Merge pull request #105 from ReactionMechanismGenerator/fixTrees

Fix trees
ReactionMechanismGenerator · Jun 15, 2016 · 6ba1c55 · 6ba1c55
2 parents 6213eb4 + 253b662
commit 6ba1c55
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Showing 15 changed files with 4,566 additions and 4,296 deletions.
diff --git a/input/kinetics/families/Cyclic_Ether_Formation/groups.py b/input/kinetics/families/Cyclic_Ether_Formation/groups.py
@@ -1245,26 +1245,26 @@
         L3: R3OOJ
         L3: R3OOH
             L4: R3OOH_SS
-            L4: R3OOH_SSCO
+                L5: R3OOH_SSCO
             L4: R3OOH_SD
             L4: R3OOH_DS
         L3: R3OOR
             L4: R3OOR_SS
-            L4: R3OOR_SSCO
+                L5: R3OOR_SSCO
             L4: R3OOR_SD
             L4: R3OOR_DS
     L2: R4OO
         L3: R4OOJ
         L3: R4OOH
             L4: R4OOH_SSS
-            L4: R4OOH_SSSCO
+                L5: R4OOH_SSSCO
             L4: R4OOH_SSD
             L4: R4OOH_SDS
             L4: R4OOH_DSS
             L4: R4OOH_DSD
         L3: R4OOR
             L4: R4OOR_SSS
-            L4: R4OOR_SSSCO
+                L5: R4OOR_SSSCO
             L4: R4OOR_SSD
             L4: R4OOR_SDS
             L4: R4OOR_DSS
@@ -1273,7 +1273,7 @@
         L3: R5OOJ
         L3: R5OOH
             L4: R5OOH_SSSS
-            L4: R5OOH_SSSSCO
+                L5: R5OOH_SSSSCO
             L4: R5OOH_SSSD
             L4: R5OOH_SSDS
             L4: R5OOH_SDSS
@@ -1282,7 +1282,7 @@
             L4: R5OOH_DSDS
         L3: R5OOR
             L4: R5OOR_SSSS
-            L4: R5OOR_SSSSCO
+                L5: R5OOR_SSSSCO
             L4: R5OOR_SSSD
             L4: R5OOR_SSDS
             L4: R5OOR_SDSS

diff --git a/input/kinetics/families/Disproportionation/groups.py b/input/kinetics/families/Disproportionation/groups.py
@@ -2720,13 +2720,12 @@
     L2: Y_2centerbirad
         L3: O2b
         L3: C2b
-		L3: S2b
+        L3: S2b
     L2: Y_1centerbirad
         L3: CO_birad_triplet
         L3: O_atom_triplet
         L3: CH2_triplet
         L3: NH_triplet
-    L2: H_rad
     L2: Y_rad
         L3: Ct_rad
             L4: Ct_rad/Ct
@@ -2811,6 +2810,7 @@
                 L5: N3d_rad/N
         L3: N5_rad
             L4: N5d_rad
+        L3: H_rad
 L1: XH_Rrad_birad
     L2: XH_Rrad
         L3: XH_s_Rrad
@@ -2852,7 +2852,7 @@
                     L6: C/H2/Nd_COrad
                     L6: C/H2/Nd_Orad
                     L6: C/H2/Nd_Nrad
-		            L6: C/H2/Nd_Srad
+                    L6: C/H2/Nd_Srad
                 L5: C/H2/De_Rrad
                     L6: C/H2/De_Csrad
                         L7: C/H2/De_Csrad/H/Cd

diff --git a/input/kinetics/families/H_Abstraction/groups.py b/input/kinetics/families/H_Abstraction/groups.py
@@ -533,10 +533,10 @@
     label = "Cd/H/OneDe",
     group = 
 """
-1 *1 C                  u0 {2,D} {3,S} {4,S}
-2    Cd                  u0 {1,D} {5,S}
-3 *2 H                  u0 {1,S}
-4    [Cd,Ct,Cb,CO,CS,N] u0 {1,S}
+1 *1 C                                             u0 {2,D} {3,S} {4,S}
+2    Cd                                            u0 {1,D} {5,S}
+3 *2 H                                             u0 {1,S}
+4    [Cd,Ct,Cb,CO,CS,N3d,N3t,N3b,N5d,N5dd,N5t,N5b] u0 {1,S}
 5 R u0 {2,S}
 """,
     kinetics = None,
@@ -6678,8 +6678,8 @@
                             L8: O_rad/Cd\Cs_Cd\H2
                             L8: O_rad/Cd\Cs_Cd\H\Cs
                             L8: O_rad/Cd\Cs_Cd\Cs2
-                    L6: InChI=1S/NO3/c2-1(3)4
                     L6: O_rad/OneDeN
+                        L7: InChI=1S/NO3/c2-1(3)4
         L3: S_rad
             L4: S_pri_rad
             L4: S_sec_rad

diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py
@@ -1079,32 +1079,34 @@
     group = 
 """
 1 *1 Cs u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
 )
 
 entry(
     index = 182,
-    label = "radadd_intra_csHNd",
+    label = "radadd_intra_csHHNd",
     group = 
 """
-1 *1 Cs     u0 {2,S} {3,S}
-2 *2 H      u0 {1,S}
+1 *1 Cs     u0 {2,S} {3,S} {4,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
+4    H      u0 {1,S}
 """,
     kinetics = None,
 )
 
