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nyeenyee
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Merge pull request #183 from ReactionMechanismGenerator/NS_updates
Nitrogen and Sulfur updates
2 parents 7ff5cd5 + e44b41a commit b0c5993

17 files changed

Lines changed: 1574 additions & 321 deletions

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‎input/kinetics/families/1,4_Linear_birad_scission/groups.py‎

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Original file line numberDiff line numberDiff line change
@@ -38,3 +38,39 @@
3838
"""
3939
)
4040

41+
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forbidden(
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label = "N2O2a",
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group =
45+
"""
46+
multiplicity [3]
47+
1 *3 O u0 p2 c0 {2,S} {3,S}
48+
2 *2 N u0 p1 c0 {1,S} {4,D}
49+
3 *4 O u1 p2 c0 {1,S}
50+
4 *1 N u1 p1 c0 {2,D}
51+
""",
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shortDesc = u"""""",
53+
longDesc =
54+
u"""
55+
N2O2 reacts in this family to form a singlet O2 (O=O)
56+
See RMG-Py issue #1020
57+
""",
58+
)
59+
60+
forbidden(
61+
label = "N2O2b",
62+
group =
63+
"""
64+
multiplicity [3]
65+
1 *2 O u0 p2 c0 {2,S} {3,S}
66+
2 *3 N u0 p1 c0 {1,S} {4,D}
67+
3 *1 O u1 p2 c0 {1,S}
68+
4 *4 N u1 p1 c0 {2,D}
69+
""",
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shortDesc = u"""""",
71+
longDesc =
72+
u"""
73+
Same as above, inverse atom labeling
74+
""",
75+
)
76+

input/kinetics/families/Oa_R_Recombination/NIST/dictionary.txt renamed to input/kinetics/families/Birad_R_Recombination/NIST/dictionary.txt

File renamed without changes.

input/kinetics/families/Oa_R_Recombination/NIST/reactions.py renamed to input/kinetics/families/Birad_R_Recombination/NIST/reactions.py

File renamed without changes.

input/kinetics/families/Oa_R_Recombination/groups.py renamed to input/kinetics/families/Birad_R_Recombination/groups.py

Lines changed: 138 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,16 @@
11
#!/usr/bin/env python
22
# encoding: utf-8
33

4-
name = "Oa_R_Recombination/groups"
4+
name = "Birad_R_Recombination/groups"
55
shortDesc = u""
66
longDesc = u"""
7-
This reaction family is reserved for O_atom (triplet only). The forbidden groups
8-
at the bottom prevent it from reacting with other forms of O.
7+
This reaction family is reserved for recombination of O_atom, S_atom, N_R_birad (triplets only).
8+
The forbidden groups at the bottom prevent it from reacting with other forms of O, S, NH.
99
"""
1010

11-
template(reactants=["Y_rad", "Oa"], products=["YO."], ownReverse=False)
11+
template(reactants=["Y_rad", "Birad"], products=["YOS."], ownReverse=False)
1212

13-
reverse = "RO_Bond_Dissociation"
13+
reverse = "ROS_Bond_Dissociation"
1414

1515
recipe(actions=[
1616
['FORM_BOND', '*1', 1, '*2'],
@@ -30,10 +30,95 @@
3030

