Merge pull request #169 from ReactionMechanismGenerator/bimolAccessibility

Bimol accessibility

Author: KEHANG

input/kinetics/families/1,2_Insertion_CO/groups.py

@@ -7,7 +7,7 @@
 Reaction site *1 should always be a singlet in this family.
 """
 
-template(reactants=["CO_birad", "RR'"], products=["R_CO_R'"], ownReverse=False)
+template(reactants=["CO", "RR'"], products=["R_CO_R'"], ownReverse=False)
 
 reverse = "1,1_Elimination"
 
@@ -22,11 +22,11 @@
 
 entry(
     index = 3,
-    label = "CO_birad",
+    label = "CO",
     group = 
 """
-1 *1 C u0 p1 {2,T}
-2 *4 O u0 p1 {1,T}
+1 *1 C u0 p1 c-1 {2,T}
+2 *4 O u0 p1 c+1 {1,T}
 """,
     kinetics = None,
 )
@@ -764,7 +764,7 @@
 
 tree(
 """
-L1: CO_birad
+L1: CO
 L1: RR'
     L2: R_H
         L3: H2

input/kinetics/families/1,2_Insertion_CO/rules.py

@@ -8,7 +8,7 @@
 """
 entry(
     index = 553,
-    label = "CO_birad;RR'",
+    label = "CO;RR'",
     kinetics = ArrheniusEP(
         A = (100000, 'cm^3/(mol*s)'),
         n = 2,
@@ -28,7 +28,7 @@
 
 entry(
     index = 554,
-    label = "CO_birad;C_methyl_C_methyl",
+    label = "CO;C_methyl_C_methyl",
     kinetics = ArrheniusEP(
         A = (538, 'cm^3/(mol*s)'),
         n = 3.29,
@@ -48,7 +48,7 @@
 
 entry(
     index = 555,
-    label = "CO_birad;H2",
+    label = "CO;H2",
     kinetics = ArrheniusEP(
         A = (2.89e+09, 'cm^3/(mol*s)'),
         n = 1.16,
@@ -68,7 +68,7 @@
 
 entry(
     index = 556,
-    label = "CO_birad;C_methane",
+    label = "CO;C_methane",
     kinetics = ArrheniusEP(
         A = (16400, 'cm^3/(mol*s)'),
         n = 2.86,
@@ -88,7 +88,7 @@
 
 entry(
     index = 557,
-    label = "CO_birad;C_pri/NonDeC",
+    label = "CO;C_pri/NonDeC",
     kinetics = ArrheniusEP(
         A = (91400, 'cm^3/(mol*s)'),
         n = 2.53,
@@ -108,7 +108,7 @@
 
 entry(
     index = 558,
-    label = "CO_birad;C/H2/NonDeC",
+    label = "CO;C/H2/NonDeC",
     kinetics = ArrheniusEP(
         A = (766000, 'cm^3/(mol*s)'),
         n = 2.07,
@@ -128,7 +128,7 @@
 
 entry(
     index = 559,
-    label = "CO_birad;C/H/Cs3",
+    label = "CO;C/H/Cs3",
     kinetics = ArrheniusEP(
         A = (8.89e+07, 'cm^3/(mol*s)'),
         n = 1.51,
@@ -143,7 +143,7 @@
 
 entry(
     index = 560,
-    label = "CO_birad;CsO_H",
+    label = "CO;CsO_H",
     kinetics = ArrheniusEP(
         A = (0.127, 'cm^3/(mol*s)'),
         n = 3.7,

input/kinetics/families/1,3_Insertion_ROR/groups.py

@@ -21,7 +21,7 @@
 entry(
     index = 1,
     label = "doublebond",
-    group = "OR{Cd_Cdd, Cdd_Cd, Cd_Cd, Sd_Cd, N3d_N3d, N3d_Cd}",
+    group = "OR{Cd_Cdd, Cdd_Cd, Cd_Cd, Sd_Cd, N1d_N5dd, N3d_Cd}",
     kinetics = None,
 )
 
@@ -975,7 +975,7 @@
 """
 1 *1 Sd  u0 {2,D}
 2 *2 Cdd u0 {1,D} {3,D}
-3    R   u0 {2,D}
+3    R!H u0 {2,D}
 """,
     kinetics = None,
 )
@@ -1175,12 +1175,12 @@
 
 entry(
     index = 97,
-    label = "N3d_N3d",
+    label = "N1d_N5dd",
     group = 
 """
-1 *1 N3d u0 {2,D}
-2 *2 N3d u0 {1,D} {3,D}
-3    Od  u0 {2,D}
+1 *1 N1d  u0 {2,D}
+2 *2 N5dd u0 {1,D} {3,D}
+3    Od   u0 {2,D}
 """,
     kinetics = None,
 )
@@ -1545,7 +1545,7 @@
                     L6: Sd_Cd/CsOs
                 L5: Sd_Cd/Nd/De
                 L5: Sd_Cd/De2
-    L2: N3d_N3d
+    L2: N1d_N5dd
     L2: N3d_Cd
 L1: R_OR
     L2: H_OR

input/kinetics/families/1,3_Insertion_RSR/groups.py

@@ -943,7 +943,7 @@
 """
 1 *1 Od  u0 {2,D}
 2 *2 Cdd u0 {1,D} {3,D}
-3    R   u0 {2,D}
+3    R!H   u0 {2,D}
 """,
     kinetics = None,
 )
@@ -1144,7 +1144,7 @@
 """
 1 *1 Sd  u0 {2,D}
 2 *2 Cdd u0 {1,D} {3,D}
-3    R   u0 {2,D}
+3    R!H   u0 {2,D}
 """,
     kinetics = None,
 )