 entry(
     index = 183,
-    label = "radadd_intra_csHDe",
+    label = "radadd_intra_csHHDe",
     group = 
 """
-1 *1 Cs            u0 {2,S} {3,S}
-2 *2 H             u0 {1,S}
+1 *1 Cs            u0 {2,S} {3,S} {4,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
+4    H             u0 {1,S}
 """,
     kinetics = None,
 )
@@ -1115,7 +1117,7 @@
     group = 
 """
 1 *1 Cs     u0 {2,S} {3,S} {4,S}
-2 *2 H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 4    [Cs,O] u0 {1,S}
 """,
@@ -1128,7 +1130,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cs,O]        u0 {1,S}
 4    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
@@ -1141,7 +1143,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 4    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
@@ -1174,7 +1176,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    R  u0 {1,S}
 """,
     kinetics = None,
@@ -1186,7 +1188,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
@@ -1198,7 +1200,7 @@
     group = 
 """
 1 *1 Cd     u0 {2,S} {3,S}
-2 *2 H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 """,
     kinetics = None,
@@ -1210,7 +1212,7 @@
     group = 
 """
 1 *1 Cd            u0 {2,S} {3,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
     kinetics = None,
@@ -1222,7 +1224,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,D}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    Cd u0 {1,D}
 """,
     kinetics = None,
@@ -1234,7 +1236,7 @@
     group = 
 """
 1 *1 CO u0 {2,S} {3,D}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    O  u0 {1,D}
 """,
     kinetics = None,
@@ -1246,7 +1248,7 @@
     group = 
 """
 1 *1 Ct u0 {2,S} {3,T}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    Ct u0 {1,T}
 """,
     kinetics = None,
@@ -1324,8 +1326,8 @@
 L1: radadd_intra
     L2: radadd_intra_cs
         L3: radadd_intra_cs2H
-        L3: radadd_intra_csHNd
-        L3: radadd_intra_csHDe
+            L4: radadd_intra_csHHNd
+            L4: radadd_intra_csHHDe
         L3: radadd_intra_csNdNd
         L3: radadd_intra_csNdDe
         L3: radadd_intra_csDeDe

diff --git a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py
@@ -2548,32 +2548,34 @@
     group = 
 """
 1 *1 Cs u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
 )
 
 entry(
     index = 182,
-    label = "radadd_intra_csHNd",
+    label = "radadd_intra_csHHNd",
     group = 
 """
-1 *1 Cs     u0 {2,S} {3,S}
-2 *2 H      u0 {1,S}
+1 *1 Cs     u0 {2,S} {3,S} {4,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
+4    H      u0 {1,S}
 """,
     kinetics = None,
 )
 
 entry(
     index = 183,
-    label = "radadd_intra_csHDe",
+    label = "radadd_intra_csHHDe",
     group = 
 """
-1 *1 Cs            u0 {2,S} {3,S}
-2 *2 H             u0 {1,S}
+1 *1 Cs            u0 {2,S} {3,S} {4,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
+4    H             u0 {1,S}
 """,
     kinetics = None,
 )
@@ -2584,7 +2586,7 @@
     group = 
 """
 1 *1 Cs     u0 {2,S} {3,S} {4,S}
-2 *2 H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 4    [Cs,O] u0 {1,S}
 """,
@@ -2597,7 +2599,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cs,O]        u0 {1,S}
 4    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
@@ -2610,7 +2612,7 @@
     group = 
 """
 1 *1 Cs            u0 {2,S} {3,S} {4,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 4    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
@@ -2643,7 +2645,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    R  u0 {1,S}
 """,
     kinetics = None,
@@ -2655,7 +2657,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,S}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    H  u0 {1,S}
 """,
     kinetics = None,
@@ -2667,7 +2669,7 @@
     group = 
 """
 1 *1 Cd     u0 {2,S} {3,S}
-2 *2 H      u0 {1,S}
+2 *4 H      u0 {1,S}
 3    [Cs,O] u0 {1,S}
 """,
     kinetics = None,
@@ -2679,7 +2681,7 @@
     group = 
 """
 1 *1 Cd            u0 {2,S} {3,S}
-2 *2 H             u0 {1,S}
+2 *4 H             u0 {1,S}
 3    [Cd,Ct,Cb,CO] u0 {1,S}
 """,
     kinetics = None,
@@ -2691,7 +2693,7 @@
     group = 
 """
 1 *1 Cd u0 {2,S} {3,D}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    Cd u0 {1,D}
 """,
     kinetics = None,
@@ -2703,7 +2705,7 @@
     group = 
 """
 1 *1 CO u0 {2,S} {3,D}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    O  u0 {1,D}
 """,
     kinetics = None,
@@ -2715,7 +2717,7 @@
     group = 
 """
 1 *1 Ct u0 {2,S} {3,T}
-2 *2 H  u0 {1,S}
+2 *4 H  u0 {1,S}
 3    Ct u0 {1,T}
 """,
     kinetics = None,
@@ -2886,8 +2888,8 @@
 L1: radadd_intra
     L2: radadd_intra_cs
         L3: radadd_intra_cs2H
-        L3: radadd_intra_csHNd
-        L3: radadd_intra_csHDe
+            L4: radadd_intra_csHHNd
+            L4: radadd_intra_csHHDe
         L3: radadd_intra_csNdNd
         L3: radadd_intra_csNdDe
         L3: radadd_intra_csDeDe