Using Val5, and opening RMG-Py #2929

Author: kirkbadger18

input/kinetics/families/Surface_Abstraction_Charge_Separation/groups.py

@@ -11,7 +11,7 @@
 
  *1   *4[-]-*3[+]          *1=*4  *3
  |||          |      ---->  |      |
-~*2~~ +    ~*5~~          ~*2~ + ~*5~~
+~*2~~ +     ~*5~~         ~*2~ + ~*5~~
 
 The rate, which should be in mol/m2/s,
 will be given by k * (mol/m2) * (mol/m2)
@@ -31,8 +31,8 @@
     ['CHANGE_BOND', '*1', -1, '*2'],
     ['LOSE_PAIR','*4','1'],
     ['GAIN_PAIR', '*3', '1'],
- #   ['LOSE_CHARGE','*3','1'],
- #   ['GAIN_CHARGE', '*4', '1'],
+    ['LOSE_CHARGE','*3','1'],
+    ['GAIN_CHARGE', '*4', '1'],
 ])
 
 entry(
@@ -52,7 +52,7 @@
     group =
 """
 1 *4 R!H u0 p[1,2,3] c-1 {2,S}
-2 *3 N u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
 3 *5 Xo u0 p0 c0 {2,[S,D]}
 4 R u0 px c0 {2,[S,D]}
 """,
@@ -72,7 +72,7 @@
     group =
 """
 1 *4 R!H u0 p[1,2,3] c-1 {2,S} {5,[S,D,T]}
-2 *3 N u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
 3 *5 Xo u0 p0 c0 {2,[S,D]}
 4 R u0 px c0 {2,[S,D]}
 5 Xo u0 c0 {1,[S,D,T]}

input/kinetics/families/Surface_Abstraction_Charge_Single/groups.py

@@ -31,6 +31,8 @@
     ['CHANGE_BOND', '*3', -1, '*5'],
     ['LOSE_PAIR','*6','1'],
     ['GAIN_PAIR', '*3', '1'],
+    ['LOSE_CHARGE','*3','1'],
+    ['GAIN_CHARGE', '*6', '1'],
 ])
 
 entry(
@@ -50,7 +52,7 @@
     group =
 """
 1 *4 R u0 px c0 {2,S}
-2 *3 N u0 p0 c+1 {1,S} {3,D} {4,S}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,D} {4,S}
 3 *5 Xo u0 p0 c0 {2,D}
 4 *6 R!H u0 p[1,2,3] c-1 {2,S}
 """,
@@ -69,7 +71,7 @@
     group =
 """
 1 *4 R u0 px c0 {2,S} {5,[S,D,T]}
-2 *3 N u0 p0 c+1 {1,S} {3,D} {4,S}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,D} {4,S}
 3 *5 Xo u0 p0 c0 {2,D}
 4 *6 R!H u0 p[1,2,3] c-1 {2,S}
 5 Xo u0 c0 {1,[S,D,T]}

input/kinetics/families/Surface_Dissociation_Charge_Separation/groups.py

@@ -40,7 +40,7 @@
     label = "Combined",
     group =
 """
-1 *1 R!H u0 p0 c+1 {2,S} {3,[S,D]}
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
 2 *2 R!H u0 p[1,2,3] c-1 {1,S}
 3 *3 Xo u0 p0 c0 {1,[S,D]}
 """,
@@ -68,7 +68,7 @@
     label = "Surf",
     group =
 """
-1 *1 R!H u0 p0 c+1 {2,S} {3,[S,D]}
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
 2 *2 R!H u0 p[1,2,3] c-1 {1,S} {4,[S,D,T]}
 3 *3 Xo u0 p0 c0 {1,[S,D]}
 4 Xo u0 c0 {2,[S,D,T]}

input/kinetics/families/Surface_Dissociation_Charge_Single/groups.py

@@ -41,7 +41,7 @@
     label = "Combined",
     group =
 """
-1 *1 N u0 p0 c+1 {2,S} {3,D} {4,S}
+1 *1 Val5 u0 p0 c+1 {2,S} {3,D} {4,S}
 2 *2 R u0 px c0 {1,S}
 3 *3 Xo u0 p0 c0 {1,D}
 4 *4 R!H u0 p[1,2,3] c-1 {1,S}
@@ -70,7 +70,7 @@
     label = "Surf",
     group =
 """
-1 *1 N u0 p0 c+1 {2,S} {3,D} {4,S}
+1 *1 Val5 u0 p0 c+1 {2,S} {3,D} {4,S}
 2 *2 R u0 px c0 {1,S} {5,[S,D,T]}
 3 *3 Xo u0 p0 c0 {1,D}
 4 *4 R!H u0 px c-1 {1,S}