Skip to content

Commit fbdbc4e

Browse files
kblondalChrisBNEU
kblondal
authored and
ChrisBNEU
committed
Added Surface_Dissociation_to_Bidentate family
and three training reactions belonging to it.
1 parent 5bce9c3 commit fbdbc4e

5 files changed

Lines changed: 230 additions & 0 deletions

File tree

‎input/kinetics/families/Surface_Dissociation_to_Bidentate/groups.py‎

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,71 @@
1+
#!/usr/bin/env python
2+
# encoding: utf-8
3+
4+
name = "Surface_Dissociation_to_Bidentate/groups"
5+
shortDesc = u""
6+
longDesc = u"""
7+
A monodentate species becomes bidentate as H dissociates from it and both form a new bond with the surface instead.
8+
9+
*1--*2--*3 *1--*2 *3
10+
| ----> | | |
11+
~*4~ + ~*5~ + ~*6 ~*4~~*5 + ~*6~~
12+
13+
The rate, which should be in mol/m2/s,
14+
will be given by k * (mol/m2) * (mol/m2) * (mol/m2)
15+
so k should be in (m4/mol2/s)
16+
"""
17+
18+
template(reactants=["Combined", "VacantSite1", "VacantSite2"], products=["Adsorbate1", "Adsorbate2"], ownReverse=False)
19+
20+
reverse = "Surface_Bidentate_Association_to_Monodentate"
21+
22+
recipe(actions=[
23+
['BREAK_BOND', '*2', 1, '*3'],
24+
['FORM_BOND', '*2', 1, '*5'],
25+
['FORM_BOND', '*3', 1, '*6'],
26+
])
27+
28+
entry(
29+
index = 1,
30+
label = "Combined",
31+
group =
32+
"""
33+
1 *1 R!H u0 {2,[S,D,T]} {4,[S,D,T]}
34+
2 *2 R!H u0 {1,[S,D,T]} {3,[S]}
35+
3 *3 H u0 {2,[S]}
36+
4 *4 Xo u0 {1,[S,D,T]}
37+
38+
""",
39+
kinetics = None,
40+
)
41+
42+
entry(
43+
index = 2,
44+
label="VacantSite1",
45+
group =
46+
"""
47+
1 *5 Xv u0
48+
""",
49+
kinetics = None,
50+
)
51+
52+
entry(
53+
index = 3,
54+
label="VacantSite2",
55+
group =
56+
"""
57+
1 *6 Xv u0
58+
""",
59+
kinetics = None,
60+
)
61+
62+
63+
tree(
64+
"""
65+
L1: Combined
66+
67+
L1: VacantSite1
68+
69+
L1: VacantSite2
70+
"""
71+
)

‎input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
1+
#!/usr/bin/env python
2+
# encoding: utf-8
3+
4+
name = "Surface_Dissociation_to_Bidentate/rules"
5+
shortDesc = u""
6+
longDesc = u"""
7+
"""
8+
9+
entry(
10+
index = 1,
11+
label = "Combined;VacantSite1;VacantSite2",
12+
kinetics = SurfaceArrheniusBEP(
13+
A = (2.528E19, 'm^4/(mol^2*s)'),
14+
n = 0.698,
15+
alpha = 0.075,
16+
E0 = (11.12, 'kcal/mol'),
17+
Tmin = (200, 'K'),
18+
Tmax = (3000, 'K'),
19+
),
20+
rank = 0,
21+
shortDesc = u"""Default""",
22+
longDesc = u"""
23+
A and n factors are from the average rates of training reactions 1-3, and alpha and E0 are BEP
24+
parameters from training reactions 1-3 (in the Surface_Dissociation_to_Bidentate
25+
forward direction).
26+
The A factor has been divided by 2.33 here to account for the average degeneracy of the training reactions.
27+
"""
28+
)

