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Enhancing heteroatoms in RMG-database #194

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8601ece
Replaced Ss and Sd with S2s and S2d
alongd Apr 20, 2017
1992dd6
Minor: filled in citation data in intra_H_migration training reactions
alongd Jun 2, 2017
6378231
Added the SOxNOx kinetic and thermo libraries
alongd Mar 9, 2017
926b11a
Added the Low T SOxNOx sub-library
alongd Apr 28, 2017
79df70e
Added the Sulfur Glarborg-Bozzelli kinetic and thermo libraries
alongd Jan 26, 2017
33e9c8c
Added the Sulfur GlarborgMarshall kinetic and thermo libraries
alongd Jan 28, 2017
2148a1d
Added the Sulfur GlarborgNS kinetic and thermo libraries
alongd Jan 30, 2017
26690a3
Added the Sulfur GlarborgH2S kinetic and thermo libraries
alongd Feb 1, 2017
3dd3ceb
Added the BurcatNS thermo library
alongd Mar 31, 2017
5ce890b
Added a training reaction to Disprop family
alongd Apr 20, 2017
13ba645
Added training reactions to R_Addition_MultipleBond from SOxNOx library
alongd Apr 20, 2017
0bd8729
Added training reactions to R_Recombination from SOxNOx library
alongd May 11, 2017
d445c39
Added training reactions to H_Abstraction from SOxNOx library
alongd May 11, 2017
9f790e4
Solvation sulfur-related thermo groups changes (abraham.py, nonacente…
alongd Apr 21, 2017
e22bdab
Radical corrections for several sulfur oxygenated groups
alongd Apr 26, 2017
02a9954
Sulfur/Oxygen Extension to Thermo GAV
rgillis8 May 2, 2017
7a8dcca
Thermo GAV tree modifications so that adjacent sulfur atoms are match…
rgillis8 May 8, 2017
8bdf525
Added sulfur groups to 1+2_Cycloaddition Family
alongd May 17, 2017
9d93472
Added sulfur groups to 1,2-Birad_to_alkene Family
alongd May 17, 2017
0e50b76
Added sulfur groups to 1,2_Insertion_carbene Family
alongd May 18, 2017
a2e8cbc
Added sulfur groups to 1,2_Insertion_CO Family
alongd May 18, 2017
c1ec4f0
Added sulfur groups to 1,2_shiftS Family
alongd May 18, 2017
f0a290a
Added sulfur groups to 1,3_Insertion_CO2 Family
alongd May 18, 2017
e36fe75
Added sulfur groups to 1,3_Insertion_ROR Family
alongd May 18, 2017
9aa185c
Added sulfur groups to 1,3_Insertion_RSR Family
alongd May 18, 2017
87dc6f6
Added sulfur groups to 2+2_cycloaddition_CCO Family
alongd May 18, 2017
9e4a485
Added sulfur groups to 2+2_cycloaddition_Cd Family
alongd May 18, 2017
18c6d8c
Added sulfur groups to 2+2_cycloaddition_CO Family
alongd May 19, 2017
99ebad8
Added the 2+2_cycloaddition_CS Family
alongd May 19, 2017
ae9b10c
Additions to reccomended.py:
alongd May 19, 2017
d21a18f
Added sulfur groups to Birad_R_Recombination Family
alongd May 19, 2017
681af4e
Added sulfur groups to Birad_recombination Family
alongd May 19, 2017
b6cc164
Added sulfur groups to CO_Disprop Family
alongd May 19, 2017
20a555f
Added sulfur groups to Cyclic_Ether_Formation Family
alongd Jun 2, 2017
34bec85
Added the Cyclic_Thioether_Formation family
alongd Jun 1, 2017
7407961
Added sulfur groups to Diels_alder_addition Family
alongd May 19, 2017
a388321
Added sulfur groups to Disproportionation Family
alongd Apr 20, 2017
b856469
Added sulfur groups to H_Abstraction Family
alongd May 18, 2017
cb2c7c0
Added sulfur groups to HO2_Elimination_from_PeroxyRadical Family
alongd May 20, 2017
c4ba9d9
Added sulfur groups to Intra_Disproportionation Family
alongd May 20, 2017
86c16b2
Added CH3NO2 group to intra_NO2_ONO_conversion Family
alongd Apr 20, 2017
13b9140
Added sulfur groups to intra_OH_migration Family
alongd May 20, 2017
27c2aa5
Added sulfur groups to Intra_R_Add_Endocyclic Family
alongd May 20, 2017
13ecb2e
Added sulfur groups to Intra_R_Add_Exocyclic Family
alongd May 20, 2017
69d20a3
