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ran BM fitting notebook
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@jonwzheng @JacksonBurns
jonwzheng authored and JacksonBurns committed Aug 14, 2024
1 parent 24451a0 commit 250e300
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256 changes: 47 additions & 209 deletions input/kinetics/families/Singlet_Carbene_Intra_Disproportionation/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,18 @@
# encoding: utf-8

name = "Singlet_Carbene_Intra_Disproportionation/groups"
shortDesc = u"Convert a singlet carbene to a closed-shell molecule through a concerted 1,2-H shift + 1,2-bond formation"
longDesc = u"""
shortDesc = "Convert a singlet carbene to a closed-shell molecule through a concerted 1,2-H shift + 1,2-bond formation"
longDesc = """
Reaction site *1 should always be a singlet in this family.
"""

template(reactants=["singletcarbene_CH"], products=["CH_C_unsaturated"], ownReverse=False)
template(reactants=["Root"], products=["CH_C_unsaturated"], ownReverse=False)

reverse = "SingletCarbenefromMultipleBond"

reversible = True

autoGenerated = False

recipe(actions=[
['LOSE_PAIR', '*1', '1'],
['FORM_BOND', '*1', 1, '*3'],
Expand All @@ -23,259 +25,95 @@

entry(
index = 0,
label = "singletcarbene_CH",
label = "Root",
group =
"""
1 *1 C u0 p1 c0 {2,[S,D]}
2 *2 C u0 {1,[S,D]} {3,S}
3 *3 H u0 {2,S}
1 *2 C u0 {2,S} {3,[S,D]}
2 *3 H u0 {1,S}
3 *1 C u0 p1 c0 {1,[S,D]}
""",
kinetics = None,
)

entry(
index = 1,
label = "singletcarbene",
label = "Root_Ext-3C-R_Ext-4R!H-R_Sp-4R!H-1C",
group =
"""
1 *1 C u0 p1 c0
1 *2 C u0 {2,S} {3,[S,D]} {4,S}
2 *3 H u0 {1,S}
3 *1 C u0 p1 c0 {1,[S,D]}
4 C u0 {1,S}
""",
kinetics = None,
)

entry(
index = 2,
label = "CH",
label = "Root_Ext-3C-R_Ext-4R!H-R_Sp-4R!H-1C_Ext-4R!H-R_Ext-4R!H-R",
group =
"""
1 *2 C u0 {2,S}
2 *3 H u0 {1,S}
1 *2 C u0 r1 {2,S} {3,[S,D]} {4,S}
2 *3 H u0 {1,S}
3 *1 C u0 p1 c0 r1 {1,[S,D]}
4 C u0 r1 {1,S} {5,[S,D,T,B]} {6,[S,D,T,B]}
5 R!H ux {4,[S,D,T,B]}
6 R!H ux {4,[S,D,T,B]}
""",
kinetics = None,
)

entry(
index = 3,
label = "fulvene_backbone",
label = "Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C",
group =
"""
1 *2 C u0 {2,S} {6,S} {7,S}
2 C u0 {1,S} {3,S} {5,D}
3 C u0 {2,S} {4,D}
4 C u0 {3,D} {6,S}
5 C u0 {2,D}
6 *1 C u0 p1 c0 {1,S} {4,S}
7 *3 H u0 {1,S}
1 *2 C u0 {2,S} {3,S} {4,[B,D,T]}
2 *3 H u0 {1,S}
3 *1 C u0 p1 c0 {1,S}
4 C ux {1,[B,D,T]}
""",
kinetics = None,
)

entry(
index = 4,
label = "benzene_backbone",
label = "Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C_Ext-4R!H-R_Ext-5R!H-R_Ext-5R!H-R_Sp-6R!H-5R!H",
group =
"""
1 *2 C u0 {2,S} {6,S} {7,S}
2 C u0 {1,S} {3,D}
3 C u0 {2,D} {4,S}
4 C u0 {3,S} {5,D}
5 C u0 {4,D} {6,S}
6 *1 C u0 p1 c0 {1,S} {5,S}
7 *3 H u0 {1,S}
1 *2 C u0 r1 {2,S} {3,S} {4,[B,D,T]}
2 *3 H u0 r0 {1,S}
3 *1 C u0 p1 c0 r1 {1,S} {5,[S,D,T,B]}
4 C ux r1 {1,[B,D,T]}
5 C ux r1 {3,[S,D,T,B]} {6,S}
6 C u0 r1 {5,S}
""",
kinetics = None,
)

entry(
index = 5,
label = "CsJ2-C",
group =
"""
1 *1 C u0 p1 c0 {2,S}
2 *2 C u0 {1,S} {3,S}
3 *3 H u0 {2,S}
""",
kinetics = None,
)

