Merge pull request #655 from to correct surface reaction family trees.

Remove reaction path degeneracy adjustments in surface families.
These extra nodes and rules were earlier added to remove reaction path degeneracy factors
that we now think should be there. This PR removes them. It also therefore simplifies the trees a bit.
Only affects surface (catalysis) reaction families.

input/kinetics/families/Surface_Abstraction/rules.py

@@ -103,131 +103,4 @@
 BEP values from "Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111)", Kreitz et al., JACS Au, 2021, 1, 10, 1656-1673 DOI:10.1021/jacsau.1c00276
 Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
-
-entry(
-    index = 6,
-    label = "O;*=CH-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the BEP are from the abstraction reaction of C-H to O.
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
-    """
-)
-
-entry(
-    index = 7,
-    label = "O;*-CH-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the BEP are from the abstraction reaction of C-H to O.
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
-    """
-)
-
-entry(
-    index = 8,
-    label = "C;*-CH-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.37,
-        E0 = (99.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the general BEP are from the abstraction reaction of C-H to C.
-BEP values from "Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111)", Kreitz et al., JACS Au, 2021, 1, 10, 1656-1673 DOI:10.1021/jacsau.1c00276
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
-"""
-)
-
-entry(
-    index = 9,
-    label = "C;*=CH-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.37,
-        E0 = (99.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the general BEP are from the abstraction reaction of C-H to C.
-BEP values from "Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111)", Kreitz et al., JACS Au, 2021, 1, 10, 1656-1673 DOI:10.1021/jacsau.1c00276
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
-    """
-)
-
-
-entry(
-    index = 10,
-    label = "C;*-CH2-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.37,
-        E0 = (99.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the general BEP are from the abstraction reaction of C-H to C.
-BEP values from "Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111)", Kreitz et al., JACS Au, 2021, 1, 10, 1656-1673 DOI:10.1021/jacsau.1c00276
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-    """
-)
-
-entry(
-    index = 11,
-    label = "O;*-CH2-H",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-These numbers for the BEP are from the abstraction reaction of C-H to O.
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-    """
-)
+)

input/kinetics/families/Surface_Abstraction_Beta/rules.py

@@ -62,45 +62,4 @@
 BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
 From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
-
-entry(
-    index = 4,
-    label = "O;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
-
-entry(
-    index = 5,
-    label = "Abstracting;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u""" 
-These numbers for the general BEP are from the abstraction reaction of C-H to O.
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
+)

input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py

@@ -61,44 +61,4 @@
 BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
 From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
-
-entry(
-    index = 4,
-    label = "Abstracting;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.68,
-        E0 = (106.1, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
-
-entry(
-    index = 5,
-    label = "OH;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.68,
-        E0 = (106.1, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
+)

input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py

@@ -61,44 +61,4 @@
 BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
 From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
-
-entry(
-    index = 4,
-    label = "Abstracting;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
-
-entry(
-    index = 5,
-    label = "O;R-CH3",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.94,
-        E0 = (129.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706
-From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
-"""
-)
+)

input/kinetics/families/Surface_Dissociation/rules.py

@@ -139,84 +139,4 @@
 E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
 Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
     """
-)
-
-entry(
-    index = 8,
-    label = "CH2;VacantSite",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.57,
-        E0 = (75.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 2 because of reaction path degeneracy for CH2
-"""
-)
-
-entry(
-    index = 9,
-    label = "CH3;VacantSite",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.39e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.57,
-        E0 = (75.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 3 because of reaction path degeneracy for CH3
-"""
-)
-
-entry(
-    index = 10,
-    label = "CH2R;VacantSite",
-    kinetics = SurfaceArrheniusBEP(
-        A = (2.09e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.57,
-        E0 = (75.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom)
-"""
-)
-
-entry(
-    index = 11,
-    label = "CHR;VacantSite",
-    kinetics = SurfaceArrheniusBEP(
-        A = (4.18e17, 'm^2/(mol*s)'),
-        n = 0,
-        alpha =0.57,
-        E0 = (75.3, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom)
-"""
-)
+)

input/kinetics/families/Surface_Dissociation_Beta/rules.py

@@ -63,24 +63,4 @@
 E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374.
 Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
-
-entry(
-    index = 4,
-    label = "CH3;VacantSite",
-    kinetics = SurfaceArrheniusBEP(
-        A = (1.393e17, 'm^2/(mol*s)'),
-        n = 0.,
-        alpha =0.58,
-        E0 = (112.9, 'kJ/mol'),
-        Tmin = (200, 'K'),
-        Tmax = (3000, 'K'),
-    ),
-    rank = 0,
-    shortDesc = u"""Default""",
-    longDesc = u"""
-E0 and alpha are taken from Table 6 for oxygenates for 3x3 cell size from "A Theoretical and Computational Analysis of Linear Free Energy Relations for the Estimation of Activation Energies" Jonathan E. Sutton, Dionisios G. Vlachos, ACS Catal., 2012, 2, 1624-1634, DOI:10.1021/cs3003269.
-Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
-A divided by 3 because of reaction path degeneracy for =R-CH3 dissociation (3 equivalent H atoms)
-"""
-)
+)