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nyeenyee
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Fix errors in Disproportionation family
Errors found by checkWellFormed (and a few stumbled while making manual corrections). In rules.py - O2_birad named wrong, should be O2b -XH_Rrad_birad has been updated to a logic Or at some point, but not in the top most node -Same with Y_rad_birad_trirad_quadrad In groups.py -Deleted group N3_atom_quartet, which was an accidental duplicate group -deleted N5dd/H_d_Rrad, which was an accidental duplicate group -Changed atom type on N5d/H_d_Rrad, which was a typo or mistake from recent merge -Moved C_rad/H/O2 and C_rad/H/CsO appear to be placed under the wrong parent. They have been moved from under C_rad/H/NonDeN to under C_rad/H/NonDeO. -Changed Y_rad adj list, it used to be defined R-R* for some reason, but now I've made it just R*. This clears up several children errors. -Added H_rad to LogicOr of Y_rad_birad_trirad_quadrad. That one seems important. -Made group XH_Rrad more general by allowing single or double bonds. So that XH_d_Rrad is a child -Many groups do not include an N atom as possible atoms, restricting descending down to certain children. An N atom has been added to the following groups: O_Rrad, COpri_Rrad, C/H/DeDe_Rrad, C_rad/H/OneDe, C/H2/Nd_Rrad, Cmethyl_Rrad, C/H/NdDe_Rrad, Cdpri_Rrad, C/H2/De_Rrad, C/H/NdNd_Rrad, Cpri_Rrad, Csec_Rrad -Changed Ct_rad/Ct atom one from C to Ct so it is proper child -Changed an monoradical atom type from R to R!H in NH_s_Rrad, which must be true by definition. Also made same change for all children -For groups N3s/H/NonDe_s_Rrad and N3s/H/Deloc_s_Rrad, changed an atom from N to R!H based on name and consulting the creator bbuessar
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‎input/kinetics/families/Disproportionation/groups.py‎

