intra_OH_migration accessibility

-rearranged groups to pass accessibility tests,
-Switched a few `Cd,Cs` to `Cs,Cd`, which functionally will not change RMG performance, but now passes our unit test, unfortunately our makeSampleAtom is not as robust as we would like
-Remove atom from Cd_rad_out to prevent it from possibly being over-specified
-Remove the Cd atom and change name of Cd_rad_out_C_H, Cd_rad_out_C_ND, Cd_rad_out_C_De to Cd_rad_out_H, Cd_rad_out_ND, and Cd_rad_out_De because they were overspecified
-Replaced Cd_rad_out_C with Cd_rad_out_double because it was overspecified
1b2e040

Author: mjohnson541

input/kinetics/families/intra_OH_migration/groups.py

@@ -56,7 +56,7 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N]     u1 {2,[S,D]}
-2 *4 [Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,S}
+2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,S}
 3 *2 O                 u0 {2,S} {4,S}
 4 *3 O                 u0 {3,S} {5,S}
 5    H                 u0 {4,S}
@@ -70,7 +70,7 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N] u1 {2,S}
-2 *4 [Cd,Cs]       u0 {1,S} {3,S}
+2 *4 [Cs,Cd]       u0 {1,S} {3,S}
 3 *2 O             u0 {2,S} {4,S}
 4 *3 O             u0 {3,S} {5,S}
 5    H             u0 {4,S}
@@ -98,8 +98,8 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N]     u1 {2,[S,D]}
-2 *4 [Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
-3 *5 [Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,S}
+2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
+3 *5 [Cs,Cd,Sid,Sis,N] u0 {2,[S,D]} {4,S}
 4 *2 O                 u0 {3,S} {5,S}
 5 *3 O                 u0 {4,S} {6,S}
 6    H                 u0 {5,S}
@@ -113,8 +113,8 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N] u1 {2,S}
-2 *4 [Cd,Cs]       u0 {1,S} {3,S}
-3 *5 [Cd,Cs]       u0 {2,S} {4,S}
+2 *4 [Cs,Cd]       u0 {1,S} {3,S}
+3 *5 [Cs,Cd]       u0 {2,S} {4,S}
 4 *2 O             u0 {3,S} {5,S}
 5 *3 O             u0 {4,S} {6,S}
 6    H             u0 {5,S}
@@ -144,7 +144,7 @@
 """
 1 *1 [C,Sid,Sis,N] u1 {2,D}
 2 *4 Cd            u0 {1,D} {3,S}
-3 *5 [Cd,Cs]       u0 {2,S} {4,S}
+3 *5 [Cs,Cd]       u0 {2,S} {4,S}
 4 *2 O             u0 {3,S} {5,S}
 5 *3 O             u0 {4,S} {6,S}
 6    H             u0 {5,S}
@@ -158,9 +158,9 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N]     u1 {2,[S,D]}
-2 *4 [Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
-3 *6 [Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]}
-4 *5 [Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,S}
+2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
+3 *6 [Cs,Cd,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]}
+4 *5 [Cs,Cd,Sid,Sis,N] u0 {3,[S,D]} {5,S}
 5 *2 O                 u0 {4,S} {6,S}
 6 *3 O                 u0 {5,S} {7,S}
 7    H                 u0 {6,S}
@@ -174,9 +174,9 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N] u1 {2,S}
-2 *4 [Cd,Cs]       u0 {1,S} {3,S}
-3 *6 [Cd,Cs]       u0 {2,S} {4,S}
-4 *5 [Cd,Cs]       u0 {3,S} {5,S}
+2 *4 [Cs,Cd]       u0 {1,S} {3,S}
+3 *6 [Cs,Cd]       u0 {2,S} {4,S}
+4 *5 [Cs,Cd]       u0 {3,S} {5,S}
 5 *2 O             u0 {4,S} {6,S}
 6 *3 O             u0 {5,S} {7,S}
 7    H             u0 {6,S}
@@ -190,7 +190,7 @@
     group = 
 """
 1 *1 [C,Sid,Sis,N] u1 {2,S}
-2 *4 [Cd,Cs]       u0 {1,S} {3,S}
+2 *4 [Cs,Cd]       u0 {1,S} {3,S}
 3 *6 Cd            u0 {2,S} {4,D}
 4 *5 Cd            u0 {3,D} {5,S}
 5 *2 O             u0 {4,S} {6,S}
@@ -208,7 +208,7 @@
 1 *1 [C,Sid,Sis,N] u1 {2,S}
 2 *4 Cd            u0 {1,S} {3,D}
 3 *6 Cd            u0 {2,D} {4,S}
-4 *5 [Cd,Cs]       u0 {3,S} {5,S}
+4 *5 [Cs,Cd]       u0 {3,S} {5,S}
 5 *2 O             u0 {4,S} {6,S}
 6 *3 O             u0 {5,S} {7,S}
 7    H             u0 {6,S}
@@ -223,8 +223,8 @@
 """
 1 *1 [C,Sid,Sis,N] u1 {2,D}
 2 *4 Cd            u0 {1,D} {3,S}
-3 *6 [Cd,Cs]       u0 {2,S} {4,S}
-4 *5 [Cd,Cs]       u0 {3,S} {5,S}
+3 *6 [Cs,Cd]       u0 {2,S} {4,S}
+4 *5 [Cs,Cd]       u0 {3,S} {5,S}
 5 *2 O             u0 {4,S} {6,S}
 6 *3 O             u0 {5,S} {7,S}
 7    H             u0 {6,S}
@@ -250,29 +250,28 @@
 