3131
entry(
3232
index = 2,
33+
label = "Birad",
34+
group =
35+
"""
36+
1 *2 R!H u2
37+
""",
38+
kinetics = None,
39+
)
40+
41+
entry(
42+
index = 50,
3343
label = "Oa",
3444
group =
3545
"""
36-
1 *2 O u2
46+
1 *2 O u2 p2
47+
""",
48+
kinetics = None,
49+
)
50+
51+
entry(
52+
index = 51,
53+
label = "Sa",
54+
group =
55+
"""
56+
1 *2 S u2 p2
57+
""",
58+
kinetics = None,
59+
)
60+
61+
entry(
62+
index = 52,
63+
label = "N_R_birad",
64+
group =
65+
"""
66+
1 *2 N u2 p1
67+
""",
68+
kinetics = None,
69+
)
70+
71+
entry(
72+
index = 53,
73+
label = "N_birad/H",
74+
group =
75+
"""
76+
1 *2 N u2 p1 {2,S}
77+
2 H u0 p0 {1,S}
78+
""",
79+
kinetics = None,
80+
)
81+
82+
entry(
83+
index = 54,
84+
label = "N_birad/C",
85+
group =
86+
"""
87+
1 *2 N u2 p1 {2,S}
88+
2 C ux {1,S}
89+
""",
90+
kinetics = None,
91+
)
92+
93+
entry(
94+
index = 55,
95+
label = "N_birad/O",
96+
group =
97+
"""
98+
1 *2 N u2 p1 {2,S}
99+
2 O ux {1,S}
100+
""",
101+
kinetics = None,
102+
)
103+
104+
entry(
105+
index = 56,
106+
label = "N_birad/N",
107+
group =
108+
"""
109+
1 *2 N u2 p1 {2,S}
110+
2 N ux {1,S}
111+
""",
112+
kinetics = None,
113+
)
114+
115+
entry(
116+
index = 57,
117+
label = "N_birad/S",
118+
group =
119+
"""
120+
1 *2 N u2 p1 {2,S}
121+
2 S ux {1,S}
37122
""",
38123
kinetics = None,
39124
)
@@ -673,48 +758,82 @@
673758
L5: C_rad/Cs
674759
L5: C_rad/TDMustO
675760
L4: C_rad/ThreeDe
676-
L1: Oa
761+
L1: Birad
762+
L2: Oa
763+
L2: Sa
764+
L2: N_R_birad
765+
L3: N_birad/H
766+
L3: N_birad/C
767+
L3: N_birad/O
768+
L3: N_birad/N
769+
L3: N_birad/S
677770
"""
678771
)
679772

680773
forbidden(
681-
label = "O2_1centeredBirad",
774+
label = "O2_p1",
682775
group =
683776
"""
684-
1 *1 O u2 p1 {2,S}
685-
2 R u0 {1,S}
777+
1 *2 O u2 p1
686778
""",
687779
shortDesc = u"""""",
688780
longDesc =
689781
u"""
690-
782+
This family is intended to handle
783+
[O] u2 p2, or
784+
[S] u2 p2, or
785+
[NH] u2 p1,
786+
instances with a different number of lone pairs are forbidden
691787
""",
692788
)
693-
789+
694790
forbidden(
695-
label = "O2_birad",
791+
label = "S2_p1",
696792
group =
697793
"""
698-
1 *1 O u1 p2 {2,S}
699-
2 O u1 p2 {1,S}
794+
1 *2 S u2 p1
700795
""",
701796
shortDesc = u"""""",
702797
longDesc =
703798
u"""
704-
799+
This family is intended to handle
800+
[O] u2 p2, or
801+
[S] u2 p2, or
802+
[NH] u2 p1,
803+
instances with a different number of lone pairs are forbidden
705804
""",
706805
)
707-
806+
708807
forbidden(
709-
label = "O_atom_singlet",
808+
label = "S2_p0",
710809
group =
711810
"""
712-
1 *1 O u0 p3
811+
1 *2 S u2 p0
713812
""",
714813
shortDesc = u"""""",
715814
longDesc =
716815
u"""
816+
This family is intended to handle
817+
[O] u2 p2, or
818+
[S] u2 p2, or
819+
[NH] u2 p1,
820+
instances with a different number of lone pairs are forbidden
821+
""",
822+
)
717823

824+
forbidden(
825+
label = "OS_chain",
826+
group =
827+
"""
828+
1 *1 [O,S] u1 p2 {2,S}
829+
2 [O,S] u0 p2 {1,S} {3,S}
830+
3 [O,S] u0 p2 {2,S} {4,S}
831+
4 [O,S] u1 p2 {3,S}
832+
""",
833+
shortDesc = u"""""",
834+
longDesc =
835+
u"""
836+
Group added to forbid this family from forming S-O chains
718837
""",
719838
)
720839

