Update bidentate

input/kinetics/families/Surface_Bidentate_Dissociation/rules.py

@@ -12,14 +12,18 @@
         A = (1.187E12, '1/s'),
         n = 0.0, 
         alpha = 0.842,
-        E0 = (34.82, 'kcal/mol'),
+        E0 = (145.69, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
     longDesc = u"""
-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.
+A factors are averages of training reactions 1-4 and the reverse direction of training reactions 5-7, 
+and alpha and E0 are BEP parameters from training reactions 1-4 and the reverse of training reactions 5-7.
+
+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_Bidentate_Dissociation/training/reactions.py

@@ -8,31 +8,24 @@
 training set for generating rate rules to populate this kinetics family.
 """
 
-#!/usr/bin/env python
-# encoding: utf-8
-
-name = "Surface_Bidentate_Dissociation/training"
-shortDesc = u"Reaction kinetics used to generate rate rules"
-longDesc = u"""
-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 = "CC_2X <=> CX_3 + CX_4  ",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(2.202E12, '1/s'), 
-        n = 0.09, 
-        Ea=(103497.2, 'J/mol'),
+        A=(4.22E12, '1/s'),
+        n = 0.0,
+        Ea=(104, '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
 """,
     metal = "Pt",
 )
@@ -42,16 +35,19 @@
     label = "CCH_2X <=> CX_3 + CHX_4",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(5.272E11, '1/s'), 
+        A=(1.3E12, '1/s'),
         n = 0.126, 
-        Ea=(76699.8, 'J/mol'),
+        Ea=(77, '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 
 """,
     metal = "Pt",
 )
@@ -61,35 +57,41 @@
     label = "HCCH_2X <=> CHX_3 + CHX_4",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(7.062E11, '1/s'), 
-        n = 0.320, 
-        Ea=(88220.0, 'J/mol'),
+        A=(7.93E12, '1/s'),
+        n = 0.0,
+        Ea=(90, 'kJ/mol'),
         Tmin = (298, 'K'),
         Tmax = (2000, 'K'),
     ),
-    rank=10,
+    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
 """,
     metal = "Pt",
 )
 
 entry( 
     index = 4,
-    label = "CHX_3 + CH2X_4 <=> HCCH2_2X",
+    label = "HCCH2_2X <=> CHX_3 + CH2X_4",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(4.256E17, 'm^2/(mol*s)'),
-        n = 0.106, 
-        Ea=(138024.4, 'J/mol'),
+        A=(2.74E13, '1/s'),
+        n = 0.0,
+        Ea=(140, '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
 """,
     metal = "Pt",
 )
@@ -99,16 +101,19 @@
     label = "CH2X_3 + CH2X_4 <=> H2CCH2_2X",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(1.161E19, 'm^2/(mol*s)'),
-        n = 0.281, 
-        Ea=(152439.3, 'J/mol'),
+        A=(9.89E23, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(154, '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
 """,
     metal = "Pt",
 )
@@ -118,16 +123,19 @@
     label = "CHX_3 + OX_4 <=> HCO_2X",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(6.922E17, 'm^2/(mol*s)'),
-        n = 0.049, 
-        Ea=(142325.0, 'J/mol'),
+        A=(6.54E21, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(142, '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
 """,
     metal = "Pt",
 )
@@ -137,16 +145,19 @@
     label = "CH2X_3 + OX_4 <=> H2CO_2X",
     degeneracy = 1,
     kinetics = SurfaceArrhenius(
-        A=(1.174E18, 'm^2/(mol*s)'),
-        n = 0.082, 
-        Ea=(114251.7, 'J/mol'),
+        A=(2.2E22, 'cm^2/(mol*s)'),
+        n = 0.0,
+        Ea=(115, '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
 """,
     metal = "Pt",
-)
+)

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}