 entry(
     index = 17,
-    label = "Cd_rad_out",
+    label = "Cd_rad_out_double",
     group = 
 """
-1 *1 Cd u1 {2,D}
-2    Cd u0 {1,D}
+1 *1 [Cd,Cdd] u1 {2,D}
+2    Cd       u0 {1,D}
 """,
     kinetics = None,
 )
 
 entry(
     index = 18,
-    label = "Cdsingle_rad_out",
+    label = "Cd_rad_out",
     group = 
 """
-1 *1 Cd u1 {2,S}
-2    R  u0 {1,S}
+1 *1 [Cd,Cdd] u1
 """,
     kinetics = None,
 )
 
 entry(
     index = 19,
-    label = "CdsingleH_rad_out",
+    label = "Cd_rad_out_H",
     group = 
 """
 1 *1 Cd u1 {2,S}
@@ -283,7 +282,7 @@
 
 entry(
     index = 20,
-    label = "CdsingleND_rad_out",
+    label = "Cd_rad_out_ND",
     group = 
 """
 1 *1 Cd     u1 {2,S}
@@ -294,7 +293,7 @@
 
 entry(
     index = 21,
-    label = "CdsingleDe_rad_out",
+    label = "Cd_rad_out_De",
     group = 
 """
 1 *1 Cd            u1 {2,S}
@@ -490,16 +489,11 @@
         L3: R4OOH_DSD
 L1: Y_rad_out
     L2: Cd_rad_out
-    L2: Cdsingle_rad_out
-        L3: CdsingleH_rad_out
-        L3: CdsingleND_rad_out
-        L3: CdsingleDe_rad_out
+        L3: Cd_rad_out_double
+        L3: Cd_rad_out_H
+        L3: Cd_rad_out_ND
+        L3: Cd_rad_out_De
     L2: C_rad_out_single
-        L3: C_rad_out_2H
-        L3: C_rad_out_1H
-            L4: C_rad_out_H/NonDeC
-            L4: C_rad_out_H/NonDeO
-            L4: C_rad_out_H/OneDe
         L3: C_rad_out_noH
             L4: C_rad_out_NonDe
                 L5: C_rad_out_Cs2
@@ -508,6 +502,11 @@
                 L5: C_rad_out_OneDe/Cs
                 L5: C_rad_out_OneDe/O
             L4: C_rad_out_TwoDe
+        L3: C_rad_out_1H
+            L4: C_rad_out_H/NonDeC
+            L4: C_rad_out_H/NonDeO
+            L4: C_rad_out_H/OneDe
+        L3: C_rad_out_2H
 """
 )