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add training rxn
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‎input/kinetics/families/Surface_Dissociation_Beta_vdW/training/dictionary.txt‎

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X_5
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1 *5 X u0 p0 c0
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COOH*
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1 *2 O u0 p2 c0 {3,S} {4,S}
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2 O u0 p2 c0 {3,D}
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3 *1 C u0 p0 c0 {1,S} {2,D} {5,S}
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4 *3 H u0 p0 c0 {1,S}
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5 *4 X u0 p0 c0 {3,S}
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CO2_2*
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1 *2 O u0 p2 c0 {3,D}
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2 O u0 p2 c0 {3,D}
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3 *1 C u0 p0 c0 {1,D} {2,D}
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4 *4 X u0 p0 c0
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H*
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1 *5 X u0 p0 c0 {2,S}
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2 *3 H u0 p0 c0 {1,S}
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HCOO*
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1 *1 O u0 p2 c0 {3,S} {5,S}
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2 O u0 p2 c0 {3,D}
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3 *2 C u0 p0 c0 {1,S} {2,D} {4,S}
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4 *3 H u0 p0 c0 {3,S}
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5 *4 X u0 p0 c0 {1,S}
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CO2*
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1 *1 O u0 p2 c0 {3,D}
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2 O u0 p2 c0 {3,D}
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3 *2 C u0 p0 c0 {1,D} {2,D}
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4 *4 X u0 p0 c0
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HCOOH*
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1 O u0 p2 c0 {3,S} {5,S}
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2 *1 O u0 p2 c0 {3,D}
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3 *2 C u0 p0 c0 {1,S} {2,D} {4,S}
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4 H u0 p0 c0 {3,S}
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5 H u0 p0 c0 {1,S}
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6 *4 X u0 p0 c0
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CH3O2_2*
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1 O u0 p2 c0 {3,S} {6,S}
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2 *1 O u0 p2 c0 {3,S} {7,S}
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3 *2 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S}
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4 *3 H u0 p0 c0 {3,S}
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5 H u0 p0 c0 {3,S}
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6 H u0 p0 c0 {1,S}
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7 *4 X u0 p0 c0 {2,S}
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CH3O2*
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1 *3 O u0 p2 c0 {3,S} {6,S}
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2 *1 O u0 p2 c0 {3,S} {7,S}
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3 *2 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S}
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4 H u0 p0 c0 {3,S}
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5 H u0 p0 c0 {3,S}
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6 H u0 p0 c0 {1,S}
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7 *4 X u0 p0 c0 {2,S}
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CH2O*
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1 *1 O u0 p2 c0 {2,D}
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2 *2 C u0 p0 c0 {1,D} {3,S} {4,S}
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3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 *4 X u0 p0 c0
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OH*
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1 *3 O u0 p2 c0 {2,S} {3,S}
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2 H u0 p0 c0 {1,S}
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3 *5 X u0 p0 c0 {1,S}
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CH3O_1*
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1 *1 O u0 p2 c0 {2,S} {6,S}
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2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
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3 *3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 H u0 p0 c0 {2,S}
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6 *4 X u0 p0 c0 {1,S}
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CH2O_2*
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1 *2 O u0 p2 c0 {2,D}
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2 *1 C u0 p0 c0 {1,D} {3,S} {4,S}
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3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 *4 X u0 p0 c0
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CH2OH*
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1 *2 O u0 p2 c0 {2,S} {5,S}
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2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S}
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3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 *3 H u0 p0 c0 {1,S}
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6 *4 X u0 p0 c0 {2,S}
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CH3O_5*
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1 *3 O u0 p2 c0 {2,S} {6,S}
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2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
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3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 H u0 p0 c0 {2,S}
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6 *5 X u0 p0 c0 {1,S}
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H2COOCH3*
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1 *1 O u0 p2 c0 {2,S} {9,S}
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2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {10,S}
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3 *3 O u0 p2 c0 {2,S} {4,S}
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4 C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
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5 H u0 p0 c0 {2,S}
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6 H u0 p0 c0 {4,S}
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7 H u0 p0 c0 {4,S}
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8 H u0 p0 c0 {4,S}
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9 *4 X u0 p0 c0 {1,S}
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10 H u0 p0 c0 {2,S}
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HCOOCH3*
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1 *1 O u0 p2 c0 {2,D}
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2 *2 C u0 p0 c0 {1,D} {3,S} {5,S}
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3 O u0 p2 c0 {2,S} {4,S}
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4 C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
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5 H u0 p0 c0 {2,S}
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6 H u0 p0 c0 {4,S}
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7 H u0 p0 c0 {4,S}
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8 H u0 p0 c0 {4,S}
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9 *4 X u0 p0 c0
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H2COOCH3_2*
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1 *1 O u0 p2 c0 {2,S} {9,S}
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2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {10,S}
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3 O u0 p2 c0 {2,S} {4,S}
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4 C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
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5 *3 H u0 p0 c0 {2,S}
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6 H u0 p0 c0 {4,S}
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7 H u0 p0 c0 {4,S}
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8 H u0 p0 c0 {4,S}
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9 *4 X u0 p0 c0 {1,S}
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10 H u0 p0 c0 {2,S}