entry(
index = 6,
label = "CdJ2=C",
group =
"""
1 *1 C u0 p1 c0 {2,D}
2 *2 C u0 {1,D} {3,S}
3 *3 H u0 {2,S}
""",
kinetics = None,
)

entry(
index = 7,
label = "CdJ2",
group =
"""
1 *1 C2d u0 p1 c0
""",
kinetics = None,
)

entry(
index = 8,
label = "CsJ2H",
group =
"""
1 *1 C2s u0 p1 c0 {2,S}
2 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 9,
label = "CsJ2C",
group =
"""
1 *1 C2s u0 p1 c0 {2,S}
2 C u0 {1,S}
""",
kinetics = None,
)

entry(
index = 10,
label = "CsJ2(CsC)",
group =
"""
1 *1 C2s u0 p1 c0 {2,S}
2 Cs u0 {1,S} {3,S}
3 C u0 {2,S}
""",
kinetics = None,
)

entry(
index = 11,
label = "CsJ2(C=C)",
group =
"""
1 *1 C2s u0 p1 c0 {2,S}
2 Cd u0 {1,S} {3,D}
3 C u0 {2,D}
""",
kinetics = None,
)

entry(
index = 12,
label = "CdH2",
group =
"""
1 *2 Cd u0 {2,S} {3,S}
2 *3 H u0 {1,S}
3 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 13,
label = "CdHC",
group =
"""
1 *2 Cd u0 {2,S} {3,S}
2 *3 H u0 {1,S}
3 C u0 {1,S}
""",
kinetics = None,
)

entry(
index = 14,
label = "CH3",
group =
"""
1 *2 Cs u0 {2,S} {3,S} {4,S}
2 *3 H u0 {1,S}
3 H u0 {1,S}
4 H u0 {1,S}
""",
kinetics = None,
)

entry(
index = 15,
label = "CH2(C)",
group =
"""
1 *2 Cs u0 {2,S} {3,S} {4,S}
2 *3 H u0 {1,S}
3 H u0 {1,S}
4 C u0 {1,S}
""",
kinetics = None,
)

entry(
index = 16,
label = "CH2(C=C)",
group =
"""
1 *2 Cs u0 {2,S} {3,S} {4,S}
2 *3 H u0 {1,S}
3 H u0 {1,S}
4 Cd u0 {1,S} {5,D}
5 C u0 {4,D}
""",
kinetics = None,
)

entry(
index = 17,
label = "CH(C)C",
group =
"""
1 *2 Cs u0 {2,S} {3,S} {4,S}
2 *3 H u0 {1,S}
3 C u0 {1,S}
4 C u0 {1,S}
""",
kinetics = None,
)

entry(
index = 18,
label = "CH=C",
label = "Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C_Ext-4R!H-R_Ext-5R!H-R_Ext-5R!H-R_N-Sp-6R!H-5R!H",
group =
"""
1 *2 Cd u0 {2,S} {3,D}
2 *3 H u0 {1,S}
3 C u0 {1,D}
1 *2 C u0 r1 {2,S} {3,S} {4,[B,D,T]}
2 *3 H u0 r0 {1,S}
3 *1 C u0 p1 c0 r1 {1,S} {5,[S,D,T,B]}
4 C ux r1 {1,[B,D,T]}
5 C ux r1 {3,[S,D,T,B]} {6,[B,D,T]}
6 C u0 r1 {5,[B,D,T]}
""",
kinetics = None,
)

tree(
"""
L1: singletcarbene_CH
L2: fulvene_backbone
L2: benzene_backbone
L2: CsJ2-C
L2: CdJ2=C
L1: singletcarbene
L2: CdJ2
L2: CsJ2H
L2: CsJ2C
L3: CsJ2(CsC)
L3: CsJ2(C=C)
L1: CH
L2: CdH2
L2: CdHC
L2: CH3
L2: CH2(C)
L3: CH2(C=C)
L2: CH(C)C
L2: CH=C
L1: Root
L2: Root_Ext-3C-R_Ext-4R!H-R_Sp-4R!H-1C
L3: Root_Ext-3C-R_Ext-4R!H-R_Sp-4R!H-1C_Ext-4R!H-R_Ext-4R!H-R
L2: Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C
L3: Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C_Ext-4R!H-R_Ext-5R!H-R_Ext-5R!H-R_Sp-6R!H-5R!H
L3: Root_Ext-3C-R_Ext-4R!H-R_N-Sp-4R!H-1C_Ext-4R!H-R_Ext-5R!H-R_Ext-5R!H-R_N-Sp-6R!H-5R!H
"""
)

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