Lines changed: 28 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@
2222
entry(
2323
index = 1,
2424
label = "Y_rad_birad_trirad_quadrad",
25-
group = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad}",
25+
group = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad, H_rad}",
2626
kinetics = None,
2727
reference = None,
2828
referenceType = "",
@@ -41,8 +41,8 @@
4141
label = "XH_Rrad",
4242
group =
4343
"""
44-
1 *2 R!H 0 {2,S} {3,S}
45-
2 *3 R!H 1 {1,S}
44+
1 *2 R!H 0 {2,{S,D}} {3,S}
45+
2 *3 R!H 1 {1,{S,D}}
4646
3 *4 H 0 {1,S}
4747
""",
4848
kinetics = None,
@@ -125,8 +125,7 @@
125125
label = "Y_rad",
126126
group =
127127
"""
128-
1 *1 R 1 {2,S}
129-
2 R 0 {1,S}
128+
1 *1 R 1
130129
""",
131130
kinetics = None,
132131
reference = None,
@@ -166,8 +165,8 @@
166165
label = "Ct_rad/Ct",
167166
group =
168167
"""
169-
1 *1 C 1 {2,T}
170-
2 C 0 {1,T}
168+
1 *1 Ct 1 {2,T}
169+
2 Ct 0 {1,T}
171170
""",
172171
kinetics = None,
173172
reference = None,
@@ -1097,7 +1096,7 @@
10971096
1 *1 C 1 {2,S} {3,S} {4,S}
10981097
2 H 0 {1,S}
10991098
3 {Cd,Ct,Cb,CO} 0 {1,S}
1100-
4 {Cs,O,S} 0 {1,S}
1099+
4 {Cs,O,S,N} 0 {1,S}
11011100
""",
11021101
kinetics = None,
11031102
reference = None,
@@ -1440,7 +1439,7 @@
14401439
group =
14411440
"""
14421441
1 *2 Cd 0 {2,S} {3,S}
1443-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
1442+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
14441443
3 *4 H 0 {1,S}
14451444
""",
14461445
kinetics = None,
@@ -1550,7 +1549,7 @@
15501549
group =
15511550
"""
15521551
1 *2 CO 0 {2,S} {3,S}
1553-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
1552+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
15541553
3 *4 H 0 {1,S}
15551554
""",
15561555
kinetics = None,
@@ -1660,7 +1659,7 @@
16601659
group =
16611660
"""
16621661
1 *2 O 0 {2,S} {3,S}
1663-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
1662+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
16641663
3 *4 H 0 {1,S}
16651664
""",
16661665
kinetics = None,
@@ -1858,7 +1857,7 @@
18581857
group =
18591858
"""
18601859
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1861-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
1860+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
18621861
3 *4 H 0 {1,S}
18631862
4 H 0 {1,S}
18641863
5 H 0 {1,S}
@@ -2002,7 +2001,7 @@
20022001
group =
20032002
"""
20042003
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2005-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2004+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
20062005
3 *4 H 0 {1,S}
20072006
4 H 0 {1,S}
20082007
5 R!H 0 {1,S}
@@ -2026,7 +2025,7 @@
20262025
group =
20272026
"""
20282027
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2029-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2028+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
20302029
3 *4 H 0 {1,S}
20312030
4 H 0 {1,S}
20322031
5 {Cs,O,S} 0 {1,S}
@@ -2146,7 +2145,7 @@
21462145
group =
21472146
"""
21482147
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2149-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2148+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
21502149
3 *4 H 0 {1,S}
21512150
4 H 0 {1,S}
21522151
5 {Cd,Ct,Cb,CO} 0 {1,S}
@@ -2266,7 +2265,7 @@
22662265
group =
22672266
"""
22682267
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2269-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2268+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
22702269
3 *4 H 0 {1,S}
22712270
4 R!H 0 {1,S}
22722271
5 R!H 0 {1,S}
@@ -2290,7 +2289,7 @@
22902289
group =
22912290
"""
22922291
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2293-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2292+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
22942293
3 *4 H 0 {1,S}
22952294
4 {Cs,O,S} 0 {1,S}
22962295
5 {Cs,O,S} 0 {1,S}
@@ -2410,7 +2409,7 @@
24102409
group =
24112410
"""
24122411
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2413-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2412+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
24142413
3 *4 H 0 {1,S}
24152414
4 {Cs,O,S} 0 {1,S}
24162415
5 {Cd,Ct,Cb,CO} 0 {1,S}
@@ -2530,7 +2529,7 @@
25302529
group =
25312530
"""
25322531
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2533-
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2532+
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
25342533
3 *4 H 0 {1,S}
25352534
4 {Cd,Ct,Cb,CO} 0 {1,S}
25362535
5 {Cd,Ct,Cb,CO} 0 {1,S}
@@ -2661,26 +2660,6 @@
26612660
],
26622661
)
26632662