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

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Put kinetic parameters for specific reactions in this file to use as a
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training set for generating rate rules to populate this kinetics family.
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"""
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# in the reverse direction of family direction
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entry(
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index = 45,
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label = "CO2_2* + H* <=> COOH* + X_5",
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degeneracy = 2,
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kinetics = SurfaceArrhenius(
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A = (6.25E20, 'm^2/(mol*s)'),
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n = -0.475,
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Ea = (117200, 'J/mol'),
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Tmin = (200, 'K'),
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Tmax = (3000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""R45
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test surface mechanism: based upon Olaf Deutschmann's work:
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"Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts"
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Delgado et al
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Catalysts, 2015, 5, 871-904""",
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metal = "Ni",
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)
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# in the reverse direction of family direction
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entry(
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index = 17,
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label = "CO2* + H* <=> HCOO* + X_5",
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degeneracy = 2,
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kinetics = SurfaceArrhenius(
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A = (1.243e18, 'm^2/(mol*s)'),
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n = 0.,
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Ea = (0.87, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
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Reaction 17 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
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and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
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A factor from paper / surface site density of Cu
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3.658e13 1/s / 2.943e‐5 mol/m^2 = 1.243e18 m^2/(mol*s)
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""",
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metal = "Cu",
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)
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# in the reverse direction of family direction
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entry(
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index = 20,
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label = "HCOOH* + H* <=> CH3O2_2* + X_5",
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degeneracy = 1,
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kinetics = SurfaceArrhenius(
63+
A = (2.122e19, 'm^2/(mol*s)'),
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n = 0.,
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Ea = (1.04, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
72+
Reaction 20 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
73+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
74+
75+
A factor from paper / surface site density of Cu
76+
6.244e14 1/s / 2.943e‐5 mol/m^2 = 2.122e19 m^2/(mol*s)
77+
""",
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metal = "Cu",
79+
)
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# in the reverse direction of family direction
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entry(
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index = 23,
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label = "CH2O* + OH* <=> CH3O2* + X_5",
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degeneracy = 1,
86+
kinetics = SurfaceArrhenius(
87+
A = (3.401e17, 'm^2/(mol*s)'),
88+
n = 0.,
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Ea = (0., 'kcal/mol'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
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Reaction 23 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
97+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
98+
99+
Spontaneous in this direction, so 1e13 and barrierless assumed in paper
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101+
A factor from paper / surface site density of Cu
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1.001e13 1/s / 2.943e‐5 mol/m^2 = 3.401e17 m^2/(mol*s)
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""",
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metal = "Cu",
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)
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# in the reverse direction of family direction
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entry(
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index = 24,
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label = "CH2O* + H* <=> CH3O_1* + X_5",
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degeneracy = 1,
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kinetics = SurfaceArrhenius(
113+
A = (6.167e17, 'm^2/(mol*s)'),
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n = 0.,
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Ea = (0.24, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
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Reaction 24 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
123+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
124+
125+
A factor from paper / surface site density of Cu
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1.815e13 1/s / 2.943e‐5 mol/m^2 = 6.167e17 m^2/(mol*s)
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Erxn = -1.02 eV
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""",
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metal = "Cu",
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)
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# in the reverse direction of family direction
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entry(
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index = 31,
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label = "CH2O_2* + H* <=> CH2OH* + X_5",
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degeneracy = 1,
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kinetics = SurfaceArrhenius(
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A = (3.234e19, 'm^2/(mol*s)'),
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n = 0.,
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Ea = (0.82, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
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Reaction 31 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
148+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
149+
150+
A factor from paper / surface site density of Cu
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9.518e14 1/s / 2.943e‐5 mol/m^2 = 3.234e19 m^2/(mol*s)
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Erxn = -0.06 eV
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""",
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metal = "Cu",
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)
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# in the reverse direction of family direction
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entry(
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index = 47,
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label = "CH3O_5* + CH2O* <=> H2COOCH3* + X_5",
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degeneracy = 1,
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kinetics = SurfaceArrhenius(
163+
A = (2.176e18, 'm^2/(mol*s)'),
164+
n = 0.,
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Ea = (0.13, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
171+
longDesc = u"""
172+
Reaction 47 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
173+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
174+
175+
A factor from paper / surface site density of Cu
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6.405e13 1/s / 2.943e‐5 mol/m^2 = 2.176e18 m^2/(mol*s)
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Erxn = -0.78 eV
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""",
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metal = "Cu",
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)
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# in the reverse direction of family direction
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entry(
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index = 48,
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label = "HCOOCH3* + H* <=> H2COOCH3_2* + X_5",
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degeneracy = 1,
187+
kinetics = SurfaceArrhenius(
188+
A = (5.219e16, 'm^2/(mol*s)'),
189+
n = 0.,
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Ea = (0.94, 'eV/molecule'),
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Tmin = (298, 'K'),
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Tmax = (2000, 'K'),
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),
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rank = 10,
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shortDesc = u"""Default""",
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longDesc = u"""
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Reaction 48 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2
198+
and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d
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A factor from paper / surface site density of Cu
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1.536e12 1/s / 2.943e‐5 mol/m^2 = 5.219e16 m^2/(mol*s)
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Erxn = 0.01 eV
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""",
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metal = "Cu",
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)

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