Adding in many new surface families

input/kinetics/families/Surface_Abstraction/groups.py

@@ -18,6 +18,9 @@
 
 template(reactants=["Abstracting", "Donating"], products=["Abstracting", "Donating"], ownReverse=True)
 
+reactantNum=2
+productNum=2
+
 recipe(actions=[
     ['FORM_BOND', '*1', 1, '*4'],
     ['BREAK_BOND', '*3', 1, '*4'],

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

@@ -16,12 +16,10 @@ CH3X_4
 4    H u0 p0 {1,S}
 5 *2 X u0 p0 {1,S}
 
-
 OX_5
 1 *5 X u0 p0 c0 {2,D}
 2 *3 O u0 p2 c0 {1,D}
 
-
 CHX_1
 1 *1 C u0 p0 {2,S} {3,T}
 2    H u0 p0 {1,S}
@@ -33,7 +31,6 @@ CH2X_4
 3    H u0 p0 {1,S}
 4 *2 X u0 p0 {1,D}
 
-
 CX_1
 1 *1 C u0 p0 {2,Q}
 2 *2 X u0 p0 {1,Q}
@@ -43,3 +40,22 @@ CHX_4
 2 *4 H u0 p0 {1,S}
 3 *2 X u0 p0 {1,T}
 
+O*
+1 *2 X u0 p0 c0 {2,D}
+2 *1 O u0 p2 c0 {1,D}
+
+HCO*
+1    O u0 p2 c0 {2,D}
+2 *3 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 *4 H u0 p0 c0 {2,S}
+4 *5 X u0 p0 c0 {2,S}
+
+OH*
+1 *1 O u0 p2 c0 {2,S} {3,S}
+2 *4 H u0 p0 c0 {1,S}
+3 *2 X u0 p0 c0 {1,S}
+
+CO*
+1    O u0 p2 c0 {2,D}
+2 *3 C u0 p0 c0 {1,D} {3,D}
+3 *5 X u0 p0 c0 {2,D}

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

@@ -19,7 +19,7 @@
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
-    #rank = 3,
+    rank = 3,
     shortDesc = u"""Deutschmann Ni""",
     longDesc = u"""
 "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts"
@@ -39,7 +39,7 @@
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
-    #rank = 3,
+    rank = 3,
     shortDesc = u"""Default""",
     longDesc = u"""
 "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts"
@@ -80,7 +80,7 @@
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
-    #rank = 3,
+    rank = 3,
     shortDesc = u"""Default""",
     longDesc = u"""
 "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts"
@@ -89,3 +89,21 @@
 """
 )
 
+entry(
+    index = 39,
+    label = "O* + HCO* <=> OH* + CO*",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A=(1.0e13, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea=(0., 'kcal/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 1,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 39 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+"""
+)

input/kinetics/families/Surface_Abstraction_vdW/groups.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_vdW/groups"
+shortDesc = u""
+longDesc = u"""
+A vdW species splitting, adsorbing to the surface, and transferring a functional group to a double, triple, or
+quadruple bonded surface species.
+
+ *2-*3  *4             *2     *4-*3
+  :     ||     ---->    |      |
+~*1~ + ~*5~~          ~*1~ + ~*5~~
+
+The rate, which should be in mol/m2/s,
+will be given by k * (mol/m2) * (mol/m2)
+so k should be in (m2/mol/s).
+
+"""
+
+template(reactants=["AdsorbateVdW","Adsorbate1"], products=["Adsorbate2","Adsorbate3"], ownReverse=False)
+
+reverse = "Surface_Reverse_Abstraction_vdW"  # maybe needs a better name?
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['BREAK_BOND', '*2', 1, '*3'],
+    ['FORM_BOND', '*1', 1, '*2'],
+    ['CHANGE_BOND', '*4', -1, '*5'],
+    ['FORM_BOND', '*3', 1, '*4'],
+])
+
+entry(
+    index = 1,
+    label = "AdsorbateVdW",
+    group =
+"""
+1 *1 Xv ux px cx
+2 *2 R  ux px cx {3,S}
+3 *3 R  ux px cx {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "Adsorbate1",
+    group =
+"""
+1 *5 X   ux px cx {2,[D,T,Q]}
+2 *4 R!H ux px cx {1,[D,T,Q]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 3,
+    label = "O-R",
+    group =
+"""
+1 *1 Xv u0 p0 c0
+2 *2 O  ux p2 cx {3,S}
+3 *3 R  ux px cx {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 4,
+    label = "C-R",
+    group =
+"""
+1 *1 Xv u0 p0 c0
+2 *2 C  ux px cx {3,S}
+3 *3 R  ux px cx {2,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 5,
+    label = "O=*",
+    group =
+"""
+1 *5 X u0 p0 c0 {2,D}
+2 *4 O u0 p2 c0 {1,D}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 6,
+    label = "C=*",
+    group =
+"""
+1 *5 X u0 p0 c0 {2,[D,T,Q]}
+2 *4 C ux px cx {1,[D,T,Q]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 7,
+    label = "H-H",
+    group =
+"""
+1 *1 Xv u0 p0 c0
+2 *2 H  u0 p0 c0 {3,S}
+3 *3 R  ux px cx {2,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: AdsorbateVdW
+    L2: H-H
+    L2: O-R
+    L2: C-R
+L1: Adsorbate1
+    L2: O=*
+    L2: C=*
+"""
+)

input/kinetics/families/Surface_Abstraction_vdW/rules.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_vdW/rules"
+shortDesc = u""
+longDesc = u"""
+A vdW double bonded species dissociatively adsorbing to the surface with double
+bonds.
+"""
+
+entry(
+    index = 1,
+    label = "AdsorbateVdW;Adsorbate1",
+    kinetics = SurfaceArrheniusBEP(
+        A = (1.0e13, 'm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.5,
+        E0 = (0, 'kcal/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""Made up"""
+)
+
+# entry(
+#     index = 2,
+#     label = "O-H;O=*",
+#     kinetics = SurfaceArrheniusBEP(
+#         A = (1e13, 'm^2/(mol*s)'),
+#         n = 0,
+#         alpha = 0.65,
+#         E0 = (2.3060548, 'kcal/mol'),
+#         Tmin = (200, 'K'),
+#         Tmax = (3000, 'K'),
+#     ),
+#     rank = 1,
+#     shortDesc = u"""Default""",
+#     longDesc = u"""
+# Reaction 17 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+# and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+#
+# E0 is Ea_fwd - deltaE and A is made up
+# """
+# )