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Hydrazine pyrolysis #296

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Hydrazine pyrolysis #296

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3b780de
Added allow_pdep_route flag to N2H3+NH2<=>N2H2+NH3
alongd Jan 27, 2019
8cbd5fe
Changed two R_Rec training rxns to the forward direction
alongd Oct 24, 2018
57e59b3
Added the HydrazinePDep kinetic library
alongd Oct 24, 2018
cc45a17
Added NxHy globally forbidden structures
alongd Oct 22, 2018
326b8f0
Modified NitrogenDean&Bozzelli
alongd Jan 28, 2019
998bf0f
Rename H2NN -> H2NN(S) throughout libraries
alongd Jan 28, 2019
fb767d9
Added NxHy thermo to primaryNS
alongd Oct 13, 2018
67d1b69
Added the 1,2 and 1,3 NH3_elimination families
alongd Oct 13, 2018
80bbc7e
Added nitrogen training reactions to H_abs
alongd Jan 28, 2019
1a974c8
Added disprop mul_bonds birad forbidden groups to H_abs
alongd Oct 13, 2018
3e91e0c
Added various NxHy rates to the primaryNitrogenLibrary
alongd Oct 13, 2018
0e575fa
Fixed Disprop training rxn H2N + H3N2 <=> H3N + H2N2-2
alongd Jan 28, 2019
14911c7
Fixed H2NN(S) structure in BurcatNS
alongd Jan 28, 2019
eea5c80
Added the OneDMinN2 transport library
alongd Dec 20, 2018
454e07a
Updated H_Abs training for NH3+H with data at the HEAT level
alongd Feb 21, 2019
d243b53
Added NH2+H2 rate at HEAT level to primaryNitrogenLibrary
alongd Feb 21, 2019
b1102b3
Added N-N(S) as a forbidden species
alongd Mar 23, 2019
ffddebf
Minor: Fixed typos in primaryNitrogenLibrary
alongd Mar 23, 2019
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91 changes: 91 additions & 0 deletions input/forbiddenStructures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,6 +190,20 @@
""",
)

entry(
label = "N-N(S)",
species =
"""
1 N u0 p2 c0 {2,S}
2 N u0 p2 c0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
This structure is not a stationary point, and should quickly become N#N
""",
)

entry(
label = "[N][N]",
species =
Expand Down Expand Up @@ -349,3 +363,80 @@
without getting negative frequency/ies.
""",
)

entry(
label = "cN3HNH2",
species =
"""
multiplicity 2
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u0 p1 c0 {1,S} {4,S} {5,S}
3 N u0 p1 c0 {1,S} {6,S} {7,S}
4 N u1 p1 c0 {1,S} {2,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {3,S}
7 H u0 p0 c0 {3,S}
""",
shortDesc = u"""""",
longDesc =
u"""
Geometry could not converge at CBS-QB3
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I trust you guys have considered the implications of these forbidden groups, but it's worth noting that an inability to converge a proper geometry doesn't mean a structure couldn't be an intermediate in a concerted reaction RMG takes multiple steps to do.

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I haven't thought about that. Does it hold even if I define a forbidden Species and not a Group?

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Forbidden species would be less risky because they only apply to that one species. The issue isn't that common, but it is worth considering as forbidding a pathway that's real could be a huge problem for someone later on.

""",
)

entry(
label = "cN3HN",
group =
"""
1 N u0 p1 c0 {2,S} {3,S} {5,S}
2 N u[0,1] p1 c0 {1,S} {3,S}
3 N u0 p0 c+1 {1,S} {2,S} {4,D}
4 N u0 p2 c-1 {3,D}
5 R ux px cx {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
Geometry of the following species in this group could not converge at CBS-QB3
[N-]=[N+]1[N]N1
[N-]=[N+]1NN1
""",
)

entry(
label = "NH3NNH",
species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,S} {4,S} {5,S} {6,S}
2 N u0 p2 c-1 {1,S} {3,S}
3 N u1 p1 c0 {2,S} {7,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {3,S}
""",
shortDesc = u"""""",
longDesc =
u"""
Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1488)
""",
)

entry(
label = "NNHNH",
species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,S} {3,D} {5,S}
2 N u0 p1 c0 {1,S} {4,D}
3 N u0 p2 c-1 {1,D}
4 N u1 p1 c0 {2,D}
5 H u0 p0 c0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1492)
""",
)
135 changes: 135 additions & 0 deletions input/kinetics/families/1,2_NH3_elimination/groups.py
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@@ -0,0 +1,135 @@
#!/usr/bin/env python
# encoding: utf-8

name = "1,2_NH3_elimination/groups"
shortDesc = u""
longDesc = u"""
This family describes reactions on a singlet PES of the sort:

