add training rxn

ReactionMechanismGenerator · Sep 18, 2024 · ccdacda · ccdacda
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diff --git a/input/kinetics/families/Surface_Dissociation_Beta_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_Beta_vdW/training/dictionary.txt
@@ -0,0 +1,136 @@
+X_5
+1 *5 X u0 p0 c0
+
+COOH*
+1 *2 O u0 p2 c0 {3,S} {4,S}
+2    O u0 p2 c0 {3,D}
+3 *1 C u0 p0 c0 {1,S} {2,D} {5,S}
+4 *3 H u0 p0 c0 {1,S}
+5 *4 X u0 p0 c0 {3,S}
+
+CO2_2*
+1 *2 O u0 p2 c0 {3,D}
+2    O u0 p2 c0 {3,D}
+3 *1 C u0 p0 c0 {1,D} {2,D}
+4 *4 X u0 p0 c0
+
+H*
+1 *5 X u0 p0 c0 {2,S}
+2 *3 H u0 p0 c0 {1,S}
+
+HCOO*
+1 *1 O u0 p2 c0 {3,S} {5,S}
+2    O u0 p2 c0 {3,D}
+3 *2 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 *3 H u0 p0 c0 {3,S}
+5 *4 X u0 p0 c0 {1,S}
+
+CO2*
+1 *1 O u0 p2 c0 {3,D}
+2    O u0 p2 c0 {3,D}
+3 *2 C u0 p0 c0 {1,D} {2,D}
+4 *4 X u0 p0 c0
+
+HCOOH*
+1    O u0 p2 c0 {3,S} {5,S}
+2 *1 O u0 p2 c0 {3,D}
+3 *2 C u0 p0 c0 {1,S} {2,D} {4,S}
+4    H u0 p0 c0 {3,S}
+5    H u0 p0 c0 {1,S}
+6 *4 X u0 p0 c0
+
+CH3O2_2*
+1    O u0 p2 c0 {3,S} {6,S}
+2 *1 O u0 p2 c0 {3,S} {7,S}
+3 *2 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S}
+4 *3 H u0 p0 c0 {3,S}
+5    H u0 p0 c0 {3,S}
+6    H u0 p0 c0 {1,S}
+7 *4 X u0 p0 c0 {2,S}
+
+CH3O2*
+1 *3 O u0 p2 c0 {3,S} {6,S}
+2 *1 O u0 p2 c0 {3,S} {7,S}
+3 *2 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S}
+4    H u0 p0 c0 {3,S}
+5    H u0 p0 c0 {3,S}
+6    H u0 p0 c0 {1,S}
+7 *4 X u0 p0 c0 {2,S}
+
+CH2O*
+1 *1 O u0 p2 c0 {2,D}
+2 *2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3    H u0 p0 c0 {2,S}
+4    H u0 p0 c0 {2,S}
+5 *4 X u0 p0 c0
+
+OH*
+1 *3 O u0 p2 c0 {2,S} {3,S}
+2    H u0 p0 c0 {1,S}
+3 *5 X u0 p0 c0 {1,S}
+
+CH3O_1*
+1 *1 O u0 p2 c0 {2,S} {6,S}
+2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
+3 *3 H u0 p0 c0 {2,S}
+4    H u0 p0 c0 {2,S}
+5    H u0 p0 c0 {2,S}
+6 *4 X u0 p0 c0 {1,S}
+
+CH2O_2*
+1 *2 O u0 p2 c0 {2,D}
+2 *1 C u0 p0 c0 {1,D} {3,S} {4,S}
+3    H u0 p0 c0 {2,S}
+4    H u0 p0 c0 {2,S}
+5 *4 X u0 p0 c0
+
+CH2OH*
+1 *2 O u0 p2 c0 {2,S} {5,S}
+2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S}
+3    H u0 p0 c0 {2,S}
+4    H u0 p0 c0 {2,S}
+5 *3 H u0 p0 c0 {1,S}
+6 *4 X u0 p0 c0 {2,S}
+
+CH3O_5*
+1 *3 O u0 p2 c0 {2,S} {6,S}
+2    C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
+3    H u0 p0 c0 {2,S}
+4    H u0 p0 c0 {2,S}
+5    H u0 p0 c0 {2,S}
+6 *5 X u0 p0 c0 {1,S}
+
+H2COOCH3*
+1 *1 O u0 p2 c0 {2,S} {9,S}
+2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {10,S}
+3 *3 O u0 p2 c0 {2,S} {4,S}
+4    C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
+5    H u0 p0 c0 {2,S}
+6    H u0 p0 c0 {4,S}
+7    H u0 p0 c0 {4,S}
+8    H u0 p0 c0 {4,S}
+9 *4 X u0 p0 c0 {1,S}
+10   H u0 p0 c0 {2,S}
+
+HCOOCH3*
+1 *1 O u0 p2 c0 {2,D}
+2 *2 C u0 p0 c0 {1,D} {3,S} {5,S}
+3    O u0 p2 c0 {2,S} {4,S}
+4    C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
+5    H u0 p0 c0 {2,S}
+6    H u0 p0 c0 {4,S}
+7    H u0 p0 c0 {4,S}
+8    H u0 p0 c0 {4,S}
+9 *4 X u0 p0 c0
+
+H2COOCH3_2*
+1 *1 O u0 p2 c0 {2,S} {9,S}
+2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {10,S}
+3    O u0 p2 c0 {2,S} {4,S}
+4    C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
+5 *3 H u0 p0 c0 {2,S}
+6    H u0 p0 c0 {4,S}
+7    H u0 p0 c0 {4,S}
+8    H u0 p0 c0 {4,S}
+9 *4 X u0 p0 c0 {1,S}
+10   H u0 p0 c0 {2,S}
diff --git a/input/kinetics/families/Surface_Dissociation_Beta_vdW/training/reactions.py b/input/kinetics/families/Surface_Dissociation_Beta_vdW/training/reactions.py
@@ -7,3 +7,199 @@
 Put kinetic parameters for specific reactions in this file to use as a
 training set for generating rate rules to populate this kinetics family.
 """
+
+# in the reverse direction of family direction
+entry(
+    index = 45,
+    label = "CO2_2* + H* <=> COOH* + X_5",
