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Halogen training reactions #515

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90066e3
added halogen 1,2_Insertion_carbene training rxns
davidfarinajr Oct 22, 2021
3d0434c
added halogen 1,2_Insertion_CO training rxn
davidfarinajr Oct 22, 2021
feba6c3
added halogen CO_Dispropotionation training rxns
davidfarinajr Oct 22, 2021
539d9b9
added halogen Disproportionation training rxns
davidfarinajr Oct 22, 2021
8436b8b
added halogen H_Abstraction training rxns
davidfarinajr Oct 22, 2021
c8c06b7
added halogen intra_H_migration training rxns
davidfarinajr Oct 22, 2021
f9603ea
added halogen R_Add_COm training rxn
davidfarinajr Oct 22, 2021
3d9da8f
added halogen R_Add_multiplebond training rxns
davidfarinajr Oct 22, 2021
dca8de2
added autotst halogen R_Add_MultiBond training reactions
davidfarinajr Oct 13, 2021
083938d
added halogen R_recombination training rxns
davidfarinajr Oct 22, 2021
92d66a5
added halogen Singlet_Carbene_Intra_Disprop training rxn
davidfarinajr Oct 22, 2021
945533e
remove Cl from forbidden in R_Recombination
davidfarinajr Sep 15, 2021
8356a2d
prep 1,2_Insertion_carbene for autotree gen
davidfarinajr Jul 16, 2021
839c7de
prep 1,2_Insertion_CO for autotree gen
davidfarinajr Jul 16, 2021
fff5846
added `Val7` to 1,2-Birad_to_alkene tree
davidfarinajr Jul 16, 2021
57cf94b
added `Val7` to 1,3_Insertion_ROR
davidfarinajr Jul 16, 2021
84043a4
added `Val7` to 1,2_Cycloaddition tree
davidfarinajr Jul 16, 2021
fd585b6
added `Val7` to Birad_R_Recombination family
davidfarinajr Jul 16, 2021
efaa783
prep CO_Disproportionation for autotree gen
davidfarinajr Jul 16, 2021
32874ae
added `Val7` to Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH tree
davidfarinajr Jul 16, 2021
06b1ff2
added `Val7` to intra_ene_reaction family
davidfarinajr Jul 16, 2021
1c0887e
prep `Intra_ene_reaction` family for autotree gen
davidfarinajr Jul 16, 2021
77e1a21
added `Val7` to `intra_RH_Add_Endocyclic`
davidfarinajr Jul 16, 2021
f5d4fe8
added `Val7` to `Intra_RH_Add_Exocyclic` tree
davidfarinajr Jul 16, 2021
446c7f5
prep `R_Addition_COm` for autotree gen
davidfarinajr Jul 16, 2021
51adb03
prep `R_Addition_MultipleBond` for autotree gen
davidfarinajr Jul 16, 2021
a5af880
added `Val7` to `Singlet_Carbene_Intra_Disproportionation`
davidfarinajr Jul 16, 2021
1e19fd4
prep `Singlet_Carbene_Intra_Disproportionation` for autotree gen
davidfarinajr Jul 16, 2021
5718a99
val7 -> F,Cl,Br,I
davidfarinajr Aug 9, 2021
60ce3ab
added `1,2_Insertion_carbene` autotree and rules
davidfarinajr Aug 9, 2021
77ea201
added `1,2_Insertion_CO` autotree and rules
davidfarinajr Aug 9, 2021
5c92b6a
added `CO_disproportionation` autotree and rules
davidfarinajr Aug 9, 2021
0c1c660
added `R_Add_COm` autotree and rules
davidfarinajr Aug 9, 2021
761b5fd
added `Singlet_Carbene_Intra_Disprop` autotree and rules
davidfarinajr Aug 9, 2021
011100d
regenerated R_Recom tree with new training data
davidfarinajr Aug 9, 2021
ab908b6
added `R_add_Multibond` autogenerated groups and rules
davidfarinajr Oct 14, 2021
0c0cca1
H_abstraction tree preparation
mjohnson541 Aug 15, 2018
53a5186
fixed H Abs training rxns
davidfarinajr Oct 14, 2021
8848d43
replaced halogen literature H abs training rxns with autotst rxns
davidfarinajr Oct 20, 2021
4eacb19
removed duplicate reactions from H Abs training
davidfarinajr Oct 20, 2021
dd82995
removed H abs training reactions with violated coll limit in rev dire…
davidfarinajr Oct 20, 2021
04bf053
added Habs autotree groups and rules
davidfarinajr Oct 21, 2021
e9b73b0
retrained Disproportionation autotree groups and rules
davidfarinajr Oct 22, 2021
c751698
use `halogens_kinetics` branch for testing
davidfarinajr Aug 10, 2021
c5bea01
fixed ranks for halogen training reactions
davidfarinajr Dec 7, 2021
9c751ad
regenerated kinetics trees with new ranks
davidfarinajr Dec 9, 2021
3ab0ed8
regenerated H Abs tree with new ranks
davidfarinajr Dec 10, 2021
fd8395b
regenerated R_Add_MultipleBond with new ranks
davidfarinajr Dec 10, 2021
e635e1d
removed `CCHY` node from `Singlet_Carbene_Intra_Disproportionation`
