(T)_p1
-multiplicity 3
-1    N u0 p1 c0 {2,S} {3,S} {4,S}
-2 *1 N u2 p1 c0 {1,S}
-3    H u0 p0 c0 {1,S}
-4    H u0 p0 c0 {1,S}
-
 CH3
 multiplicity 2
 1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
@@ -3858,6 +3865,11 @@ multiplicity 2
 1 *3 O u1 p2 c0 {2,S}
 2 *2 H u0 p0 c0 {1,S}
 
+OH_r3
+multiplicity 2
+1 *3 O u1 p2 c0 {2,S}
+2    H u0 p0 c0 {1,S}
+
 SH_p1
 multiplicity 2
 1 *1 S u1 p2 c0 {2,S}
@@ -4000,10 +4012,17 @@ H2N2
 3 *2 H u0 p0 c0 {1,S}
 4    H u0 p0 c0 {2,S}
 
-OH
-multiplicity 2
-1 *3 O u1 p2 c0 {2,S}
-2    H u0 p0 c0 {1,S}
+H2N2-2
+1 *3 N u0 p1 c0 {2,D} {3,S}
+2    N u0 p1 c0 {1,D} {4,S}
+3 *2 H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {2,S}
+
+H2N2-3
+1    N u0 p1 c0 {2,S} {3,S} {4,S}
+2 *1 N u2 p1 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
 
 C2H5OS
 multiplicity 2
@@ -4475,6 +4494,24 @@ C6H12O2-4
 19    H u0 p0 c0 {7,S}
 20    H u0 p0 c0 {7,S}
 
+NH2
+multiplicity 2
+1    N u1 p1 c0 {2,S} {3,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+
+NH3
+1 N u0 p1 c0 {2,S} {3,S} {4,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {1,S}
+
+NH3_r12
+1 *1 N u0 p1 c0 {2,S} {3,S} {4,S}
+2 *2 H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4    H u0 p0 c0 {1,S}
+
 C3H6S
 1     S u0 p2 c0 {4,D}
 2  *1 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S}