‎input/kinetics/families/Birad_R_Recombination/rules.py‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,50 @@
1+
#!/usr/bin/env python
2+
# encoding: utf-8
3+
4+
name = "Birad_R_Recombination/rules"
5+
shortDesc = u""
6+
longDesc = u"""
7+
8+
"""
9+
entry(
10+
index = 1000,
11+
label = "Y_rad;Oa",
12+
kinetics = ArrheniusEP(
13+
A = (1e+13, 'cm^3/(mol*s)'),
14+
n = 0,
15+
alpha = 0,
16+
E0 = (0, 'kcal/mol'),
17+
Tmin = (300, 'K'),
18+
Tmax = (1500, 'K'),
19+
),
20+
rank = 2,
21+
)
22+
23+
entry(
24+
index = 2000,
25+
label = "Y_rad;Sa",
26+
kinetics = ArrheniusEP(
27+
A = (1e+13, 'cm^3/(mol*s)'),
28+
n = 0,
29+
alpha = 0,
30+
E0 = (0, 'kcal/mol'),
31+
Tmin = (300, 'K'),
32+
Tmax = (1500, 'K'),
33+
),
34+
rank = 2,
35+
)
36+
37+
entry(
38+
index = 2000,
39+
label = "Y_rad;N_R_birad",
40+
kinetics = ArrheniusEP(
41+
A = (1e+13, 'cm^3/(mol*s)'),
42+
n = 0,
43+
alpha = 0,
44+
E0 = (0, 'kcal/mol'),
45+
Tmin = (300, 'K'),
46+
Tmax = (1500, 'K'),
47+
),
48+
rank = 2,
49+
)
50+

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

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,57 @@
1+
O
2+
multiplicity 3
3+
1 *2 O u2 p2 c0
4+
5+
S
6+
multiplicity 3
7+
1 *2 S u2 p2 c0
8+
9+
NH
10+
multiplicity 3
11+
1 *2 N u2 p1 c0 {2,S}
12+
2 H u0 p0 c0 {1,S}
13+
14+
HSO
15+
multiplicity 2
16+
1 S u0 p2 c0 {2,S} {3,S}
17+
2 *1 O u1 p2 c0 {1,S}
18+
3 H u0 p0 c0 {1,S}
19+
20+
HSOO
21+
multiplicity 2
22+
1 S u0 p2 c0 {2,S} {4,S}
23+
2 *1 O u0 p2 c0 {1,S} {3,S}
24+
3 *2 O u1 p2 c0 {2,S}
25+
4 H u0 p0 c0 {1,S}
26+
27+
NO
28+
multiplicity 2
29+
1 *1 N u1 p1 c0 {2,D}
30+
2 O u0 p2 c0 {1,D}
31+
32+
NO2_p
33+
multiplicity 2
34+
1 *1 N u0 p1 c0 {2,D} {3,S}
35+
2 O u0 p2 c0 {1,D}
36+
3 *2 O u1 p2 c0 {1,S}
37+
38+
NO2_r
39+
multiplicity 2
40+
1 O u0 p2 c0 {2,D}
41+
2 *1 N u1 p0 c+1 {1,D} {3,S}
42+
3 O u0 p3 c-1 {2,S}
43+
44+
HNNO2
45+
multiplicity 2
46+
1 *2 N u1 p1 c0 {2,S} {3,S}
47+
2 H u0 p0 c0 {1,S}
48+
3 *1 N u0 p0 c+1 {1,S} {4,S} {5,D}
49+
4 O u0 p3 c-1 {3,S}
50+
5 O u0 p2 c0 {3,D}
51+
52+
SNO
53+
multiplicity 2
54+
1 *2 S u1 p2 c0 {2,S}
55+
2 *1 N u0 p1 c0 {1,S} {3,D}
56+
3 O u0 p2 c0 {2,D}
57+

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