+    degeneracy = 2,
+    kinetics = SurfaceArrhenius(
+        A = (6.25E20, 'm^2/(mol*s)'),
+        n = -0.475,
+        Ea = (117200, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""R45
+    test surface mechanism: based upon Olaf Deutschmann's work:
+    "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts"
+    Delgado et al
+    Catalysts, 2015, 5, 871-904""",
+	  metal = "Ni",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 17,
+    label = "CO2* + H* <=> HCOO* + X_5",
+    degeneracy = 2,
+    kinetics = SurfaceArrhenius(
+        A = (1.243e18, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0.87, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    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
+
+A factor from paper / surface site density of Cu
+3.658e13 1/s / 2.943e‐5 mol/m^2 = 1.243e18 m^2/(mol*s)
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 20,
+    label = "HCOOH* + H* <=> CH3O2_2* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (2.122e19, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (1.04, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 20 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+A factor from paper / surface site density of Cu
+6.244e14 1/s / 2.943e‐5 mol/m^2 = 2.122e19 m^2/(mol*s)
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 23,
+    label = "CH2O* + OH* <=> CH3O2* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (3.401e17, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0., 'kcal/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 23 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+Spontaneous in this direction, so 1e13 and barrierless assumed in paper
+
+A factor from paper / surface site density of Cu
+1.001e13 1/s / 2.943e‐5 mol/m^2 = 3.401e17 m^2/(mol*s)
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 24,
+    label = "CH2O* + H* <=> CH3O_1* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (6.167e17, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0.24, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 24 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+A factor from paper / surface site density of Cu
+1.815e13 1/s / 2.943e‐5 mol/m^2 = 6.167e17 m^2/(mol*s)
+Erxn = -1.02 eV
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 31,
+    label = "CH2O_2* + H* <=> CH2OH* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (3.234e19, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0.82, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 31 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+A factor from paper / surface site density of Cu
+9.518e14 1/s / 2.943e‐5 mol/m^2 = 3.234e19 m^2/(mol*s)
+Erxn = -0.06 eV
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 47,
+    label = "CH3O_5* + CH2O* <=> H2COOCH3* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (2.176e18, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0.13, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 47 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+A factor from paper / surface site density of Cu
+6.405e13 1/s / 2.943e‐5 mol/m^2 = 2.176e18 m^2/(mol*s)
+Erxn = -0.78 eV
+""",
+    metal = "Cu",
+)
+
+# in the reverse direction of family direction
+entry(
+    index = 48,
+    label = "HCOOCH3* + H* <=> H2COOCH3_2* + X_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A = (5.219e16, 'm^2/(mol*s)'),
+        n = 0.,
+        Ea = (0.94, 'eV/molecule'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 10,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Reaction 48 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
+and CO Hydrogenation", Grabow and Mavrikakis.  doi:10.1021/cs200055d
+
+A factor from paper / surface site density of Cu
+1.536e12 1/s / 2.943e‐5 mol/m^2 = 5.219e16 m^2/(mol*s)
+Erxn = 0.01 eV
+""",
+    metal = "Cu",
+)