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mjohnson541nyee
mjohnson541
authored and
nyee
committed
intra_H_mirgration accessibility
-general rearrangements to meet accessibility tests -combined two group branches of rough form R2=R1(R3)H that had separate branches for R2 and R3 -moved Cs_H_out_OOH/H to be under the Cs_H_out_OOH group rather than the Cs_H_out_H/NonDeO -Added T bonds to R2H, which is the sampleBackbone. Previously when merged with a *2 Ct.
1 parent a6033b9 commit b141932

2 files changed

Lines changed: 38 additions & 67 deletions

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‎input/kinetics/families/intra_H_migration/groups.py‎

Lines changed: 31 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -58,8 +58,8 @@
5858
label = "R2H",
5959
group =
6060
"""
61-
1 *1 R!H u1 {2,[S,D,B]}
62-
2 *2 R!H u0 {1,[S,D,B]} {3,S}
61+
1 *1 R!H u1 {2,[S,D,T,B]}
62+
2 *2 R!H u0 {1,[S,D,T,B]} {3,S}
6363
3 *3 H u0 {2,S}
6464
""",
6565
kinetics = None,
@@ -2945,17 +2945,6 @@
29452945
kinetics = None,
29462946
)
29472947

2948-
entry(
2949-
index = 190,
2950-
label = "Cd_rad_out_double",
2951-
group =
2952-
"""
2953-
1 *1 Cd u1 {2,D}
2954-
2 [Cd,Cdd] u0 {1,D}
2955-
""",
2956-
kinetics = None,
2957-
)
2958-
29592948
entry(
29602949
index = 191,
29612950
label = "Cd_rad_out_single",
@@ -3005,8 +2994,7 @@
30052994
label = "Ct_rad_out",
30062995
group =
30072996
"""
3008-
1 *1 Ct u1 {2,T}
3009-
2 Ct u0 {1,T}
2997+
1 *1 Ct u1
30102998
""",
30112999
kinetics = None,
30123000
)
@@ -3016,8 +3004,7 @@
30163004
label = "Cb_rad_out",
30173005
group =
30183006
"""
3019-
1 *1 Cb u1 {2,B}
3020-
2 [Cb,Cbf] u0 {1,B}
3007+
1 *1 Cb u1
30213008
""",
30223009
kinetics = None,
30233010
)
@@ -3427,20 +3414,6 @@
34273414
kinetics = None,
34283415
)
34293416

3430-
entry(
3431-
index = 232,
3432-
label = "Cs_H_out_2H/NonDeC",
3433-
group =
3434-
"""
3435-
1 *2 Cs u0 {2,S} {3,S} {4,S} {5,S}
3436-
2 *3 H u0 {1,S}
3437-
3 Cs u0 {1,S}
3438-
4 H u0 {1,S}
3439-
5 H u0 {1,S}
3440-
""",
3441-
kinetics = None,
3442-
)
3443-
34443417
entry(
34453418
index = 233,
34463419
label = "Cs_H_out_1H",
@@ -3913,10 +3886,6 @@
39133886
L3: R3H
39143887
L4: R3H_SR
39153888
L5: R3H_SS
3916-
L6: R3H_SS_2Cd
3917-
L6: R3H_SS_O
3918-
L6: R3H_SS_Cs
3919-
L6: R3H_SS_S
39203889
L6: R3H_SS_12cy3
39213890
L6: R3H_SS_23cy3
39223891
L6: R3H_SS_13cy4
@@ -3925,6 +3894,10 @@
39253894
L6: R3H_SS_13cy5
39263895
L6: R3H_SS_12cy5
39273896
L6: R3H_SS_23cy5
3897+
L6: R3H_SS_2Cd
3898+
L6: R3H_SS_O
3899+
L6: R3H_SS_Cs
3900+
L6: R3H_SS_S
39283901
L5: R3H_SD
39293902
L5: R3H_ST
39303903
L5: R3H_SB
@@ -4093,7 +4066,6 @@
40934066
L2: O_rad_out
40944067
L2: S_rad_out
40954068
L2: Cd_rad_out
4096-
L3: Cd_rad_out_double
40974069
L3: Cd_rad_out_single
40984070
L4: Cd_rad_out_singleH
40994071
L4: Cd_rad_out_singleNd
@@ -4103,12 +4075,6 @@
41034075
L2: CO_rad_out
41044076
L2: CS_rad_out
41054077
L2: C_rad_out_single
4106-
L3: C_rad_out_2H
4107-
L3: C_rad_out_1H
4108-
L4: C_rad_out_H/NonDeC
4109-
L4: C_rad_out_H/NonDeO
4110-
L4: C_rad_out_H/NonDeS
4111-
L4: C_rad_out_H/OneDe
41124078
L3: C_rad_out_noH
41134079
L4: C_rad_out_NonDe
41144080
L5: C_rad_out_Cs2
@@ -4121,6 +4087,12 @@
41214087
L5: C_rad_out_OneDe/O
41224088
L5: C_rad_out_OneDe/S
41234089
L4: C_rad_out_TwoDe
4090+
L3: C_rad_out_1H
4091+
L4: C_rad_out_H/NonDeC
4092+
L4: C_rad_out_H/NonDeO
4093+
L4: C_rad_out_H/NonDeS
4094+
L4: C_rad_out_H/OneDe
4095+
L3: C_rad_out_2H
41244096
L1: XH_out
41254097
L2: CO_H_out
41264098
L2: O_H_out
@@ -4134,22 +4106,9 @@
41344106
L3: Cd_H_out_singleNd
41354107
L3: Cd_H_out_singleDe
41364108
L2: Cs_H_out
4137-
L3: Cs_H_out_2H
4138-
L4: Cs_H_out_2H/NonDeC
4139-
L3: Cs_H_out_1H
4140-
L4: Cs_H_out_H/NonDeC
4141-
L5: Cs_H_out_H/(NonDeC/Cs)
4142-
L6: Cs_H_out_H/(NonDeC/Cs/Cs)
4143-
L7: Cs_H_out_H/(NonDeC/Cs/Cs/Cs)
4144-
L5: Cs_H_out_H/(NonDeC/O)
4145-
L4: Cs_H_out_H/NonDeO
4146-
L5: Cs_H_out_OOH/H
4147-
L4: Cs_H_out_H/NonDeS
4148-
L4: Cs_H_out_H/OneDe
4149-
L5: Cs_H_out_H/Ct
4150-
L5: Cs_H_out_H/CO
4151-
L5: Cs_H_out_H/CS
4152-
L5: Cs_H_out_H/Cd
4109+
L3: Cs_H_out_OOH
4110+
L4: Cs_H_out_OOH/Cs
4111+
L4: Cs_H_out_OOH/H
41534112
L3: Cs_H_out_noH
41544113
L4: Cs_H_out_NonDe
41554114
L5: Cs_H_out_Cs2
@@ -4166,8 +4125,20 @@
41664125
L5: Cs_H_out_CtCt
41674126
L5: Cs_H_out_CdCt
41684127
L5: Cs_H_out_CdCd
4169-
L3: Cs_H_out_OOH
4170-
L4: Cs_H_out_OOH/Cs
4128+
L3: Cs_H_out_1H
4129+
L4: Cs_H_out_H/NonDeC
4130+
L5: Cs_H_out_H/(NonDeC/Cs)
4131+
L6: Cs_H_out_H/(NonDeC/Cs/Cs)
4132+
L7: Cs_H_out_H/(NonDeC/Cs/Cs/Cs)
4133+
L5: Cs_H_out_H/(NonDeC/O)
4134+
L4: Cs_H_out_H/NonDeO
4135+
L4: Cs_H_out_H/NonDeS
4136+
L4: Cs_H_out_H/OneDe
4137+
L5: Cs_H_out_H/Ct
4138+
L5: Cs_H_out_H/CO
4139+
L5: Cs_H_out_H/CS
4140+
L5: Cs_H_out_H/Cd
4141+
L3: Cs_H_out_2H
41714142
"""
41724143
)
41734144

