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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.
2 parents ed45f13 + 8dd1ef5 commit fb75d87

8 files changed

Lines changed: 14 additions & 482 deletions

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‎input/kinetics/families/Surface_Abstraction/rules.py‎

Lines changed: 1 addition & 128 deletions
Original file line numberDiff line numberDiff line change
@@ -103,131 +103,4 @@
103103
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
104104
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)
105105
"""
106-
)
107-
108-
entry(
109-
index = 6,
110-
label = "O;*=CH-H",
111-
kinetics = SurfaceArrheniusBEP(
112-
A = (2.09e17, 'm^2/(mol*s)'),
113-
n = 0,
114-
alpha = 0.94,
115-
E0 = (129.3, 'kJ/mol'),
116-
Tmin = (200, 'K'),
117-
Tmax = (3000, 'K'),
118-
),
119-
rank = 0,
120-
shortDesc = u"""Default""",
121-
longDesc = u"""
122-
These numbers for the BEP are from the abstraction reaction of C-H to O.
123-
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
124-
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)
125-
Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
126-
"""
127-
)
128-
129-
entry(
130-
index = 7,
131-
label = "O;*-CH-H",
132-
kinetics = SurfaceArrheniusBEP(
133-
A = (2.09e17, 'm^2/(mol*s)'),
134-
n = 0,
135-
alpha = 0.94,
136-
E0 = (129.3, 'kJ/mol'),
137-
Tmin = (200, 'K'),
138-
Tmax = (3000, 'K'),
139-
),
140-
rank = 0,
141-
shortDesc = u"""Default""",
142-
longDesc = u"""
143-
These numbers for the BEP are from the abstraction reaction of C-H to O.
144-
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
145-
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)
146-
Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
147-
"""
148-
)
149-
150-
entry(
151-
index = 8,
152-
label = "C;*-CH-H",
153-
kinetics = SurfaceArrheniusBEP(
154-
A = (2.09e17, 'm^2/(mol*s)'),
155-
n = 0,
156-
alpha =0.37,
157-
E0 = (99.3, 'kJ/mol'),
158-
Tmin = (200, 'K'),
159-
Tmax = (3000, 'K'),
160-
),
161-
rank = 0,
162-
shortDesc = u"""Default""",
163-
longDesc = u"""
164-
These numbers for the general BEP are from the abstraction reaction of C-H to C.
165-
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
166-
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)
167-
Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
168-
"""
169-
)
170-
171-
entry(
172-
index = 9,
173-
label = "C;*=CH-H",
174-
kinetics = SurfaceArrheniusBEP(
175-
A = (2.09e17, 'm^2/(mol*s)'),
176-
n = 0,
177-
alpha =0.37,
178-
E0 = (99.3, 'kJ/mol'),
179-
Tmin = (200, 'K'),
180-
Tmax = (3000, 'K'),
181-
),
182-
rank = 0,
183-
shortDesc = u"""Default""",
184-
longDesc = u"""
185-
These numbers for the general BEP are from the abstraction reaction of C-H to C.
186-
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
187-
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)
188-
Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms)
189-
"""
190-
)
191-
192-
193-
entry(
194-
index = 10,
195-
label = "C;*-CH2-H",
196-
kinetics = SurfaceArrheniusBEP(
197-
A = (1.393e17, 'm^2/(mol*s)'),
198-
n = 0,
199-
alpha =0.37,
200-
E0 = (99.3, 'kJ/mol'),
201-
Tmin = (200, 'K'),
202-
Tmax = (3000, 'K'),
203-
),
204-
rank = 0,
205-
shortDesc = u"""Default""",
206-
longDesc = u"""
207-
These numbers for the general BEP are from the abstraction reaction of C-H to C.
208-
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
209-
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)
210-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
211-
"""
212-
)
213-
214-
entry(
215-
index = 11,
216-
label = "O;*-CH2-H",
217-
kinetics = SurfaceArrheniusBEP(
218-
A = (1.393e17, 'm^2/(mol*s)'),
219-
n = 0,
220-
alpha = 0.94,
221-
E0 = (129.3, 'kJ/mol'),
222-
Tmin = (200, 'K'),
223-
Tmax = (3000, 'K'),
224-
),
225-
rank = 0,
226-
shortDesc = u"""Default""",
227-
longDesc = u"""
228-
These numbers for the BEP are from the abstraction reaction of C-H to O.
229-
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
230-
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)
231-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
232-
"""
233-
)
106+
)

