update remaining families

Author: bjkreitz

input/kinetics/families/Surface_Dissociation/rules.py

@@ -30,10 +30,10 @@
     index = 2,
     label = "C-H_Bidentate;VacantSite",
     kinetics = SurfaceArrheniusBEP(
-        A = (7.250e16, 'm^2/(mol*s)'), 
+        A = (1.36e18, 'm^2/(mol*s)'),
         n = 0.0,
-        alpha = 0.961, 
-        E0 = (22.37, 'kcal/mol'), 
+        alpha = 0.85,
+        E0 = (65.61, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),

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

@@ -185,3 +185,51 @@ HCO_2X
 3    O u0 p2 {1,S} {5,S}  
 4 *3 X u0 p0 {1,D}
 5    X u0 p0 {3,S}
+
+
+XCXCH2_1
+1    C u0 p0 {2,S} {5,T}
+2 *1 C u0 p0 {1,S} {3,S} {4,S} {6,S}
+3 *2 H u0 p0 {2,S}
+4    H u0 p0 {2,S}
+5    X u0 p0 {1,T}
+6 *3 X u0 p0 {2,S}
+
+XCXCH_3
+1    C u0 p0 {2,S} {4,T}
+2 *1 C u0 p0 {1,S} {3,S} {5,D}
+3    H u0 p0 {2,S}
+4    X u0 p0 {1,T}
+5 *3 X u0 p0 {2,D}
+
+XCHXCH2_1
+1 *1 C u0 p0 {2,S} {3,S} {6,D}
+2    C u0 p0 {1,S} {4,S} {5,S} {7,S}
+3 *2 H u0 p0 {1,S}
+4    H u0 p0 {2,S}
+5    H u0 p0 {2,S}
+6 *3 X u0 p0 {1,D}
+7    X u0 p0 {2,S}
+
+XCXCH2_3
+1 *1 C u0 p0 {2,S} {5,T}
+2    C u0 p0 {1,S} {3,S} {4,S} {6,S}
+3    H u0 p0 {2,S}
+4    H u0 p0 {2,S}
+5 *3 X u0 p0 {1,T}
+6    X u0 p0 {2,S}
+
+XCHXCH_1
+1 *1 C u0 p0 {2,S} {3,S} {5,D}
+2    C u0 p0 {1,S} {4,S} {6,D}
+3 *2 H u0 p0 {1,S}
+4    H u0 p0 {2,S}
+5 *3 X u0 p0 {1,D}
+6    X u0 p0 {2,D}
+
+XCXCH_4
+1 *1 C u0 p0 {2,S} {4,T}
+2    C u0 p0 {1,S} {3,S} {5,D}
+3    H u0 p0 {2,S}
+4 *3 X u0 p0 {1,T}
+5    X u0 p0 {2,D}

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

@@ -373,16 +373,21 @@
     label = "HCCH2_2X + Ni_4 <=> HCCH_2X + HX_5",
     degeneracy = 2,
     kinetics = SurfaceArrhenius(
-        A=(1.9460e16, 'm^2/(mol*s)'),
-        n = 0.512, 
-        Ea=(69707.5, 'J/mol'),
+        A=(4.75e21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(72, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank=8,
     shortDesc = u"""Default""",
     longDesc = u"""
-Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 2 because of the degeneracy.
+
 """,
     metal = "Pt",
 )
@@ -392,16 +397,20 @@
     label = "H2CCH2_2X + Ni_4 <=> H2CCH_2X + HX_5",
     degeneracy = 2,
     kinetics = SurfaceArrhenius(
-        A=(3.034e15, 'm^2/(mol*s)'), 
-        n = 0.661, 
-        Ea=(55411.0, 'J/mol'),
+        A=(2.225e21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(59, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank=8,
     shortDesc = u"""Default""",
     longDesc = u"""
-Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 2 because of the degeneracy.
 """,
     metal = "Pt",
 )
@@ -411,16 +420,88 @@
     label = "H2CO_2X + Ni_4 <=> HCO_2X + HX_5",
     degeneracy = 2,
     kinetics = SurfaceArrhenius(
-        A=(1.438e17, 'm^2/(mol*s)'),
-        n = 0.043, 
-        Ea=(1417.1, 'J/mol'),
+        A=(0.875e21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(2, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank=8,
     shortDesc = u"""Default""",
     longDesc = u"""
-Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 2 because of the degeneracy.
 """,
     metal = "Pt",
 )
+
+entry(
+    index = 63,
+    label = "XCXCH_3 + HX_5 <=> XCXCH2_1 + Ni_4",
+    degeneracy = 2,
+    kinetics = SurfaceArrhenius(
+        A=(2.595e19, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(34, 'kJ/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank=8,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 2 because of the degeneracy.
+""",
+    metal = "Pt",
+)
+
+entry(
+    index = 64,
+    label = "XCXCH_4 + HX_5 <=> XCHXCH_1 + Ni_4",
+    degeneracy = 2,
+    kinetics = SurfaceArrhenius(
+        A=(1.66e21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(62, 'kJ/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank=8,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 2 because of the degeneracy.
+""",
+    metal = "Pt",
+)
+
+entry(
+    index = 65,
+    label = "XCHXCH2_1 + Ni_4 <=> XCXCH2_3 + HX_5",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A=(9.69e21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(48, 'kJ/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank=8,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+""",
+    metal = "Pt",
+)

