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Adding halogens to default families #562

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Adding halogens to default families #562

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2f1f74f
added halogen `H_Abstraction` tranining rxns
davidfarinajr Jan 17, 2022
d243628
added halogen `1+2_Cycloaddition` tranining rxns
davidfarinajr Jan 17, 2022
f46084f
added halogens to `1+2_Cycladdition` groups
davidfarinajr Jan 17, 2022
de7f272
added halogens to `1,2-Birad_to_alkene` groups
davidfarinajr Jan 17, 2022
fe754a6
added halogen `1,2_Insertion_carbene` training reactions
davidfarinajr Jan 17, 2022
bb3b667
added `1,2_Insertion_carbene` autotree groups and rules
davidfarinajr Jan 17, 2022
b682578
added halogen `1,2_Insertion_CO` training reactions
davidfarinajr Jan 17, 2022
45f67f2
added `1,2_Insertion_CO`autotree groups and rules
davidfarinajr Jan 17, 2022
4ca6fa6
added halogen groups to `1,3_Insertion_ROR` groups
davidfarinajr Jan 17, 2022
0c12da9
added halogens to `Birad_R_Recombination` groups
davidfarinajr Jan 17, 2022
21402b4
added halogen `CO_Disproportionation` training reactions
davidfarinajr Jan 17, 2022
65cf9cf
added `CO_Disproportionation` autotree groups and rules
davidfarinajr Jan 17, 2022
aa6f000
added halogens to `Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH`…
davidfarinajr Jan 17, 2022
0509636
added halogen `Disproportionation` training reactions
davidfarinajr Jan 17, 2022
2218080
added `Disproportionation` autotree groups and rules
davidfarinajr Jan 17, 2022
10304ef
Added `H_Abstraction` autotree groups and rules
davidfarinajr Jan 17, 2022
7575eaf
added halogens to `Intra_ene_reaction` groups
davidfarinajr Jan 17, 2022
6d1e870
added halogen `intra_H_migration` training reactions
davidfarinajr Jan 17, 2022
c6ff1da
added halogen `R_Addition_COm` training reactions
davidfarinajr Jan 17, 2022
000c9ad
added `R_Addition_COm` autotree groups and rules
davidfarinajr Jan 17, 2022
6d454dc
added halogen `R_Addition_MultipleBond` training reactions
davidfarinajr Jan 17, 2022
6e9c6f4
added halogen `R_Recombination` training reactions
davidfarinajr Jan 17, 2022
68eaf79
added `R_Recombination` autotree groups and rules
davidfarinajr Jan 17, 2022
7587a64
added halogens to `Intra_RH_Add_Endocyclic` groups
davidfarinajr Jan 17, 2022
6f7556f
added halogens to `Intra_RH_Add_Exocyclic` groups
davidfarinajr Jan 17, 2022
5d0892b
added `R_Addition_MultipleBond` autotree groups and rules
davidfarinajr Jan 17, 2022
40d3803
added `Singlet_Carbene_Intra_Disproportionation` training reactions
davidfarinajr Jan 17, 2022
489b505
added `Singlet_Carbene_Intra_Disproportionation` autotree groups and …
davidfarinajr Jan 17, 2022
ee92c13
use `halogens_kinetics` branch for testing
davidfarinajr Aug 10, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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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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