‎input/kinetics/families/Surface_Abstraction_Beta/rules.py‎

Lines changed: 1 addition & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -62,45 +62,4 @@
6262
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
6363
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)
6464
"""
65-
)
66-
67-
entry(
68-
index = 4,
69-
label = "O;R-CH3",
70-
kinetics = SurfaceArrheniusBEP(
71-
A = (1.393e17, 'm^2/(mol*s)'),
72-
n = 0.,
73-
alpha =0.94,
74-
E0 = (129.3, 'kJ/mol'),
75-
Tmin = (200, 'K'),
76-
Tmax = (3000, 'K'),
77-
),
78-
rank = 0,
79-
shortDesc = u"""Default""",
80-
longDesc = u"""
81-
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
82-
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)
83-
A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
84-
"""
85-
)
86-
87-
entry(
88-
index = 5,
89-
label = "Abstracting;R-CH3",
90-
kinetics = SurfaceArrheniusBEP(
91-
A = (1.393e17, 'm^2/(mol*s)'),
92-
n = 0.,
93-
alpha =0.94,
94-
E0 = (129.3, 'kJ/mol'),
95-
Tmin = (200, 'K'),
96-
Tmax = (3000, 'K'),
97-
),
98-
rank = 0,
99-
shortDesc = u"""Default""",
100-
longDesc = u"""
101-
These numbers for the general BEP are from the abstraction reaction of C-H to O.
102-
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
103-
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)
104-
A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
105-
"""
106-
)
65+
)

‎input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py‎

Lines changed: 1 addition & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -61,44 +61,4 @@
6161
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
6262
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)
6363
"""
64-
)
65-
66-
entry(
67-
index = 4,
68-
label = "Abstracting;R-CH3",
69-
kinetics = SurfaceArrheniusBEP(
70-
A = (1.393e17, 'm^2/(mol*s)'),
71-
n = 0.,
72-
alpha =0.68,
73-
E0 = (106.1, 'kJ/mol'),
74-
Tmin = (200, 'K'),
75-
Tmax = (3000, 'K'),
76-
),
77-
rank = 0,
78-
shortDesc = u"""Default""",
79-
longDesc = u"""
80-
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
81-
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)
82-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
83-
"""
84-
)
85-
86-
entry(
87-
index = 5,
88-
label = "OH;R-CH3",
89-
kinetics = SurfaceArrheniusBEP(
90-
A = (1.393e17, 'm^2/(mol*s)'),
91-
n = 0.,
92-
alpha =0.68,
93-
E0 = (106.1, 'kJ/mol'),
94-
Tmin = (200, 'K'),
95-
Tmax = (3000, 'K'),
96-
),
97-
rank = 0,
98-
shortDesc = u"""Default""",
99-
longDesc = u"""
100-
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
101-
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)
102-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
103-
"""
104-
)
64+
)

‎input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py‎

Lines changed: 1 addition & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -61,44 +61,4 @@
6161
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
6262
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)
6363
"""
64-
)
65-
66-
entry(
67-
index = 4,
68-
label = "Abstracting;R-CH3",
69-
kinetics = SurfaceArrheniusBEP(
70-
A = (1.393e17, 'm^2/(mol*s)'),
71-
n = 0.,
72-
alpha =0.94,
73-
E0 = (129.3, 'kJ/mol'),
74-
Tmin = (200, 'K'),
75-
Tmax = (3000, 'K'),
76-
),
77-
rank = 0,
78-
shortDesc = u"""Default""",
79-
longDesc = u"""
80-
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
81-
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)
82-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
83-
"""
84-
)
85-
86-
entry(
87-
index = 5,
88-
label = "O;R-CH3",
89-
kinetics = SurfaceArrheniusBEP(
90-
A = (1.393e17, 'm^2/(mol*s)'),
91-
n = 0.,
92-
alpha =0.94,
93-
E0 = (129.3, 'kJ/mol'),
94-
Tmin = (200, 'K'),
95-
Tmax = (3000, 'K'),
96-
),
97-
rank = 0,
98-
shortDesc = u"""Default""",
99-
longDesc = u"""
100-
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
101-
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)
102-
Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
103-
"""
104-
)
64+
)