davidfarinajr Dec 14, 2021
c1e0225
regenerated existing family rules with new Bm fitting
davidfarinajr Dec 17, 2021
c5b50ee
fixup! regenerated existing family rules with new Bm fitting
davidfarinajr Dec 18, 2021
c4255a4
C -> C2s in 1+2 cyclo add groups to prevent atomtype error
davidfarinajr Dec 22, 2021
2f98cc9
added 1+2_Cycloaddition halogen training reactions
davidfarinajr Dec 23, 2021
36d784a
added halogen groups to 1+2_Cycloaddition family
davidfarinajr Dec 23, 2021
da8a2fb
rebase H_Abs with main branch
davidfarinajr Jan 17, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
strategy:
max-parallel: 5
env: # update this if needed to match a pull request on the RMG-database
RMG_PY_BRANCH: main
RMG_PY_BRANCH: halogens_kinetics
defaults:
run:
shell: bash -l {0}
Expand Down
180 changes: 140 additions & 40 deletions input/kinetics/families/1+2_Cycloaddition/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,9 +58,9 @@
label = "carbene",
group =
"""
1 *3 C u0 p1 {2,S} {3,S}
2 H u0 {1,S}
3 H u0 {1,S}
1 *3 C2s u0 p1 {2,S} {3,S}
2 [H,Val7] u0 {1,S}
3 [H,Val7] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -71,11 +71,11 @@
group =
"""
1 Cs u0 {2,S} {3,S} {4,S} {5,S}
2 *3 C u0 p1 {1,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {1,S}
6 H u0 {2,S}
2 *3 C2s u0 p1 {1,S} {6,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {1,S}
6 [H,Val7] u0 {2,S}
""",
kinetics = None,
)
Expand All @@ -85,9 +85,9 @@
label = "ph_carbene",
group =
"""
1 *3 C u0 p1 {2,S} {3,S}
1 *3 C2s u0 p1 {2,S} {3,S}
2 Cb u0 {1,S} {4,B} {5,B}
3 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 Cb u0 {2,B} {6,B}
5 Cb u0 {2,B} {7,B}
6 Cb u0 {4,B} {8,B}
Expand All @@ -104,13 +104,13 @@
"""
1 Cs u0 {3,S} {4,S} {5,S} {6,S}
2 Cs u0 {3,S} {7,S} {8,S} {9,S}
3 *3 C u0 p1 {1,S} {2,S}
4 H u0 {1,S}
5 H u0 {1,S}
6 H u0 {1,S}
7 H u0 {2,S}
8 H u0 {2,S}
9 H u0 {2,S}
3 *3 C2s u0 p1 {1,S} {2,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {1,S}
6 [H,Val7] u0 {1,S}
7 [H,Val7] u0 {2,S}
8 [H,Val7] u0 {2,S}
9 [H,Val7] u0 {2,S}
""",
kinetics = None,
)
Expand Down Expand Up @@ -144,8 +144,8 @@
"""
1 *1 CO u0 {2,D} {3,S} {4,S}
2 *2 O u0 {1,D}
3 H u0 {1,S}
4 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -157,7 +157,7 @@
"""
1 *1 CO u0 {2,D} {3,S} {4,S}
2 *2 O u0 {1,D}
3 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [Cs,O] u0 {1,S}
""",
kinetics = None,
Expand All @@ -170,7 +170,7 @@
"""
1 *1 CO u0 {2,D} {3,S} {4,S}
2 *2 O u0 {1,D}
3 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [Cd,Ct,Cb,CO] u0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -222,8 +222,8 @@
"""
1 *1 CS u0 {2,D} {3,S} {4,S}
2 *2 S u0 {1,D}
3 H u0 {1,S}
4 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
""",
kinetics = None,
)
Expand All @@ -235,7 +235,7 @@
"""
1 *1 CS u0 {2,D} {3,S} {4,S}
2 *2 S u0 {1,D}
3 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [Cs,O,S] u0 {1,S}
""",
kinetics = None,
Expand All @@ -248,7 +248,7 @@
"""
1 *1 CS u0 {2,D} {3,S} {4,S}
2 *2 S u0 {1,D}
3 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [Cd,Ct,Cb,CO,CS] u0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -323,10 +323,10 @@
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {2,S}
6 H u0 {2,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {2,S}
6 [H,Val7] u0 {2,S}
""",
kinetics = None,
)
Expand All @@ -338,9 +338,9 @@
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {2,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {2,S}
6 R!H u0 {2,S}
""",
kinetics = None,
Expand All @@ -353,9 +353,9 @@
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {2,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {2,S}
6 [Cs,O,S] u0 {2,S}
""",
kinetics = None,
Expand All @@ -368,9 +368,9 @@
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {2,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 [H,Val7] u0 {2,S}
6 [Cd,Ct,Cb,CO,CS] u0 {2,S}
""",
kinetics = None,
Expand All @@ -383,8 +383,8 @@
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
3 [H,Val7] u0 {1,S}
4 [H,Val7] u0 {1,S}
5 R!H u0 {2,S}
6 R!H u0 {2,S}
""",
Expand Down Expand Up @@ -782,12 +782,109 @@
kinetics = None,
)