2664-
entry(
2665-
index = 201,
2666-
label = "N3_atom_quartet",
2667-
group =
2668-
"""
2669-
1 *1 N3s 3
2670-
""",
2671-
kinetics = None,
2672-
reference = None,
2673-
referenceType = "",
2674-
shortDesc = u"""""",
2675-
longDesc =
2676-
u"""
2677-
2678-
""",
2679-
history = [
2680-
("Mon Nov 4 10:25:25 2013","Beat Buesser <bbuesser@mit.edu>","action","""Beat Buesser <bbuesser@mit.edu> created this value."""),
2681-
],
2682-
)
2683-
26842663
entry(
26852664
index = 202,
26862665
label = "CH_quartet",
@@ -3639,7 +3618,7 @@
36393618
group =
36403619
"""
36413620
1 *2 N 0 {2,S} {3,S}
3642-
2 *3 R 1 {1,S}
3621+
2 *3 R!H 1 {1,S}
36433622
3 *4 H 0 {1,S}
36443623
""",
36453624
kinetics = None,
@@ -3661,7 +3640,7 @@
36613640
group =
36623641
"""
36633642
1 *2 N3s 0 {2,S} {3,S}
3664-
2 *3 R 1 {1,S}
3643+
2 *3 R!H 1 {1,S}
36653644
3 *4 H 0 {1,S}
36663645
""",
36673646
kinetics = None,
@@ -3683,7 +3662,7 @@
36833662
group =
36843663
"""
36853664
1 *2 N3s 0 {2,S} {3,S} {4,S}
3686-
2 *3 R 1 {1,S}
3665+
2 *3 R!H 1 {1,S}
36873666
3 *4 H 0 {1,S}
36883667
4 H 0 {1,S}
36893668
""",
@@ -3821,7 +3800,7 @@
38213800
group =
38223801
"""
38233802
1 *2 N3s 0 {2,S} {3,S} {4,S}
3824-
2 *3 N 1 {1,S}
3803+
2 *3 R!H 1 {1,S}
38253804
3 *4 H 0 {1,S}
38263805
4 {Cs,N3s,Os} 0 {1,S}
38273806
""",
@@ -3844,7 +3823,7 @@
38443823
group =
38453824
"""
38463825
1 *2 N3s 0 {2,S} {3,S} {4,S}
3847-
2 *3 N 1 {1,S}
3826+
2 *3 R!H 1 {1,S}
38483827
3 *4 H 0 {1,S}
38493828
4 {Cd,Ct,Cb,CO} 0 {1,S}
38503829
""",
@@ -3867,7 +3846,7 @@
38673846
group =
38683847
"""
38693848
1 *2 {N5s,N5d} 0 {2,S} {3,S}
3870-
2 *3 R 1 {1,S}
3849+
2 *3 R!H 1 {1,S}
38713850
3 *4 H 0 {1,S}
38723851
""",
38733852
kinetics = None,
@@ -4276,7 +4255,7 @@
42764255
label = "N5d/H_d_Rrad",
42774256
group =
42784257
"""
4279-
1 *2 N3d 0 {2,D} {3,S}
4258+
1 *2 N5d 0 {2,D} {3,S}
42804259
2 *3 R!H 1 {1,D}
42814260
3 *4 H 0 {1,S}
42824261
""",
@@ -4292,29 +4271,7 @@
42924271
("Mon Nov 4 10:25:25 2013","Beat Buesser <bbuesser@mit.edu>","action","""Beat Buesser <bbuesser@mit.edu> created this value."""),
42934272
],
42944273
)
4295-
4296-
entry(
4297-
index = 275,
4298-
label = "N5dd/H_d_Rrad",
4299-
group =
4300-
"""
4301-
1 *2 N3d 0 {2,D} {3,S}
4302-
2 *3 R!H 1 {1,D}
4303-
3 *4 H 0 {1,S}
4304-
""",
4305-
kinetics = None,
4306-
reference = None,
4307-
referenceType = "",
4308-
shortDesc = u"""""",
4309-
longDesc =
4310-
u"""
4311-
4312-
""",
4313-
history = [
4314-
("Mon Nov 4 10:25:25 2013","Beat Buesser <bbuesser@mit.edu>","action","""Beat Buesser <bbuesser@mit.edu> created this value."""),
4315-
],
4316-
)
4317-
4274+
43184275
entry(
43194276
index = 276,
43204277
label = "XH_Rbirad",
@@ -4874,9 +4831,9 @@
48744831
L4: C_sec_rad
48754832
L5: C_rad/H/NonDeC
48764833
L5: C_rad/H/NonDeO
4877-
L5: C_rad/H/NonDeN
48784834
L6: C_rad/H/CsO
48794835
L6: C_rad/H/O2
4836+
L5: C_rad/H/NonDeN
48804837
L5: C_rad/H/NonDeS
48814838
L6: C_rad/H/CsS
48824839
L6: C_rad/H/S2
@@ -5007,8 +4964,7 @@
50074964
L5: N3d/H_d_Rrad
50084965
L6: N3d/H_d_Crad
50094966
L6: N3d/H_d_Nrad
5010-
L5: N5d/H_d_Rrad
5011-
L5: N5dd/H_d_Rrad
4967+
L5: N5d/H_d_Rrad
50124968
L2: XH_Rbirad
50134969
L3: XH_s_Rbirad
50144970
L4: CH_s_Rbirad