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

Lines changed: 64 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,64 @@
1+
Pt_5
2+
1 *5 X u0 p0 c0
3+
4+
Pt_6
5+
1 *6 X u0 p0 c0
6+
7+
H2CCH3_X
8+
1 *1 C u0 p0 {2,S} {3,S} {4,S} {8,S}
9+
2 H u0 p0 {1,S}
10+
3 H u0 p0 {1,S}
11+
4 *2 C u0 p0 {1,S} {5,S} {6,S} {7,S}
12+
5 H u0 p0 {4,S}
13+
6 H u0 p0 {4,S}
14+
7 *3 H u0 p0 {4,S}
15+
8 *4 X u0 p0 {1,S}
16+
17+
18+
H2CCH2_2X
19+
1 *1 C u0 p0 {2,S} {3,S} {4,S} {7,S}
20+
2 H u0 p0 {1,S}
21+
3 H u0 p0 {1,S}
22+
4 *2 C u0 p0 {1,S} {5,S} {6,S} {8,S}
23+
5 H u0 p0 {4,S}
24+
6 H u0 p0 {4,S}
25+
7 *4 X u0 p0 {1,S}
26+
8 *5 X u0 p0 {4,S}
27+
28+
H_X
29+
1 *3 H u0 p0 {2,S}
30+
2 *6 X u0 p0 {1,S}
31+
32+
HCCH3_X
33+
1 *1 C u0 p0 {2,S} {3,S} {7,D}
34+
2 H u0 p0 {1,S}
35+
3 *2 C u0 p0 {1,S} {4,S} {5,S} {6,S}
36+
4 H u0 p0 {3,S}
37+
5 H u0 p0 {3,S}
38+
6 *3 H u0 p0 {3,S}
39+
7 *4 X u0 p0 {1,D}
40+
41+
HCCH2_2X
42+
1 *1 C u0 p0 {2,S} {3,S} {6,D}
43+
2 H u0 p0 {1,S}
44+
3 *2 C u0 p0 {1,S} {4,S} {5,S} {7,S}
45+
4 H u0 p0 {3,S}
46+
5 H u0 p0 {3,S}
47+
6 *4 X u0 p0 {1,D}
48+
7 *5 X u0 p0 {3,S}
49+
50+
H2COH_X
51+
1 *1 C u0 p0 {2,S} {3,S} {4,S} {6,S}
52+
2 H u0 p0 {1,S}
53+
3 H u0 p0 {1,S}
54+
4 *2 O u0 p2 {1,S} {5,S}
55+
5 *3 H u0 p0 {4,S}
56+
6 *4 X u0 p0 {1,S}
57+
58+
H2CO_2X
59+
1 *1 C u0 p0 {2,S} {3,S} {4,S} {5,S}
60+
2 H u0 p0 {1,S}
61+
3 H u0 p0 {1,S}
62+
4 *2 O u0 p2 {1,S} {6,S}
63+
5 *4 X u0 p0 {1,S}
64+
6 *5 X u0 p0 {4,S}

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

Lines changed: 66 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,66 @@
1+
#!/usr/bin/env python
2+
# encoding: utf-8
3+
4+
name = "Surface_Dissociation_to_Bidentate/training"
5+
shortDesc = u"Reaction kinetics used to generate rate rules"
6+
longDesc = u"""
7+
Put kinetic parameters for specific reactions in this file to use as a
8+
training set for generating rate rules to populate this kinetics family.
9+
"""
10+
11+
entry(
12+
index = 1,
13+
label = "H2CCH3_X + Pt_5 + Pt_6 <=> H2CCH2_2X + H_X",
14+
degeneracy = 3,
15+
kinetics = SurfaceArrhenius(
16+
A=(1.163E20, 'm^4/(mol^2*s)'),
17+
n = 0.644,
18+
Ea=(42144.629, 'J/mol'),
19+
Tmin = (298, 'K'),
20+
Tmax = (2000, 'K'),
21+
),
22+
rank = 8,
23+
shortDesc = u"""Deutschmann Ni""",
24+
longDesc = u"""
25+
Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
26+
""",
27+
metal = "Pt",
28+
)
29+
30+
entry(
31+
index = 2,
32+
label = "HCCH3_X + Pt_5 + Pt_6 <=> HCCH2_2X + H_X",
33+
degeneracy = 3,
34+
kinetics = SurfaceArrhenius(
35+
A=(2.057E20, 'm^4/(mol^2*s)'),
36+
n = 0.598,
37+
Ea=(45301.1, 'J/mol'),
38+
Tmin = (298, 'K'),
39+
Tmax = (2000, 'K'),
40+
),
41+
rank = 8,
42+
shortDesc = u"""Default""",
43+
longDesc = u"""
44+
Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
45+
""",
46+
metal = "Pt",
47+
)
48+
49+
entry(
50+
index = 3,
51+
label = "H2CO_2X + H_X <=> H2COH_X + Pt_5 + Pt_6",
52+
degeneracy = 1,
53+
kinetics = SurfaceArrhenius(
54+
A=(4.857E16, 'm^2/(mol*s)'),
55+
n = 0.063,
56+
Ea=(28353.5, 'J/mol'),
57+
Tmin = (298, 'K'),
58+
Tmax = (2000, 'K'),
59+
),
60+
rank = 8,
61+
shortDesc = u"""Default""",
62+
longDesc = u"""
63+
Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.
64+
""",
65+
metal = "Pt",
66+
)

‎input/kinetics/families/recommended.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -121,6 +121,7 @@
121121
'Surface_Adsorption_Bidentate',
122122
'Surface_Bidentate_Dissociation',
123123
'Surface_DoubleBond_to_Bidentate',
124+
'Surface_Dissociation_to_Bidentate',
124125
'Surface_vdW_to_Bidentate',
125126
'Surface_Abstraction_Single_vdW',
126127
'Surface_Adsorption_Dissociative_Double',

0 commit comments

Comments
 (0)