Merge PR #646 to update bidentate surface reaction families.

@bjkreitz writes:

I updated the BEP rate rules and training reactions for the following bidentate reaction families
 Surface_Dissociation, Surface_Bidentate_Dissociation, Surface_Dissociation_to_Bidentate, 
Surface_vdW_to_Bidentate based on new data that we published in our latest paper 
DOI: 10.1039/d3dd00184a. The original data compiled by Katrin was in the modified Arrhenius format, 
but a regular Arrhenius format has a sufficient accuracy and makes the manual evaluation of the 
microkinetics easier. Accordingly, I changed the training reaction format.
I also added comments to the training reactions and rate rules to point to the publication.

Kirk reviewed:
I looked through the new values and they all seem to match up with what is in the paper. Additionally I ran a mechanism with both the main branch and this branch for the dehydrogenation reaction that was outlined in the paper. I used 5% CH3CH3, and 95% N2, and ran until a conversion of 0.1 was reached. Both core models were very similar, only differing by one species, and their thermo values stayed the same as expected. When looking at the reactions, both models had at least one reaction from each of these 6 reaction families. The new model generated 22 reactions that were within these 6 families, and the old model generated 24 reactions within these families. The reactions found were identical except for the old model having 2 extra. As expected the heats of reaction did not change. Also the rates of reaction changed by very little; when looking at log10, the differences were under 0.5.

Chris reviewed:
This looks good. I ran the attached example, using the compare tool it looks like the changes aren't huge. Where they are different, the bidentate-forming reactions are generally a little slower (which is a good thing, I think the general feeling was they were too fast before).

Author: rwest

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}