input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py

@@ -10,19 +10,21 @@
     index = 1,
     label = "Combined;VacantSite1;VacantSite2",
     kinetics = SurfaceArrheniusBEP(
-        A = (5.726E21, 'm^4/(mol^2*s)'), 
-        n = 0.0,  
-        alpha = 0.0824, 
-        E0 = (12.11, 'kcal/mol'), 
+        A = (1.41E30, 'cm^4/(mol^2*s)'),
+        n = 0.0,
+        alpha = 0.87,
+        E0 = (77.188, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
     longDesc = u"""
-A and n factors are from the average rates of training reactions 1-3, and alpha and E0 are BEP
-parameters from training reactions 1-3 (in the Surface_Dissociation_to_Bidentate 
-forward direction).
-The A factor has been divided by 2.33 here to account for the average degeneracy of the training reactions.
+A and n factors are from the average rates of training reactions 1-2 and reverse of 3-4, and alpha and E0 are BEP
+parameters from training reactions 1-2 and reverse of 3-4.
+
+Details on the computational method to derive the rate constants for the BEP relation are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
 """
 )

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

@@ -62,3 +62,19 @@ H2CO_2X
 4 *2 O u0 p2 {1,S} {6,S}  
 5 *4 X u0 p0 {1,S}
 6 *5 X u0 p0 {4,S}
+
+XCXCH2
+1 *1 C u0 p0 {2,S} {5,T}
+2 *2 C u0 p0 {1,S} {3,S} {4,S} {6,S}
+3    H u0 p0 {2,S}
+4    H u0 p0 {2,S}
+5 *4 X u0 p0 {1,T}
+6 *5 X u0 p0 {2,S}
+
+XCCH3
+1 *1 C u0 p0 {2,S} {6,T}
+2 *2 C u0 p0 {1,S} {3,S} {4,S} {5,S}
+3 *3 H u0 p0 {2,S}
+4    H u0 p0 {2,S}
+5    H u0 p0 {2,S}
+6 *4 X u0 p0 {1,T}

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

@@ -13,16 +13,20 @@
     label = "H2CCH3_X + Pt_5 + Pt_6 <=> H2CCH2_2X + H_X",
     degeneracy = 3,
     kinetics = SurfaceArrhenius(
-        A=(1.163E20, 'm^4/(mol^2*s)'), 
-        n = 0.644,
-        Ea=(42144.629, 'J/mol'),
+        A=(0.557E30, 'cm^4/(mol^2*s)'),
+        n = 0.0,
+        Ea=(46, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank = 8,
     shortDesc = u"""Deutschmann Ni""",
     longDesc = u"""
-Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 3 due to the degeneracy.
 """,
 	metal = "Pt",
 )
@@ -32,16 +36,20 @@
     label = "HCCH3_X + Pt_5 + Pt_6 <=> HCCH2_2X + H_X",
     degeneracy = 3,
     kinetics = SurfaceArrhenius(
-        A=(2.057E20, 'm^4/(mol^2*s)'),
-        n = 0.598,
-        Ea=(45301.1, 'J/mol'),
+        A=(0.65E30, 'cm^4/(mol^2*s)'),
+        n = 0.0,
+        Ea=(49, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank = 8,
     shortDesc = u"""Default""",
     longDesc = u"""
-Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+A divided by 3 due to the degeneracy.
 """,
 	metal = "Pt",
 )
@@ -51,16 +59,41 @@
     label = "H2CO_2X + H_X <=> H2COH_X + Pt_5 + Pt_6",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(4.857E16, 'm^2/(mol*s)'),
-        n = 0.063,
-        Ea=(28353.5, 'J/mol'),
+        A=(8.22E20, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(29, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
     rank = 8,
     shortDesc = u"""Default""",
     longDesc = u"""
-Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
 """,
 	metal = "Pt",
 )
+
+entry(
+    index = 4,
+    label = "XCXCH2 + H_X <=> XCCH3 + Pt_5 + Pt_6",
+    degeneracy = 1,
+    kinetics = SurfaceArrhenius(
+        A=(1.07E22, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(72, 'kJ/mol'),
+        Tmin = (298, 'K'),
+        Tmax = (2000, 'K'),
+    ),
+    rank = 8,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. 
+Details on the computational method to derive the rate constants are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+""",
+	metal = "Pt",
+)

input/kinetics/families/Surface_vdW_to_Bidentate/rules.py

@@ -9,14 +9,20 @@
     index = 1,
     label = "Combined;VacantSite",
     kinetics = SurfaceArrheniusBEP(
-        A = (1.0e17, 'm^2/(mol*s)'),
+        A = (1.78e21, 'cm^2/(mol*s)'),
         n = 0,
         alpha = 0.0,
-        E0 = (7, 'kcal/mol'),
+        E0 = (12, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
-    longDesc = u"""These values are made up."""
+    longDesc = u"""
+These values are based on training reaction 2. 
+The other training reactions are barrierless.
+Details on the computational method to derive the rate constants for the BEP relation are provided in "Automatic mechanism generation involving 
+kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173
+doi:10.1039/d3dd00184a
+"""
 )