Added sulfur groups to Intra_R_Add_ExoTetCyclic Family
alongd May 20, 2017
61d64c6
Added sulfur groups to Intra_RH_Add_Endocyclic Family
alongd May 20, 2017
504219d
Added sulfur groups to Intra_RH_Add_Exocyclic Family
alongd May 20, 2017
a001782
Added sulfur groups to intra_substitutionCS_cyclization Family
alongd May 20, 2017
9c9d346
Added sulfur groups to intra_substitutionCS_isomerization Family
alongd May 20, 2017
d6aa641
Added sulfur groups to intra_subsitutionS_cyclization Family
alongd May 20, 2017
6f70160
Added sulfur groups to intra_substitutionS_isomerization Family
alongd May 20, 2017
06a9d44
Added sulfur group to ketoenol Family
alongd May 20, 2017
f693fce
Added sulfur groups to R_Addition_COm Family
alongd May 20, 2017
f748cf8
Added sulfur groups to R_Addition_CSm Family
alongd May 21, 2017
94b7587
Added sulfur groups to R_Recombination Family
alongd Apr 20, 2017
6ec6b2b
Added sulfur groups to R_Addition_Multiple_Bond Family
alongd May 10, 2017
b477e47
Added sulfur groups to Substitution_O Family
alongd May 21, 2017
864ab3b
Added sulfur groups to Substitution_S Family
alongd May 31, 2017
92a2d9c
Addition to SulfurGAV
rgillis8 Jul 6, 2017
5c661d3
Addition to radical corrections for SulfurGAV
rgillis8 Jul 6, 2017
12168df
Further Additions to SulfurGAVs
rgillis8 Jul 10, 2017
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Added sulfur groups to intra_OH_migration Family
  • Loading branch information
alongd committed Jul 5, 2017
commit 13b914055d9815273a60e942fedc274a0e56f6a9
116 changes: 59 additions & 57 deletions input/kinetics/families/intra_OH_migration/groups.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
name = "intra_OH_migration/groups"
shortDesc = u""
longDesc = u"""

Sulfur was added to this family, and is treated the same as oxygen.
Ideally we would like to branch this into a new family "intra_SH_migration"
once relevant kinetic data is available
"""

template(reactants=["RnOOH"], products=["HORO."], ownReverse=False)
Expand Down Expand Up @@ -43,8 +45,8 @@
group =
"""
1 *1 [C,Sid,Sis,N] u1 {2,S}
2 *2 O u0 {1,S} {3,S}
3 *3 O u0 {2,S} {4,S}
2 *2 [O,S] u0 {1,S} {3,S}
3 *3 [O,S] u0 {2,S} {4,S}
4 H u0 {3,S}
""",
kinetics = None,
Expand All @@ -57,8 +59,8 @@
"""
1 *1 [C,Sid,Sis,N] u1 {2,[S,D]}
2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,S}
3 *2 O u0 {2,S} {4,S}
4 *3 O u0 {3,S} {5,S}
3 *2 [O,S] u0 {2,S} {4,S}
4 *3 [O,S] u0 {3,S} {5,S}
5 H u0 {4,S}
""",
kinetics = None,
Expand All @@ -71,8 +73,8 @@
"""
1 *1 [C,Sid,Sis,N] u1 {2,S}
2 *4 [Cs,Cd] u0 {1,S} {3,S}
3 *2 O u0 {2,S} {4,S}
4 *3 O u0 {3,S} {5,S}
3 *2 [O,S] u0 {2,S} {4,S}
4 *3 [O,S] u0 {3,S} {5,S}
5 H u0 {4,S}
""",
kinetics = None,
Expand All @@ -85,8 +87,8 @@
"""
1 *1 [C,Sid,Sis,N] u1 {2,D}
2 *4 Cd u0 {1,D} {3,S}
3 *2 O u0 {2,S} {4,S}
4 *3 O u0 {3,S} {5,S}
3 *2 [O,S] u0 {2,S} {4,S}
4 *3 [O,S] u0 {3,S} {5,S}
5 H u0 {4,S}
""",
kinetics = None,
Expand All @@ -100,8 +102,8 @@
1 *1 [C,Sid,Sis,N] u1 {2,[S,D]}
2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
3 *5 [Cs,Cd,Sid,Sis,N] u0 {2,[S,D]} {4,S}
4 *2 O u0 {3,S} {5,S}
5 *3 O u0 {4,S} {6,S}
4 *2 [O,S] u0 {3,S} {5,S}
5 *3 [O,S] u0 {4,S} {6,S}
6 H u0 {5,S}
""",
kinetics = None,
Expand All @@ -115,8 +117,8 @@
1 *1 [C,Sid,Sis,N] u1 {2,S}
2 *4 [Cs,Cd] u0 {1,S} {3,S}
3 *5 [Cs,Cd] u0 {2,S} {4,S}
4 *2 O u0 {3,S} {5,S}
5 *3 O u0 {4,S} {6,S}
4 *2 [O,S] u0 {3,S} {5,S}
5 *3 [O,S] u0 {4,S} {6,S}
6 H u0 {5,S}
""",
kinetics = None,
Expand All @@ -130,8 +132,8 @@
1 *1 [C,Sid,Sis,N] u1 {2,S}
2 *4 Cd u0 {1,S} {3,D}
3 *5 Cd u0 {2,D} {4,S}
4 *2 O u0 {3,S} {5,S}
5 *3 O u0 {4,S} {6,S}
4 *2 [O,S] u0 {3,S} {5,S}
5 *3 [O,S] u0 {4,S} {6,S}
6 H u0 {5,S}
""",
kinetics = None,
Expand All @@ -145,8 +147,8 @@