input/kinetics/families/1,4_Cyclic_birad_scission/groups.py

@@ -31,11 +31,11 @@
     label = "R5JJ",
     group = 
 """
-1 *1 R u1 {2,[S,D]} {5,S}
-2 *2 R u0 {1,[S,D]} {3,S}
-3 *3 R u0 {2,S} {4,[S,D]}
-4 *4 R u1 {3,[S,D]} {5,S}
-5    R u0 {1,S} {4,S}
+1 *1 R!H u1 {2,[S,D]} {5,S}
+2 *2 R!H u0 {1,[S,D]} {3,S}
+3 *3 R!H u0 {2,S} {4,[S,D]}
+4 *4 R!H u1 {3,[S,D]} {5,S}
+5    R!H u0 {1,S} {4,S}
 """,
     kinetics = None,
 )
@@ -45,12 +45,12 @@
     label = "R6JJ",
     group = 
 """
-1 *1 R u1 {2,[S,D]} {5,S}
-2 *2 R u0 {1,[S,D]} {3,S}
-3 *3 R u0 {2,S} {4,[S,D]}
-4 *4 R u1 {3,[S,D]} {6,S}
-5    R u0 {1,S} {6,S}
-6    R u0 {4,S} {5,S}
+1 *1 R!H u1 {2,[S,D]} {5,S}
+2 *2 R!H u0 {1,[S,D]} {3,S}
+3 *3 R!H u0 {2,S} {4,[S,D]}
+4 *4 R!H u1 {3,[S,D]} {6,S}
+5    R!H u0 {1,S} {6,S}
+6    R!H u0 {4,S} {5,S}
 """,
     kinetics = None,
 )
@@ -60,13 +60,13 @@
     label = "R7JJ",
     group = 
 """
-1 *1 R u1 {2,[S,D]} {5,S}
-2 *2 R u0 {1,[S,D]} {3,S}
-3 *3 R u0 {2,S} {4,[S,D]}
-4 *4 R u1 {3,[S,D]} {7,S}
-5    R u0 {1,S} {6,S}
-6    R u0 {5,S} {7,S}
-7    R u0 {4,S} {6,S}
+1 *1 R!H u1 {2,[S,D]} {5,S}
+2 *2 R!H u0 {1,[S,D]} {3,S}
+3 *3 R!H u0 {2,S} {4,[S,D]}
+4 *4 R!H u1 {3,[S,D]} {7,S}
+5    R!H u0 {1,S} {6,S}
+6    R!H u0 {5,S} {7,S}
+7    R!H u0 {4,S} {6,S}
 """,
     kinetics = None,
 )

input/kinetics/families/1,4_Linear_birad_scission/groups.py

@@ -24,10 +24,10 @@
     label = "RJJ",
     group = 
 """
-1 *1 R u1 {2,[S,D]}
-2 *2 R u0 {1,[S,D]} {3,S}
-3 *3 R u0 {2,S} {4,[S,D]}
-4 *4 R u1 {3,[S,D]}
+1 *1 R!H u1 {2,[S,D]}
+2 *2 R!H u0 {1,[S,D]} {3,S}
+3 *3 R!H u0 {2,S} {4,[S,D]}
+4 *4 R!H u1 {3,[S,D]}
 """,
     kinetics = None,
 )

input/kinetics/families/Disproportionation/groups.py

@@ -1207,26 +1207,6 @@
     kinetics = None,
 )
 
-entry(
-    index = 232,
-    label = "N5_rad",
-    group = 
-"""
-1 *1 [N5d,N5dd,N5t] u1
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 233,
-    label = "N5d_rad",
-    group = 
-"""
-1 *1 N5d u1
-""",
-    kinetics = None,
-)
-
 entry(
     index = 2,
     label = "XH_Rrad",
@@ -2695,13 +2675,13 @@
 
 entry(
     index = 288,
-    label = "Cd_Cdrad",
+    label = "Cds/H/R!H",
     group = 
 """
-1 *2 Cd u0 {2,D} {3,S}
-2 *3 Cd u1 {1,D}
-3 *4 H u0 {1,S}
-
+1 *2 C   u0 {2,D} {3,S} {4,S}
+2 *3 R!H u1 {1,D}
+3 *4 H   u0 {1,S}
+4    R!H u0 {1,S}
 """,
     kinetics = None,
 )
@@ -2809,8 +2789,7 @@
                 L5: N3d_rad/C
                 L5: N3d_rad/O
                 L5: N3d_rad/N
-        L3: N5_rad
-            L4: N5d_rad
+        L3: H_rad
 L1: XH_Rrad_birad
     L2: XH_Rrad
         L3: XH_s_Rrad
@@ -2895,7 +2874,6 @@
                 L5: N5H_s_Rrad
         L3: XH_d_Rrad
             L4: CH_d_Rrad
-                L5: Cd_Cdrad
                 L5: Cds/H2_d_Rrad
                     L6: Cds/H2_d_Crad
                     L6: Cds/H2_d_N3rad
@@ -2905,8 +2883,9 @@
                             L8: Cds/H2_d_N5ddrad/C
                             L8: Cds/H2_d_N5ddrad/O
                             L8: Cds/H2_d_N5ddrad/N
-                L5: Cds/H/NonDe_d_Rrad
-                L5: Cds/H/Deloc_d_Rrad
+                L5: Cds/H/R!H
+                    L6: Cds/H/NonDe_d_Rrad
+                    L6: Cds/H/Deloc_d_Rrad
             L4: NH_d_Rrad
                 L5: N3d/H_d_Rrad
                     L6: N3d/H_d_Crad