Merge pull request #569 from ReactionMechanismGenerator/bidentate_reaction_data

Bidentate reaction data

Author: xiaoruiDong

input/forbiddenStructures.py

@@ -456,3 +456,71 @@
 becuase we do not have good thermo for `Ctc` (C u0 p0 c+1 {1,T}) atomtype
 """,
 )
+
+entry(
+    label = "CO2X2",
+    species =
+"""
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 X u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+We assume that CO2 binds only via physisorption to the surface
+""",
+)
+
+entry(
+    label = "CO2X3",
+    species =
+"""
+1 O u0 p2 c0 {3,S} {6,S}
+2 O u0 p2 c0 {3,S} {5,S}
+3 C u0 p0 c0 {1,S} {2,S} {4,D}
+4 X u0 p0 c0 {3,D}
+5 X u0 p0 c0 {2,S}
+6 X u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+We assume that CO2 binds only via physisorption to the surface
+""",
+)
+
+
+entry(
+    label = "O2X2",
+    species =
+"""
+1 O u0 p2 c0 {2,S} {3,S}
+2 O u0 p2 c0 {1,S} {4,S}
+3 X u0 p0 c0 {1,S}
+4 X u0 p0 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+O2 dissociates upon adsorption
+""",
+)
+
+entry(
+    label = "OCX2",
+    species =
+"""
+1 O u0 p2 c0 {2,S} {3,S}
+2 C u0 p0 c0 {1,S} {4,T}
+3 X u0 p0 c0 {1,S}
+4 X u0 p0 c0 {2,T}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+CO binds in a monodentate configuration
+""",
+)

input/kinetics/families/Surface_Adsorption_Bidentate/rules.py

@@ -10,7 +10,7 @@
     index = 1,
     label = "Adsorbate;VacantSite1;VacantSite2",
     kinetics = StickingCoefficientBEP(
-        A = 0.1,
+        A = 0.2,
         n = 0,
         alpha = 0,
         E0 = (0, 'kcal/mol'),

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

@@ -0,0 +1,51 @@
+X_3
+1 *3 X u0 p0 c0
+
+X_4
+1 *4 X u0 p0 c0
+
+HCCH
+1 *1 C u0 p0 c0 {2,S} {3,T}
+2    H u0 p0 c0 {1,S}
+3 *2 C u0 p0 c0 {1,T} {4,S}
+4    H u0 p0 c0 {3,S}
+
+HCCH_2X
+1 *1 C u0 p0 c0 {2,S} {3,D} {5,S}
+2    H u0 p0 c0 {1,S}
+3 *2 C u0 p0 c0 {1,D} {4,S} {6,S}
+4    H u0 p0 c0 {3,S}
+5 *3 X u0 p0 c0 {1,S}
+6 *4 X u0 p0 c0 {3,S}
+
+H2CCH2
+1 *1 C u0 p0 c0 {2,S} {3,S} {4,D}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4 *2 C u0 p0 c0 {1,D} {5,S} {6,S}
+5    H u0 p0 c0 {4,S}
+6    H u0 p0 c0 {4,S}
+
+H2CCH2_2X
+1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4 *2 C u0 p0 c0 {1,S} {5,S} {6,S} {8,S}
+5    H u0 p0 c0 {4,S}
+6    H u0 p0 c0 {4,S}
+7 *3 X u0 p0 c0 {1,S}
+8 *4 X u0 p0 c0 {4,S}
+
+H2CO
+1 *1 C u0 p0 c0 {2,S} {3,S} {4,D}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4 *2 O u0 p2 c0 {1,D}
+
+H2CO_2X
+1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
+2    H u0 p0 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+4 *2 O u0 p2 c0 {1,S} {6,S}
+5 *3 X u0 p0 c0 {1,S}
+6 *4 X u0 p0 c0 {4,S}

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

@@ -7,3 +7,59 @@
 Put kinetic parameters for specific reactions in this file to use as a
 training set for generating rate rules to populate this kinetics family.
 """
+
+entry(
+    index = 1,
+    label = "HCCH + X_3 + X_4 <=> HCCH_2X",
+    kinetics = StickingCoefficient(
+        A = 8.3E-1,
+        n = 0,
+        Ea = (0, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 1,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+    Experimental value with single-crystal adsorption calorimetry (SCAC) for initial sticking probability:
+    "Energetics and kinetics of the interaction of acetylene and ethylene with Pd{100} and Ni{100}"
+    Vattuone et al
+    Surface Science, 2000, 447, 1-14""",
+	metal = "Pd",
+)
+
+entry(
+    index = 2,
+    label = "H2CCH2 + X_3 + X_4 <=> H2CCH2_2X",
+    kinetics = StickingCoefficient(
+        A = 6.9E-1,
+        n = 0,
+        Ea = (0, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 1,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+    Experimental value with microcalorimetry for initial sticking probability:
+    "Microcalorimetric study of ethylene adsorption at 300 K on Pt{100}-hex and Pt{100}-(11)"
+    Yeo et al
+    Journal of Molecular Catalysis A: Chemical, 1998, 131, 31-38""",
+	metal = "Pt",
+)
+
+entry(
+    index = 3,
+    label = "H2CO + X_3 + X_4 <=> H2CO_2X",
+    kinetics = StickingCoefficient(
+        A = 2.0E-1,
+        n = 0,
+        Ea = (0, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""Made up""",
+	metal = "Pt",
+)