1 *1 [C,Sid,Sis,N] u1 {2,D}
2 *4 Cd u0 {1,D} {3,S}
3 *5 [Cs,Cd] u0 {2,S} {4,S}
4 *2 O u0 {3,S} {5,S}
5 *3 O u0 {4,S} {6,S}
4 *2 [O,S] u0 {3,S} {5,S}
5 *3 [O,S] u0 {4,S} {6,S}
6 H u0 {5,S}
""",
kinetics = None,
Expand All @@ -161,8 +163,8 @@
2 *4 [Cs,Cd,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]}
3 *6 [Cs,Cd,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]}
4 *5 [Cs,Cd,Sid,Sis,N] u0 {3,[S,D]} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand All @@ -177,8 +179,8 @@
2 *4 [Cs,Cd] u0 {1,S} {3,S}
3 *6 [Cs,Cd] u0 {2,S} {4,S}
4 *5 [Cs,Cd] u0 {3,S} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand All @@ -193,8 +195,8 @@
2 *4 [Cs,Cd] u0 {1,S} {3,S}
3 *6 Cd u0 {2,S} {4,D}
4 *5 Cd u0 {3,D} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand All @@ -209,8 +211,8 @@
2 *4 Cd u0 {1,S} {3,D}
3 *6 Cd u0 {2,D} {4,S}
4 *5 [Cs,Cd] u0 {3,S} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand All @@ -225,8 +227,8 @@
2 *4 Cd u0 {1,D} {3,S}
3 *6 [Cs,Cd] u0 {2,S} {4,S}
4 *5 [Cs,Cd] u0 {3,S} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand All @@ -241,8 +243,8 @@
2 *4 Cd u0 {1,D} {3,S}
3 *6 Cd u0 {2,S} {4,D}
4 *5 Cd u0 {3,D} {5,S}
5 *2 O u0 {4,S} {6,S}
6 *3 O u0 {5,S} {7,S}
5 *2 [O,S] u0 {4,S} {6,S}
6 *3 [O,S] u0 {5,S} {7,S}
7 H u0 {6,S}
""",
kinetics = None,
Expand Down Expand Up @@ -285,8 +287,8 @@
label = "Cd_rad_out_ND",
group =
"""
1 *1 Cd u1 {2,S}
2 [Cs,O] u0 {1,S}
1 *1 Cd u1 {2,S}
2 [Cs,O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -296,8 +298,8 @@
label = "Cd_rad_out_De",
group =
"""
1 *1 Cd u1 {2,S}
2 [Cd,Ct,Cb,CO] u0 {1,S}
1 *1 Cd u1 {2,S}
2 [Cd,Ct,Cb,CO,CS] u0 {1,S}
""",
kinetics = None,
)
Expand Down Expand Up @@ -355,9 +357,9 @@
label = "C_rad_out_H/NonDeO",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 H u0 {1,S}
3 O u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 H u0 {1,S}
3 [O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -367,9 +369,9 @@
label = "C_rad_out_H/OneDe",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 H u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 H u0 {1,S}
3 [Cd,Ct,Cb,CO,CS] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -391,9 +393,9 @@
label = "C_rad_out_NonDe",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 [Cs,O] u0 {1,S}
3 [Cs,O] u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 [Cs,O,S] u0 {1,S}
3 [Cs,O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -415,9 +417,9 @@
label = "C_rad_out_NDMustO",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 O u0 {1,S}
3 [Cs,O] u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 O u0 {1,S}
3 [Cs,O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -427,9 +429,9 @@
label = "C_rad_out_OneDe",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO] u0 {1,S}
3 [Cs,O] u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO,CS] u0 {1,S}
3 [Cs,O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -439,9 +441,9 @@
label = "C_rad_out_OneDe/Cs",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO] u0 {1,S}
3 Cs u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO,CS] u0 {1,S}
3 Cs u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -451,9 +453,9 @@
label = "C_rad_out_OneDe/O",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO] u0 {1,S}
3 O u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO,CS] u0 {1,S}
3 [O,S] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -463,9 +465,9 @@
label = "C_rad_out_TwoDe",
group =
"""
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO] u0 {1,S}
3 [Cd,Ct,Cb,CO] u0 {1,S}
1 *1 C u1 {2,S} {3,S}
2 [Cd,Ct,Cb,CO,CS] u0 {1,S}
3 [Cd,Ct,Cb,CO,CS] u0 {1,S}
""",
kinetics = None,
)
Expand Down