‎input/kinetics/families/intra_H_migration/rules.py‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -628,7 +628,7 @@
628628

629629
entry(
630630
index = 645,
631-
label = "R2H_S;Cd_rad_out_double;Cs_H_out_2H",
631+
label = "R2H_S;Cd_rad_out;Cs_H_out_2H",
632632
kinetics = ArrheniusEP(
633633
A = (2.44e+09, 's^-1'),
634634
n = 1.12,
@@ -666,7 +666,7 @@
666666

667667
entry(
668668
index = 647,
669-
label = "R2H_S;Cd_rad_out_double;Cs_H_out_H/OneDe",
669+
label = "R2H_S;Cd_rad_out;Cs_H_out_H/OneDe",
670670
kinetics = ArrheniusEP(
671671
A = (7.24e+09, 's^-1'),
672672
n = 0.82,
@@ -704,7 +704,7 @@
704704

705705
entry(
706706
index = 649,
707-
label = "R2H_S;Cd_rad_out_double;Cs_H_out_OneDe",
707+
label = "R2H_S;Cd_rad_out;Cs_H_out_OneDe",
708708
kinetics = ArrheniusEP(
709709
A = (1.67e+10, 's^-1'),
710710
n = 0.79,
@@ -1939,7 +1939,7 @@
19391939

19401940
entry(
19411941
index = 715,
1942-
label = "R3H_SS;Cd_rad_out_double;Cs_H_out_2H",
1942+
label = "R3H_SS;Cd_rad_out;Cs_H_out_2H",
19431943
kinetics = ArrheniusEP(
19441944
A = (7.68e+08, 's^-1'),
19451945
n = 1.24,
@@ -1977,7 +1977,7 @@
19771977

19781978
entry(
19791979
index = 717,
1980-
label = "R3H_SS;Cd_rad_out_double;Cs_H_out_H/NonDeC",
1980+
label = "R3H_SS;Cd_rad_out;Cs_H_out_H/NonDeC",
19811981
kinetics = ArrheniusEP(
19821982
A = (1.66e+09, 's^-1'),
19831983
n = 0.99,
@@ -2015,7 +2015,7 @@
20152015

20162016
entry(
20172017
index = 719,
2018-
label = "R3H_SS;Cd_rad_out_double;Cs_H_out_Cs2",
2018+
label = "R3H_SS;Cd_rad_out;Cs_H_out_Cs2",
20192019
kinetics = ArrheniusEP(
20202020
A = (1.1e+10, 's^-1'),
20212021
n = 0.78,
@@ -4317,7 +4317,7 @@
43174317

43184318
entry(
43194319
index = 871,
4320-
label = "R4H_SDS;Cd_rad_out_double;Cs_H_out_2H",
4320+
label = "R4H_SDS;Cd_rad_out;Cs_H_out_2H",
43214321
kinetics = ArrheniusEP(
43224322
A = (1.11e+08, 's^-1'),
43234323
n = 1.1915,

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