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WIP - Cathub kinetics #499

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86bd818
use the `surface_arrbm` py branch for tests
davidfarinajr Jun 23, 2021
cefc7b0
added cathub Pt kinetics library
davidfarinajr Jun 22, 2021
cbdfad6
added kinetics libraries for a variety of metals from cathub
davidfarinajr Jun 23, 2021
b0f5ab1
re-estimation of A factors cathub kinetics libraries
davidfarinajr Jul 14, 2021
f1249cb
added cathub training reactions
davidfarinajr Jul 20, 2021
8446261
added cathub seed mechs
davidfarinajr Jul 20, 2021
12b6e1c
added Surface_Bidentate_Dissocation autotree and rules
davidfarinajr Jul 21, 2021
0c2f197
added Surface_Dissocation autotree and rules
davidfarinajr Jul 21, 2021
035cda3
added Surface_Dissocation_vdw autotree and rules
davidfarinajr Jul 21, 2021
7d91ee8
MultiArr -> Arr for cathub reactions
davidfarinajr Jul 26, 2021
25d5b34
removed metal and facet from surface thermo group entries
davidfarinajr Jul 26, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
strategy:
max-parallel: 5
env: # update this if needed to match a pull request on the RMG-database
RMG_PY_BRANCH: main
RMG_PY_BRANCH: surface_arrbm
defaults:
run:
shell: bash -l {0}
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24 changes: 24 additions & 0 deletions input/kinetics/families/Surface_Adsorption_Bidentate/training/dictionary.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
X
1 *3 X u0 p0 c0

X-2
1 *4 X u0 p0 c0

C2H4
1 *1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 *2 C u0 p0 c0 {1,D} {5,S} {6,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}

C2H4X2
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
2 *2 C u0 p0 c0 {1,S} {5,S} {6,S} {8,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 *3 X u0 p0 c0 {1,S}
8 *4 X u0 p0 c0 {2,S}

72 changes: 72 additions & 0 deletions input/kinetics/families/Surface_Adsorption_Bidentate/training/reactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,75 @@
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 = "X + X-2 + C2H4 <=> C2H4X2",
# degeneracy = 1.0,
# kinetics = SurfaceArrhenius(A=(2.50073e+17,'m^5/(mol^2*s)'), n=0, Ea=(-0.172641,'eV/molecule'), T0=(1,'K')),
# rank = 3,
# shortDesc = """cathub_id:UmVhY3Rpb246MzM4NDg0""",
# longDesc =
# """
# Training reaction from kinetics library: Surface/cathub/Ni
# Original entry: X + C2H4 + X <=> CH2CH2X
# equation : C2H4(g) + * -> CH2CH2*,
# dft_code : Quantum ESPRESSO 5.1,
# dftFunctional : BEEF-vdW,
# pubId: HansenFirst2018,
# reactionEnergy: -0.5288464656041469 eV

# Could not determine reaction type estimating A = kb/298/h = 6.21e+12
# A/=2.483e-5 mol/m^2 (Pt111 site density)
# """,
# metal = "Ni",
# facet = "111",
# )

# entry(
# index = 2,
# label = "X + X-2 + C2H4 <=> C2H4X2",
# degeneracy = 1.0,
# kinetics = SurfaceArrhenius(A=(2.50073e+17,'m^5/(mol^2*s)'), n=0, Ea=(-0.171177,'eV/molecule'), T0=(1,'K')),
# rank = 3,
# shortDesc = """cathub_id:UmVhY3Rpb246MzM4ODQ2""",
# longDesc =
# """
# Training reaction from kinetics library: Surface/cathub/Ru
# Original entry: X + C2H4 + X <=> CH2CH2X
# equation : C2H4(g) + * -> CH2CH2*
# dft_code : Quantum ESPRESSO 5.1
# dftFunctional : BEEF-vdW
# pubId: HansenFirst2018
# reactionEnergy: -0.7945991106244037 eV

# Could not determine reaction type estimating A = kb/298/h = 6.21e+12
# A/=2.483e-5 mol/m^2 (Pt111 site density)
# """,
# metal = "Ru",
# facet = "001",
# )