NNHNH2 <=> N=N + NH3

where a terminal NH2 group and an H atom on an adjacent N are eliminated as NH3, leaving a multiple bond.

atom labeling:
*1 - the eliminated N
*2 - N adjacent to N *1, has the eliminated H *4
*3 - N adjacent to N *2
*4 - the eliminated H from N *2
"""

template(reactants=["NNHNH2"], products=["NN", "NH3"], ownReverse=False)

reverse = "1,2_NH3_addition"

reversible = True

recipe(actions=[
['FORM_BOND', '*1', 1, '*4'],
['BREAK_BOND', '*1', 1, '*2'],
['BREAK_BOND', '*2', 1, '*4'],
['GAIN_PAIR', '*2', '1'],
['LOSE_PAIR', '*3', '1'],
['CHANGE_BOND', '*2', 1, '*3'],
])

entry(
index = 0,
label = "NNHNH2",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 px cx {1,S} {4,S} {3,[S,D]}
3 *3 N u0 px cx {2,[S,D]}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "non_charged",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p1 c0 {1,S} {4,S} {3,S}
3 *3 N u0 p1 c0 {2,S}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "non_charged4",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p1 c0 {1,S} {4,S} {3,S}
3 *3 N u0 p1 c0 {2,S} {7,S}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 N ux px cx {3,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "charged",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {4,S} {3,[S,D]}
3 *3 N u0 p2 c-1 {2,[S,D]}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "chargedS",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {4,S} {3,S}
3 *3 N u0 p2 c-1 {2,S}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "chargedD",
group =
"""
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {4,S} {3,D}
3 *3 N u0 p2 c-1 {2,D}
4 *4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
""",
kinetics = None,
)

tree(
"""
L1: NNHNH2
L2: non_charged
L3: non_charged4
L2: charged
L3: chargedS
L3: chargedD
"""
)
8 changes: 8 additions & 0 deletions input/kinetics/families/1,2_NH3_elimination/rules.py
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@@ -0,0 +1,8 @@
#!/usr/bin/env python
# encoding: utf-8

name = "1,2_NH3_elimination/rules"
shortDesc = u""
longDesc = u"""

"""
73 changes: 73 additions & 0 deletions input/kinetics/families/1,2_NH3_elimination/training/dictionary.txt
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NH3
1 *1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 *4 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}

N4
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p1 c0 {1,S} {3,S} {7,S}
3 *3 N u0 p1 c0 {2,S} {4,S} {8,S}
4 N u0 p1 c0 {3,S} {9,S} {10,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 *4 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {4,S}
10 H u0 p0 c0 {4,S}

N4c
1 *1 N u0 p1 c0 {2,S} {7,S} {8,S}
2 *2 N u0 p0 c+1 {1,S} {3,S} {4,S} {5,S}
3 *4 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 *3 N u0 p2 c-1 {2,S} {6,S}
6 N u0 p1 c0 {5,S} {9,S} {10,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {6,S}
10 H u0 p0 c0 {6,S}

NH2NHN_r
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {3,S} {4,D}
3 *4 H u0 p0 c0 {2,S}
4 *3 N u0 p2 c-1 {2,D}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}

NH2NHN_p
1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *3 N u0 p0 c+1 {1,S} {3,S} {4,D}
3 H u0 p0 c0 {2,S}
4 *2 N u0 p2 c-1 {2,D}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}

NH2NNH
1 N u0 p1 c0 {2,S} {4,S} {5,S}
2 *3 N u0 p1 c0 {1,S} {3,D}
3 *2 N u0 p1 c0 {2,D} {6,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {3,S}

