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RMG-database v2.1.9 release
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mliu49 committed May 15, 2018
2 parents 7ca5cca + 28e7df3 commit 68b5ec3
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Showing 41 changed files with 33,937 additions and 1,313 deletions.
145 changes: 136 additions & 9 deletions input/forbiddenStructures.py
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@

entry(
label = "C_quintet",
group =
molecule =
"""
1 C u4 p0
""",
Expand Down Expand Up @@ -483,9 +483,9 @@

entry(
label = "CO_birad",
group =
species =
"""
multiplicity [3]
multiplicity 3
1 C u2 p0 c0 {2,D}
2 O u0 p2 c0 {1,D}
""",
Expand All @@ -501,9 +501,9 @@

entry(
label = "CS_birad",
group =
species =
"""
multiplicity [3]
multiplicity 3
1 C u2 p0 c0 {2,D}
2 S u0 p2 c0 {1,D}
""",
Expand All @@ -519,15 +519,142 @@

entry(
label = "[N][N]",
group =
species =
"""
multiplicity [5]
1 N u2 p0 c0 {2,S}
2 N u2 p0 c0 {1,S}
multiplicity 5
1 N u2 p1 c0 {2,S}
2 N u2 p1 c0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
N#N can be excited to [N]=[N], but we shouldn't allow it to reach [N][N]
""",
)

entry(
label = "SOO2",
species =
"""
multiplicity 3
1 S u0 p2 c0 {2,S} {3,S}
2 O u0 p2 c0 {1,S} {4,S}
3 O u1 p2 c0 {1,S}
4 O u1 p2 c0 {2,S}
""",
shortDesc = u"""""",
longDesc =
u"""
The SO--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable SO--OO bond length),
yet it is predicted by RMG, e.g, by R_Recombination of [S][O] and [O][O].
Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 S u1 p1 c0 {2,S} {3,D}
2 O u0 p2 c0 {1,S} {4,S}
3 O u0 p2 c0 {1,D}
4 O u1 p2 c0 {2,S}
""",
)

entry(
label = "SO2O2",
species =
"""
multiplicity 3
1 S u0 p1 c0 {2,S} {3,S} {4,D}
2 O u0 p2 c0 {1,S} {5,S}
3 O u1 p2 c0 {1,S}
4 O u0 p2 c0 {1,D}
5 O u1 p2 c0 {2,S}
""",
shortDesc = u"""""",
longDesc =
u"""
The SO2--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable O2S--OO bond length),
yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of O=S=O and [O][O].
Also, it is described as a TS in doi: 10.1021/jp067499p (Fig. 1 structure 5, Fig. 2)
Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 S u1 p0 c0 {2,S} {3,D} {4,D}
2 O u0 p2 c0 {1,S} {5,S}
3 O u0 p2 c0 {1,D}
4 O u0 p2 c0 {1,D}
5 O u1 p2 c0 {2,S}
""",
)

entry(
label = "S2O2",
species =
"""
multiplicity 3
1 O u0 p2 c0 {2,S} {3,S}
2 S u0 p2 c0 {1,S} {4,S}
3 O u1 p2 c0 {1,S}
4 S u1 p2 c0 {2,S}
""",
shortDesc = u"""""",
longDesc =
u"""
The S2--O2 complex isn't a sable species (has an imaginary frequency),
yet it is predicted by RMG, e.g, by R_Recombination of [S][S] and [O][O].
Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 O u0 p2 c0 {2,S} {3,S}
2 S u1 p1 c0 {1,S} {4,D}
3 O u1 p2 c0 {1,S}
4 S u0 p2 c0 {2,D}
""",
)

entry(
label = "N2SH",
species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,D} {3,D}
2 S u1 p1 c0 {1,D} {4,S}
3 N u0 p2 c-1 {1,D}
4 H u0 p0 c0 {2,S}
""",
shortDesc = u"""""",
longDesc =
u"""
The S2--SH complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable NN--SH bond length),
yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of [SH] to N#N.
Other resonance structures of it which are forbidden as well via this entry are:
multiplicity 2
1 N u0 p1 c0 {2,S} {3,D}
2 S u0 p2 c0 {1,S} {4,S}
3 N u1 p1 c0 {1,D}
4 H u0 p0 c0 {2,S}
multiplicity 2
1 N u1 p0 c+1 {2,S} {3,D}
2 S u0 p2 c0 {1,S} {4,S}
3 N u0 p2 c-1 {1,D}
4 H u0 p0 c0 {2,S}
""",
)

entry(
label = "SO3(T)",
species =
"""
multiplicity 3
1 O u0 p2 c0 {2,D}
2 S u1 p0 c0 {1,D} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 O u1 p2 c0 {2,S}
""",
shortDesc = u"""""",
longDesc =
u"""
The geometry of SO3(T) could not be stabilized at either B3LYP/6-311G(2d,d,p) nor M06-2x
without getting negative frequency/ies.
""",
)
37 changes: 0 additions & 37 deletions input/kinetics/families/1,4_Linear_birad_scission/groups.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,40 +37,3 @@
L1: RJJ
"""
)


forbidden(
label = "N2O2a",
group =
"""
multiplicity [3]
1 *3 O u0 p2 c0 {2,S} {3,S}
2 *2 N u0 p1 c0 {1,S} {4,D}
3 *4 O u1 p2 c0 {1,S}
4 *1 N u1 p1 c0 {2,D}
""",
shortDesc = u"""""",
longDesc =
u"""
N2O2 reacts in this family to form a singlet O2 (O=O)
See RMG-Py issue #1020
""",
)

forbidden(
label = "N2O2b",
group =
"""
multiplicity [3]
1 *2 O u0 p2 c0 {2,S} {3,S}
2 *3 N u0 p1 c0 {1,S} {4,D}
3 *1 O u1 p2 c0 {1,S}
4 *4 N u1 p1 c0 {2,D}
""",
shortDesc = u"""""",
longDesc =
u"""
Same as above, inverse atom labeling
""",
)

Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,9 @@
degeneracy = 1,
kinetics = Arrhenius(A=(1.42e+16, 'cm^3/(mol*s)'), n=-0.75, Ea=(1226, 'cal/mol'), T0=(1, 'K')),
rank = 3,
shortDesc = u"""Training reaction from kinetics library: SOxNOx""",
shortDesc = u"""Training reaction from kinetics library: primaryNitrogenLibrary""",
longDesc =
u"""
Part of the "NOx" subset
T range: 500-3000 K
calculations done at the B3LYP/6-311D(d,p)//B3LYP/6-311D(d,p) level of theory
D. Chakraborty, C.C. Hsu, M.C. Lin, J. Chem. Phys., 1998, 109, 8887, doi: 10.1063/1.477560
Expand All @@ -32,7 +31,7 @@
degeneracy = 1,
kinetics = Arrhenius(A=(1.3e+14, 'cm^3/(mol*s)'), n=0.24, Ea=(0, 'cal/mol'), T0=(1, 'K'), Tmin = (300, 'K'), Tmax = (800, 'K')),
rank = 1,
shortDesc = u"""Training reaction from kinetics library: SOxNOx""",
shortDesc = u"""Training reaction from kinetics library: N-S_interactions""",
longDesc =
u"""
A. Goumri, D.D. Shao, P. Marshall, J. Chem. Phys., 2004, 121, 9999, doi: 10.1063/1.1806419
Expand All @@ -54,7 +53,7 @@
# degeneracy = 1,
# kinetics = Arrhenius(A=(2.01e+19, 's^-1'), n=-1.07, Ea=(28377, 'cal/mol'), T0=(1, 'K'), Tmin = (200, 'K'), Tmax = (2000, 'K')),
# rank = 2,
# shortDesc = u"""Training reaction from kinetics library: SOx""",
# shortDesc = u"""Training reaction from kinetics library: primarySulfurLibrary""",
# longDesc =
#u"""
#T range: 200-2000 K
Expand All @@ -71,7 +70,7 @@
degeneracy = 1,
kinetics = Arrhenius(A=(3.98e+14, 's^-1'), n=0, Ea=(71700, 'cal/mol'), T0=(1, 'K'), Tmin = (1350, 'K'), Tmax = (2100, 'K')),
rank = 1,
shortDesc = u"""Training reaction from kinetics library: SOx""",
shortDesc = u"""Training reaction from kinetics library: primarySulfurLibrary""",
longDesc =
u"""
T range: 1350-2100 K
Expand Down
81 changes: 77 additions & 4 deletions input/kinetics/families/H_Abstraction/groups.py
Original file line number Diff line number Diff line change
Expand Up @@ -7056,6 +7056,28 @@
kinetics = None,
)

entry(
index = 442,
label = "Cl_rad",
group =
"""
1 *3 Cl1s u1
""",
kinetics = None,
)

entry(
index = 443,
label = "HCl",
group =
"""
1 *1 Cl1s u0 {2,S}
2 *2 H u0 {1,S}
""",
kinetics = None,
)


tree(
"""
L1: X_H_or_Xrad_H_Xbirad_H_Xtrirad_H
Expand Down Expand Up @@ -7329,6 +7351,7 @@
L3: N5_H
L4: N5dc_H
L5: N5dc/H/NonDeOO
L3: HCl
L1: Y_rad_birad_trirad_quadrad
L2: Y_1centerquadrad
L3: C_quintet
Expand Down Expand Up @@ -7584,20 +7607,70 @@
L7: N3d_rad/OneDeCdd_O
L3: N5_rad
L4: N5dc_rad
L3: Cl_rad
"""
)

forbidden(
label = "disprop1",
label = "disprop1_base_case",
group =
"""
1 *1 R u0 {2,S} {3,S}
2 C u1 {1,S}
3 *2 H u0 {1,S}
1 *1 R u0 {2,S} {3,S}
2 [C,N] u1 {1,S}
3 *2 H u0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
Generally, we'd like to forbid `HR[R].` from reacting here (`.` marks a radical), since this is a disprop reaction.
However, the following specific cases must not be forbidden here: `HO2`, `HSS`, `HOS`, `HSO`
(since they form the ground state triplets O2, S2, and SO).
This group forbids `HR[C,N].`, where the radical site isn't O or S
""",
)

forbidden(
label = "disprop1_OS_rad",
group =
"""
1 *1 [C,N] u0 {2,S} {3,S}
2 [O,S] u1 {1,S}
3 *2 H u0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
This group forbids `H[C,N][O,S].`, where the radical site is O or S, but the non-rad site isn't
""",
)

forbidden(
label = "disprop1_hyperS_H",
group =
"""
1 *1 S u0 p[0,1] {2,S} {3,S}
2 [O,S] u1 {1,S}
3 *2 H u0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
This group forbids `H[S p0,1][O,S].`, where hypervalance S is allowed at the H site
""",
)

forbidden(
label = "disprop1_hyperS_rad",
group =
"""
1 *1 [O,S] u0 {2,S} {3,S}
2 S u1 p[0,1] {1,S}
3 *2 H u0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""
This group forbids `H[O,S][S p0,1].`, where hypervalance S is allowed at the rad site
""",
)

Expand Down
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