‎input/kinetics/families/Disproportionation/rules.py‎

Lines changed: 12 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -11,13 +11,8 @@
1111
entry(
1212
index = 485,
1313
label = "Y_rad_birad_trirad_quadrad;XH_Rrad_birad",
14-
group1 = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad}",
15-
group2 =
16-
"""
17-
1 *2 R!H 0 {2,S} {3,S}
18-
2 *3 R!H 1 {1,S}
19-
3 *4 H 0 {1,S}
20-
""",
14+
group1 = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad, H_rad}",
15+
group2 ="OR{XH_Rrad, XH_Rbirad}",
2116
kinetics = ArrheniusEP(
2217
A = (300000000000.0, 'cm^3/(mol*s)'),
2318
n = 0,
@@ -41,7 +36,7 @@
4136

4237
entry(
4338
index = 487,
44-
label = "O2_birad;Cmethyl_Csrad",
39+
label = "O2b;Cmethyl_Csrad",
4540
group1 =
4641
"""
4742
1 *1 O 1 {2,S}
@@ -715,7 +710,7 @@
715710

716711
entry(
717712
index = 501,
718-
label = "O2_birad;C/H2/Nd_Csrad",
713+
label = "O2b;C/H2/Nd_Csrad",
719714
group1 =
720715
"""
721716
1 *1 O 1 {2,S}
@@ -1295,7 +1290,7 @@
12951290

12961291
entry(
12971292
index = 513,
1298-
label = "O2_birad;C/H/NdNd_Csrad",
1293+
label = "O2b;C/H/NdNd_Csrad",
12991294
group1 =
13001295
"""
13011296
1 *1 O 1 {2,S}
@@ -1835,7 +1830,7 @@
18351830

18361831
entry(
18371832
index = 524,
1838-
label = "O2_birad;Cdpri_Csrad",
1833+
label = "O2b;Cdpri_Csrad",
18391834
group1 =
18401835
"""
18411836
1 *1 O 1 {2,S}
@@ -2261,7 +2256,7 @@
22612256

22622257
entry(
22632258
index = 533,
2264-
label = "O2_birad;O_Csrad",
2259+
label = "O2b;O_Csrad",
22652260
group1 =
22662261
"""
22672262
1 *1 O 1 {2,S}
@@ -2304,7 +2299,7 @@
23042299

23052300
entry(
23062301
index = 534,
2307-
label = "O2_birad;O_Csrad",
2302+
label = "O2b;O_Csrad",
23082303
group1 =
23092304
"""
23102305
1 *1 O 1 {2,S}
@@ -2347,7 +2342,7 @@
23472342

23482343
entry(
23492344
index = 535,
2350-
label = "O2_birad;O_Csrad",
2345+
label = "O2b;O_Csrad",
23512346
group1 =
23522347
"""
23532348
1 *1 O 1 {2,S}
@@ -3260,7 +3255,7 @@
32603255

32613256
entry(
32623257
index = 555,
3263-
label = "O2_birad;O_Csrad",
3258+
label = "O2b;O_Csrad",
32643259
group1 =
32653260
"""
32663261
1 *1 O 1 {2,S}
@@ -3326,18 +3321,13 @@
33263321

33273322
entry(
33283323
index = 556,
3329-
label = "O2_birad;XH_Rrad_birad",
3324+
label = "O2b;XH_Rrad_birad",
33303325
group1 =
33313326
"""
33323327
1 *1 O 1 {2,S}
33333328
2 O 1 {1,S}
33343329
""",
3335-
group2 =
3336-
"""
3337-
1 *2 R!H 0 {2,S} {3,S}
3338-
2 *3 R!H 1 {1,S}
3339-
3 *4 H 0 {1,S}
3340-
""",
3330+
group2 = "OR{XH_Rrad, XH_Rbirad}",
33413331
kinetics = ArrheniusEP(
33423332
A = (300000000000.0, 'cm^3/(mol*s)'),
33433333
n = 0,

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