N2
1 *2 N u0 p1 c0 {2,T}
2 *3 N u0 p1 c0 {1,T}

N3
1 *1 N u0 p1 c0 {2,S} {4,S} {5,S}
2 *2 N u0 p1 c0 {1,S} {3,S} {6,S}
3 *3 N u0 p1 c0 {2,S} {7,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 *4 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}

H2NN(S)
1 *3 N u0 p0 c+1 {2,S} {3,S} {4,D}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 *2 N u0 p2 c-1 {1,D}
77 changes: 77 additions & 0 deletions input/kinetics/families/1,2_NH3_elimination/training/reactions.py
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#!/usr/bin/env python
# encoding: utf-8

name = "1,2_NH3_elimination/training"
shortDesc = u"Kinetics used to train group additivity values"

entry(
index = 1,
label = "N4 <=> NH3 + NH2NHN_p",
degeneracy = 2,
kinetics = Arrhenius(A=(1.31e+12, 's^-1'), n=0.78, Ea=(173.6, 'kJ/mol'),
T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K'),
comment = 'Fitted to 51 data points; dA = *|/ 2.33413, dn = +|- 0.105743, dEa = +|- 0.801565 kJ/mol'),
rank = 3,
shortDesc = u"""CCSD(T)-F12a/aug-cc-pVTZ//wB97x-D3/6-311++G(3df,3pd)""",
longDesc =
u"""
Calculated by alongd (xq1343)
opt, freq: wB97x-D3/6-311++G(3df,3pd)
sp: CCSD(T)-F12a/aug-cc-pVTZ
rotors: B3LYP/6-311++G(3df,3pd)
""",
)

entry(
index = 2,
label = "N4c <=> NH3 + NH2NNH",
degeneracy = 2,
kinetics = Arrhenius(A=(2.30e+13, 's^-1'), n=0.42, Ea=(37.1, 'kJ/mol'),
T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K'),
comment = 'Fitted to 51 data points; dA = *|/ 1.173, dn = +|- 0.0199062, dEa = +|- 0.150895 kJ/mol'),
rank = 3,
shortDesc = u"""CCSD(T)-F12a/aug-cc-pVTZ//wB97x-D3/6-311++G(3df,3pd)""",
longDesc =
u"""
Calculated by alongd (xq1344)
opt, freq: wB97x-D3/6-311++G(3df,3pd)
sp: CCSD(T)-F12a/aug-cc-pVTZ
rotors: B3LYP/6-311++G(3df,3pd)
""",
)

entry(
index = 3,
label = "NH2NHN_r <=> NH3 + N2",
degeneracy = 1,
kinetics = Arrhenius(A=(7.17e+08, 's^-1'), n=3.54, Ea=(48.2, 'kJ/mol'),
T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K'),
comment = 'Fitted to 51 data points; dA = *|/ 2.36471, dn = +|- 0.107367, dEa = +|- 0.813875 kJ/mol'),
rank = 3,
shortDesc = u"""CCSD(T)-F12a/aug-cc-pVTZ//wB97x-D3/6-311++G(3df,3pd)""",
longDesc =
u"""
Calculated by alongd (xq1444)
opt, freq: wB97x-D3/6-311++G(3df,3pd)
sp: CCSD(T)-F12a/aug-cc-pVTZ
rotors: B3LYP/6-311++G(3df,3pd)
""",
)

entry(
index = 4,
label = "N3 <=> H2NN(S) + NH3",
degeneracy = 2,
kinetics = Arrhenius(A=(2.26e+08, 's^-1'), n=1.68, Ea=(171.3, 'kJ/mol'),
T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K'),
comment = 'Fitted to 51 data points; dA = *|/ 1.13644, dn = +|- 0.0159552, dEa = +|- 0.120945 kJ/mol'),
rank = 3,
shortDesc = u"""CCSD(T)-F12a/aug-cc-pVTZ//wB97x-D3/6-311++G(3df,3pd)""",
longDesc =
u"""
Calculated by alongd (xq1457)
opt, freq: wB97x-D3/6-311++G(3df,3pd)
sp: CCSD(T)-F12a/aug-cc-pVTZ
rotors: B3LYP/6-311++G(3df,3pd)
""",
)
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