input/kinetics/families/Surface_Bidentate_Dissociation/rules.py

@@ -9,32 +9,17 @@
     index = 1,
     label = "Combined",
     kinetics = SurfaceArrheniusBEP(
-        A = (8.96e10, '1/s'),
-        n = 0.422,
-        alpha = 0,
-        E0 = (0.0, 'kcal/mol'),
+        A = (1.187E12, '1/s'),
+        n = 0.0, 
+        alpha = 0.842,
+        E0 = (34.82, 'kcal/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
     longDesc = u"""
-Pre-exponential value, n and E0 are from R42 in Table 1 of "A Catalytic Reaction Mechanism for Methane 
-Partial Oxidation at Short ContactTimes, Reforming, and Combustion, and 
-for Oxygenate Decomposition and Oxidation on Platinum"
-Authors:  A.B. Mhadeshwar and D.G. Vlachos
-doi:10.1021/ie070322c
-
-The reaction is
-   HCOO** -> CO2* + H*
-They report a nonlinear dependence of the activation energy on specific coverage (of H*)
-and temperature, but don't say what this dependence is.
-Note that this reaction is not actually an example of this reaction family!
-It the dissociation of a bidentate adsorbate, but the H* that ends up adsorbed was not 
-one of the initial adatoms.
-However, in the absence of better data, it is currently our best estimate. (KB, CFG, RHW, 2020-11-30).
+A and n factors are averages of training reactions 1-3 and the reverse direction of training reactions 4-7, 
+and alpha and E0 are BEP parameters from training reactions 1-3 and the reverse of training reactions 4-7.
 """
 )
-
-
-

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

@@ -0,0 +1,88 @@
+CC_2X
+1 *1 C u0 p0 {2,S} {3,T}
+2 *2 C u0 p0 {1,S} {4,T}
+3 *3 X u0 p0 {1,T} 
+4 *4 X u0 p0 {2,T}
+
+CX_3
+1 *1 C u0 p0 {2,Q}
+2 *3 X u0 p0 {1,Q}  
+
+CX_4
+1 *2 C u0 p0 {2,Q}
+2 *4 X u0 p0 {1,Q}  
+
+CCH_2X
+1 *1 C u0 p0 {2,S} {3,S} {4,D}
+2    H u0 p0 {1,S}
+3 *2 C u0 p0 {1,S} {5,T}
+4 *3 X u0 p0 {1,D}
+5 *4 X u0 p0 {3,T}
+
+CHX_4
+1 *2 C u0 p0 {2,S} {3,T}
+2    H u0 p0 {1,S}
+3 *4 X u0 p0 {1,T}  
+
+HCCH_2X
+1 *1 C u0 p0 {2,S} {3,S} {5,D}
+2    H u0 p0 {1,S}
+3 *2 C u0 p0 {1,S} {4,S} {6,D}
+4    H u0 p0 {3,S}
+5 *3 X u0 p0 {1,D}
+6 *4 X u0 p0 {3,D}
+
+CHX_3
+1 *1 C u0 p0 {2,S} {3,T}
+2    H u0 p0 {1,S}
+3 *3 X u0 p0 {1,T} 
+
+HCCH2_2X
+1 *1 C u0 p0 {2,S} {3,S} {4,S} {6,S}
+2    H u0 p0 {1,S}
+3    H u0 p0 {1,S}
+4 *2 C u0 p0 {1,S} {5,S} {7,D}
+5    H u0 p0 {4,S}
+6 *3 X u0 p0 {1,S}
+7 *4 X u0 p0 {4,D}
+
+CH2X_4
+1 *2 C u0 p0 {2,S} {3,S} {4,D}
+2    H u0 p0 {1,S}
+3    H u0 p0 {1,S}
+4 *4 X u0 p0 {1,D}  
+
+H2CCH2_2X
+1 *1 C u0 p0 {2,S} {3,S} {4,S} {7,S}
+2    H u0 p0 {1,S}
+3    H u0 p0 {1,S}
+4 *2 C u0 p0 {1,S} {5,S} {6,S} {8,S}
+5    H u0 p0 {4,S}
+6    H u0 p0 {4,S}
+7 *3 X u0 p0 {1,S}
+8 *4 X u0 p0 {4,S}
+
+CH2X_3
+1 *1 C u0 p0 {2,S} {3,S} {4,D}
+2    H u0 p0 {1,S}
+3    H u0 p0 {1,S}
+4 *3 X u0 p0 {1,D}  
+
+HCO_2X
+1 *1 C u0 p0 {2,S} {3,S} {4,D}
+2    H u0 p0 {1,S}
+3 *2 O u0 p2 {1,S} {5,S}
+4 *3 X u0 p0 {1,D}
+5 *4 X u0 p0 {3,S}
+
+OX_4
+1 *2 O u0 p2 {2,D}
+2 *4 X u0 p0 {1,D}
+
+H2CO_2X
+1 *1 C u0 p0 {2,S} {3,S} {4,S} {5,S}
+2    H u0 p0 {1,S}
+3    H u0 p0 {1,S}
+4 *2 O u0 p2 {1,S} {6,S}
+5 *3 X u0 p0 {1,S}
+6 *4 X u0 p0 {4,S}