‎input/kinetics/families/Surface_Dissociation/rules.py‎

Lines changed: 1 addition & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -139,84 +139,4 @@
139139
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.
140140
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)
141141
"""
142-
)
143-
144-
entry(
145-
index = 8,
146-
label = "CH2;VacantSite",
147-
kinetics = SurfaceArrheniusBEP(
148-
A = (2.09e17, 'm^2/(mol*s)'),
149-
n = 0,
150-
alpha =0.57,
151-
E0 = (75.3, 'kJ/mol'),
152-
Tmin = (200, 'K'),
153-
Tmax = (3000, 'K'),
154-
),
155-
rank = 0,
156-
shortDesc = u"""Default""",
157-
longDesc = u"""
158-
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.
159-
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)
160-
A divided by 2 because of reaction path degeneracy for CH2
161-
"""
162-
)
163-
164-
entry(
165-
index = 9,
166-
label = "CH3;VacantSite",
167-
kinetics = SurfaceArrheniusBEP(
168-
A = (1.39e17, 'm^2/(mol*s)'),
169-
n = 0,
170-
alpha =0.57,
171-
E0 = (75.3, 'kJ/mol'),
172-
Tmin = (200, 'K'),
173-
Tmax = (3000, 'K'),
174-
),
175-
rank = 0,
176-
shortDesc = u"""Default""",
177-
longDesc = u"""
178-
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.
179-
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)
180-
A divided by 3 because of reaction path degeneracy for CH3
181-
"""
182-
)
183-
184-
entry(
185-
index = 10,
186-
label = "CH2R;VacantSite",
187-
kinetics = SurfaceArrheniusBEP(
188-
A = (2.09e17, 'm^2/(mol*s)'),
189-
n = 0,
190-
alpha =0.57,
191-
E0 = (75.3, 'kJ/mol'),
192-
Tmin = (200, 'K'),
193-
Tmax = (3000, 'K'),
194-
),
195-
rank = 0,
196-
shortDesc = u"""Default""",
197-
longDesc = u"""
198-
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.
199-
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)
200-
A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom)
201-
"""
202-
)
203-
204-
entry(
205-
index = 11,
206-
label = "CHR;VacantSite",
207-
kinetics = SurfaceArrheniusBEP(
208-
A = (4.18e17, 'm^2/(mol*s)'),
209-
n = 0,
210-
alpha =0.57,
211-
E0 = (75.3, 'kJ/mol'),
212-
Tmin = (200, 'K'),
213-
Tmax = (3000, 'K'),
214-
),
215-
rank = 0,
216-
shortDesc = u"""Default""",
217-
longDesc = u"""
218-
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.
219-
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)
220-
A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom)
221-
"""
222-
)
142+
)

‎input/kinetics/families/Surface_Dissociation_Beta/rules.py‎

Lines changed: 1 addition & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -63,24 +63,4 @@
6363
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.
6464
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)
6565
"""
66-
)
67-
68-
entry(
69-
index = 4,
70-
label = "CH3;VacantSite",
71-
kinetics = SurfaceArrheniusBEP(
72-
A = (1.393e17, 'm^2/(mol*s)'),
73-
n = 0.,
74-
alpha =0.58,
75-
E0 = (112.9, 'kJ/mol'),
76-
Tmin = (200, 'K'),
77-
Tmax = (3000, 'K'),
78-
),
79-
rank = 0,
80-
shortDesc = u"""Default""",
81-
longDesc = u"""
82-
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.
83-
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)
84-
A divided by 3 because of reaction path degeneracy for =R-CH3 dissociation (3 equivalent H atoms)
85-
"""
86-
)
66+
)

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