# entry(
# index = 3,
# label = "X + X-2 + C2H4 <=> C2H4X2",
# degeneracy = 1.0,
# kinetics = SurfaceArrhenius(A=(2.50073e+17,'m^5/(mol^2*s)'), n=0, Ea=(-0.161351,'eV/molecule'), T0=(1,'K')),
# rank = 3,
# shortDesc = """cathub_id:UmVhY3Rpb246MzM4ODAy""",
# longDesc =
# """
# Training reaction from kinetics library: Surface/cathub/Rh
# Original entry: X + C2H4 + X <=> CH2CH2X
# equation : C2H4(g) + * -> CH2CH2*
# dft_code : Quantum ESPRESSO 5.1
# dftFunctional : BEEF-vdW
# pubId: HansenFirst2018
# reactionEnergy: -0.7351978815859184 eV

# Could not determine reaction type estimating A = kb/298/h = 6.21e+12
# A/=2.483e-5 mol/m^2 (Pt111 site density)
# """,
# metal = "Rh",
# facet = "111",
# )

149 changes: 143 additions & 6 deletions input/kinetics/families/Surface_Adsorption_Dissociative/training/dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -9,19 +9,156 @@ H2
2 *2 H u0 p0 c0 {1,S}

HX_3
1 *1 H u0 p0 {2,S}
2 *3 X u0 p0 {1,S}
1 *1 H u0 p0 c0 {2,S}
2 *3 X u0 p0 c0 {1,S}

HX_4
1 *2 H u0 p0 {2,S}
2 *4 X u0 p0 {1,S}
1 *2 H u0 p0 c0 {2,S}
2 *4 X u0 p0 c0 {1,S}

HOX_1
1 *1 O u0 p2 c0 {2,S} {3,S}
2 *3 X u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
2 H u0 p0 c0 {1,S}
3 *3 X u0 p0 c0 {1,S}

H2O
1 *1 O u0 p2 c0 {2,S} {3,S}
2 *2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}

CH4O
1 O u0 p2 c0 {2,S} {6,S}
2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3 *2 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {1,S}

CH3OX
1 O u0 p2 c0 {2,S} {5,S}
2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 *3 X u0 p0 c0 {2,S}

H3N
1 *1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 *2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}

H2NX
1 *1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 *3 X u0 p0 c0 {1,S}

CH2O2
1 O u0 p2 c0 {3,S} {5,S}
2 O u0 p2 c0 {3,D}
3 *1 C u0 p0 c0 {1,S} {2,D} {4,S}
4 *2 H u0 p0 c0 {3,S}
5 H u0 p0 c0 {1,S}

CHO2X
1 O u0 p2 c0 {3,S} {4,S}
2 O u0 p2 c0 {3,D}
3 *1 C u0 p0 c0 {1,S} {2,D} {5,S}
4 H u0 p0 c0 {1,S}
5 *3 X u0 p0 c0 {3,S}

CH2O2-2
1 *1 O u0 p2 c0 {3,S} {5,S}
2 O u0 p2 c0 {3,D}
3 C u0 p0 c0 {1,S} {2,D} {4,S}
4 H u0 p0 c0 {3,S}
5 *2 H u0 p0 c0 {1,S}

CHO2X-2
1 *1 O u0 p2 c0 {3,S} {5,S}
2 O u0 p2 c0 {3,D}
3 C u0 p0 c0 {1,S} {2,D} {4,S}
4 H u0 p0 c0 {3,S}
5 *3 X u0 p0 c0 {1,S}

CH4O-2
1 *1 O u0 p2 c0 {2,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {2,S}
6 *2 H u0 p0 c0 {1,S}

CH3OX-2
1 *1 O u0 p2 c0 {2,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {2,S}
6 *3 X u0 p0 c0 {1,S}

C2H6
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 *2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}

CH3X
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 *3 X u0 p0 c0 {1,S}

CH3X-2
1 *2 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 *4 X u0 p0 c0 {1,S}

C2H6-2
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 *2 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}

C2H5X
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 *1 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 *3 X u0 p0 c0 {2,S}

CH4
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 *2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}

C3H8
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 *2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}

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