Update surface reaction families (Merge PR #628)

Update list of default surface reaction families and restrict Abstraction_Single_vdW.

1. Turn off the reaction families for which we currently only have made up rules or a single training reactions in the recommended.py file by default. The reactions include Surface_EleyRideal_Addition_Multiple_Bond, Surface_Migration, Surface_DoubleBond_to_Bidentate, and Surface_Addition_Single_vdW. We anticipate that the elementary steps discovered by these families will cause problems in the microkinetic models due to the unreasonable rate estimates.

2. Additionally, we restricted the Surface_Abstraction_Single_vdW to not abstract other atoms with an adsorbed H and removed physisorbed H2 from the tree (see discussion #2494)

3. We updated the top level BEP rule of Surface_Abstraction_Single_vdW with the BEP from Surface_Abstraction_Beta_vdW to provide better rate estimates.

input/kinetics/families/Surface_Abstraction_Single_vdW/groups.py

@@ -35,7 +35,7 @@
 """
 multiplicity [1]
 1 *1 Xv u0 p0 c0
-2 *2 R  u0 px cx {3,S}
+2 *2 R!H  u0 px cx {3,S}
 3 *3 R  u0 px cx {2,S}
 """,
     # Note: shuold we restrict it so atoms *2 and *3 have no charge?
@@ -48,21 +48,8 @@
     label = "Abstracting",
     group =
 """
-1 *5 X u0 p0 c0 {2,S}
-2 *4 R ux px cx {1,S}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 3,
-    label = "H-H",
-    group =
-"""
-multiplicity [1]
-1 *1 Xv u0 p0 c0
-2 *2 H  u0 p0 c0 {3,S}
-3 *3 H  u0 p0 c0 {2,S}
+1 *5 X   u0 p0 c0 {2,S}
+2 *4 R!H ux px cx {1,S}
 """,
     kinetics = None,
 )
@@ -588,7 +575,6 @@
 tree(
 """
 L1: Donating
-    L2: H-H
     L2: O-R
         L3: O-H
             L4: H2O

input/kinetics/families/Surface_Abstraction_Single_vdW/rules.py

@@ -12,14 +12,18 @@
     index = 1,
     label = "Donating;Abstracting",
     kinetics = SurfaceArrheniusBEP(
-        A = (1.0e13, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.5,
-        E0 = (0, 'kcal/mol'),
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.94,
+        E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
-    longDesc = u"""Made up"""
+    longDesc = u""" 
+These numbers for the general BEP are from the abstraction reaction of C-H to O.
+BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
+From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
+"""
 )

input/kinetics/families/Surface_Abstraction_vdW/rules.py

@@ -12,14 +12,18 @@
     index = 1,
     label = "AdsorbateVdW;Adsorbate1",
     kinetics = SurfaceArrheniusBEP(
-        A = (1.0e13, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.5,
-        E0 = (0, 'kcal/mol'),
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.94,
+        E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
-    longDesc = u"""Made up"""
+    longDesc = u""" 
+These numbers for the general BEP are from the abstraction reaction of C-H to O.
+BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
+From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
+"""
 )

input/kinetics/families/recommended.py

@@ -109,25 +109,21 @@
     'Surface_Adsorption_Dissociative',
     'Surface_Dissociation',
     'Surface_Abstraction',
-    'Surface_EleyRideal_Addition_Multiple_Bond',
-    'Surface_Migration',
     'Surface_Dissociation_Double_vdW',
-    'Surface_Addition_Single_vdW',
     'Surface_Dissociation_vdW',
     'Surface_Abstraction_vdW',
     'Surface_Dissociation_Beta',
     'Surface_Adsorption_Bidentate',
     'Surface_Bidentate_Dissociation',
-    'Surface_DoubleBond_to_Bidentate', 
     'Surface_Dissociation_to_Bidentate', 
     'Surface_vdW_to_Bidentate',
-    'Surface_Abstraction_Single_vdW',
     'Surface_Adsorption_Dissociative_Double',
     'Surface_Abstraction_Beta',
     'Surface_Abstraction_Beta_double_vdW',
     'Surface_Dissociation_Double',
     'Surface_Dissociation_Beta_vdW',
     'Surface_Abstraction_Beta_vdW',
+    'Surface_Abstraction_Single_vdW',
 }
 
 # reaction families for halogen chemistry only
@@ -147,4 +143,8 @@
 # Surface chemistry families that are under development and not yet working well.
 surface_development = {
     #'Surface_Adsorption_Double',
+    'Surface_EleyRideal_Addition_Multiple_Bond',
+    'Surface_Migration',
+    'Surface_DoubleBond_to_Bidentate',
+    'Surface_Addition_Single_vdW',
 }