entry(
index = 56,
label = "CH2",
group =
"""
1 *3 C2s u0 p1 {2,S} {3,S}
2 H u0 p0 {1,S}
3 H u0 p0 {1,S}
""",
kinetics = None,
)

entry(
index = 57,
label = "CF2",
group =
"""
1 *3 C2s u0 p1 {2,S} {3,S}
2 F1s u0 p3 {1,S}
3 F1s u0 p3 {1,S}
""",
kinetics = None,
)

entry(
index = 58,
label = "CCl2",
group =
"""
1 *3 C2s u0 p1 {2,S} {3,S}
2 Cl1s u0 p3 {1,S}
3 Cl1s u0 p3 {1,S}
""",
kinetics = None,
)

entry(
index = 59,
label = "CBr2",
group =
"""
1 *3 C2s u0 p1 {2,S} {3,S}
2 Br1s u0 p3 {1,S}
3 Br1s u0 p3 {1,S}
""",
kinetics = None,
)

entry(
index = 60,
label = "C2H4",
group =
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 H u0 {2,S}
6 H u0 {2,S}
""",
kinetics = None,
)

entry(
index = 61,
label = "CH2CF2",
group =
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 H u0 {1,S}
4 H u0 {1,S}
5 F u0 {2,S}
6 F u0 {2,S}
""",
kinetics = None,
)

entry(
index = 62,
label = "CF2CF2",
group =
"""
1 *1 Cd u0 {2,D} {3,S} {4,S}
2 *2 Cd u0 {1,D} {5,S} {6,S}
3 F u0 {1,S}
4 F u0 {1,S}
5 F u0 {2,S}
6 F u0 {2,S}
""",
kinetics = None,
)

tree(
"""
L1: elec_def
L2: o_atom_singlet
L2: S_atom_singlet
L2: carbene
L3: CH2
L3: CF2
L3: CCl2
L3: CBr2
L2: me_carbene
L2: ph_carbene
L2: dime_carbene
Expand All @@ -809,6 +906,9 @@
L2: mb_db
L3: mb_db_dbSub
L3: mb_db_unsub
L4: C2H4
L4: CH2CF2
L4: CF2CF2
L3: mb_db_monosub
L4: mb_db_monosub_Nd
L4: mb_db_monosub_De
Expand Down
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