From af4e38cbec9736a9503b3fc4cdd759ef53260375 Mon Sep 17 00:00:00 2001 From: Matt Johnson Date: Sat, 3 Jun 2023 19:17:52 -0700 Subject: [PATCH] fix LithiumPrimaryKinetics2 --- .../LithiumPrimaryKinetics2/dictionary.txt | 37 ---------- .../LithiumPrimaryKinetics2/reactions.py | 69 +++++++++---------- 2 files changed, 34 insertions(+), 72 deletions(-) diff --git a/input/kinetics/libraries/LithiumPrimaryKinetics2/dictionary.txt b/input/kinetics/libraries/LithiumPrimaryKinetics2/dictionary.txt index 2ee56d9ed1..ad683e0fde 100644 --- a/input/kinetics/libraries/LithiumPrimaryKinetics2/dictionary.txt +++ b/input/kinetics/libraries/LithiumPrimaryKinetics2/dictionary.txt @@ -82,20 +82,6 @@ multiplicity 2 10 H u0 p0 c0 {5,S} 11 H u0 p0 c0 {5,S} -[Li]OC[=O]OC[CH2] -multiplicity 2 -1 O u0 p2 c0 {4,S} {6,S} -2 O u0 p2 c0 {6,S} {7,S} -3 O u0 p2 c0 {6,D} -4 C u0 p0 c0 {1,S} {5,S} {8,S} {9,S} -5 C u1 p0 c0 {4,S} {10,S} {11,S} -6 C u0 p0 c0 {1,S} {2,S} {3,D} -7 Li u0 p0 c0 {2,S} -8 H u0 p0 c0 {4,S} -9 H u0 p0 c0 {4,S} -10 H u0 p0 c0 {5,S} -11 H u0 p0 c0 {5,S} - [Li]OC[=O]OCCO[C]1OCCO1 multiplicity 2 1 O u0 p2 c0 {8,S} {11,S} @@ -120,20 +106,6 @@ multiplicity 2 20 H u0 p0 c0 {10,S} 21 H u0 p0 c0 {10,S} -[Li]OC[=O]OCC[Li] -1 O u0 p2 c0 {4,S} {6,S} -2 O u0 p2 c0 {6,S} {8,S} -3 O u0 p2 c0 {6,D} -4 C u0 p0 c0 {1,S} {5,S} {9,S} {10,S} -5 C u0 p0 c0 {4,S} {7,S} {11,S} {12,S} -6 C u0 p0 c0 {1,S} {2,S} {3,D} -7 Li u0 p0 c0 {5,S} -8 Li u0 p0 c0 {2,S} -9 H u0 p0 c0 {4,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {5,S} -12 H u0 p0 c0 {5,S} - [Li]OC[=O]OCCC1[O[Li]]OCCO1 1 O u0 p2 c0 {7,S} {10,S} 2 O u0 p2 c0 {7,S} {11,S} @@ -334,14 +306,6 @@ multiplicity 2 12 H u0 p0 c0 {3,S} 13 H u0 p0 c0 {3,S} -[Li]OC[=O]O[Li] -1 O u0 p2 c0 {4,S} {5,S} -2 O u0 p2 c0 {4,S} {6,S} -3 O u0 p2 c0 {4,D} -4 C u0 p0 c0 {1,S} {2,S} {3,D} -5 Li u0 p0 c0 {1,S} -6 Li u0 p0 c0 {2,S} - [Li]OC(=O)OCC[Li] 1 O u0 p2 c0 {4,S} {6,S} 2 O u0 p2 c0 {6,S} {8,S} @@ -423,4 +387,3 @@ N=C 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {3,S} 8 H u0 p0 c0 {3,S} - diff --git a/input/kinetics/libraries/LithiumPrimaryKinetics2/reactions.py b/input/kinetics/libraries/LithiumPrimaryKinetics2/reactions.py index ea986a8a16..6efe9748b3 100644 --- a/input/kinetics/libraries/LithiumPrimaryKinetics2/reactions.py +++ b/input/kinetics/libraries/LithiumPrimaryKinetics2/reactions.py @@ -12,7 +12,7 @@ label = "O=C1OCCO1 + [Li] <=> [Li]OC(=O)OC[CH2]", degeneracy = 1.0, kinetics = Arrhenius(A=(6.40229e+07,'cm^3/(mol*s)'), n=2.08453, Ea=(2.45304,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS1 in O=C1OCCO1 + [Li] <=> [Li]OC(=O)OC[CH2]: @@ -45,7 +45,7 @@ label = "[Li]OC1OCC1 <=> O=CCCO[Li]", degeneracy = 1.0, kinetics = Arrhenius(A=(6.68965e+12,'s^-1'), n=-0.134733, Ea=(38.4756,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS4 in [Li]OC1OCC1 <=> O=CCCO[Li]: @@ -80,7 +80,7 @@ label = "[Li]O[C]1OCCO1 <=> O=[C]OCCO[Li]", degeneracy = 1.0, kinetics = Arrhenius(A=(2.97927e+12,'s^-1'), n=0.00494054, Ea=(1.80157,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS1 in [Li]O[C]1OCCO1 <=> O=[C]OCCO[Li]: @@ -110,10 +110,10 @@ entry( index = 3, - label = "O=C1OCCO1 + [Li]OC[=O]OC[CH2] <=> [Li]OC[=O]OCCO[C]1OCCO1", + label = "O=C1OCCO1 + [Li]OC(=O)OC[CH2] <=> [Li]OC[=O]OCCO[C]1OCCO1", degeneracy = 1.0, kinetics = Arrhenius(A=(0.00568213,'cm^3/(mol*s)'), n=3.08997, Ea=(92.7056,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS2 in O=C1OCCO1 + [Li]OC[=O]OC[CH2] <=> [Li]OC[=O]OCCO[C]1OCCO1: @@ -146,11 +146,11 @@ H 2.03853228 -2.45935310 -1.24367327 1D rotors: -* Invalidated! pivots: [2, 3], dihedral: [1, 2, 3, 4], invalidation reason: -* Invalidated! pivots: [3, 5], dihedral: [2, 3, 5, 6], invalidation reason: -* Invalidated! pivots: [5, 6], dihedral: [3, 5, 6, 7], invalidation reason: -* Invalidated! pivots: [6, 7], dihedral: [5, 6, 7, 12], invalidation reason: -* Invalidated! pivots: [7, 12], dihedral: [6, 7, 12, 13], invalidation reason: +* Invalidated! pivots: [2, 3], dihedral: [1, 2, 3, 4], invalidation reason: +* Invalidated! pivots: [3, 5], dihedral: [2, 3, 5, 6], invalidation reason: +* Invalidated! pivots: [5, 6], dihedral: [3, 5, 6, 7], invalidation reason: +* Invalidated! pivots: [6, 7], dihedral: [5, 6, 7, 12], invalidation reason: +* Invalidated! pivots: [7, 12], dihedral: [6, 7, 12, 13], invalidation reason: * Invalidated! pivots: [12, 13], dihedral: [7, 12, 13, 14], invalidation reason: ccsd(t)-f12/cc-pvdz-f12//wb97x-d3/def2-tzvp """, @@ -158,10 +158,10 @@ entry( index = 4, - label = "[Li]OC[=O]OCC[Li] + O=C1OCCO1 <=> [Li]OC[=O]OCCC1[O[Li]]OCCO1", + label = "[Li]OC(=O)OCC[Li] + O=C1OCCO1 <=> [Li]OC[=O]OCCC1[O[Li]]OCCO1", degeneracy = 1.0, kinetics = Arrhenius(A=(2.21675,'cm^3/(mol*s)'), n=2.94197, Ea=(-82.2275,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS4 in [Li]OC[=O]OCC[Li] + O=C1OCCO1 <=> [Li]OC[=O]OCCC1[O[Li]]OCCO1: @@ -195,10 +195,10 @@ H -1.80327947 -1.91854114 -0.38464998 1D rotors: -* Invalidated! pivots: [2, 3], dihedral: [9, 2, 3, 4], invalidation reason: -* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: -* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: -* Invalidated! pivots: [5, 7], dihedral: [4, 5, 7, 8], invalidation reason: +* Invalidated! pivots: [2, 3], dihedral: [9, 2, 3, 4], invalidation reason: +* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: +* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: +* Invalidated! pivots: [5, 7], dihedral: [4, 5, 7, 8], invalidation reason: * Invalidated! pivots: [13, 14], dihedral: [1, 13, 14, 15], invalidation reason: ccsd(t)-f12/cc-pvdz-f12//wb97x-d3/def2-tzvp """, @@ -209,7 +209,7 @@ label = "COCCOC + [Li] <=> [Li]OCCOC + [CH3]", degeneracy = 1.0, kinetics = Arrhenius(A=(62816.3,'cm^3/(mol*s)'), n=2.80799, Ea=(51.0438,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS8 in COCCOC + [Li] <=> [Li]OCCOC + [CH3]: @@ -251,7 +251,7 @@ label = "O=C1OCC[F]O1 + [Li] <=> O=C1OC[CH]O1 + [Li]F", degeneracy = 1.0, kinetics = Arrhenius(A=(5.84579e+07,'cm^3/(mol*s)'), n=2.04554, Ea=(28.3364,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS11 in O=C1OCC[F]O1 + [Li] <=> O=C1OC[CH]O1 + [Li]F: @@ -284,7 +284,7 @@ label = "C=C + [Li] <=> [Li]C[CH2]", degeneracy = 1.0, kinetics = Arrhenius(A=(2.10799e+08,'cm^3/(mol*s)'), n=1.74038, Ea=(37.7145,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS12 in C=C + [Li] <=> [Li]C[CH2]: @@ -313,7 +313,7 @@ label = "[Li]O[O] + CCC <=> [Li]OO + C[CH]C", degeneracy = 1.0, kinetics = Arrhenius(A=(0.0384704,'cm^3/(mol*s)'), n=4.42153, Ea=(115.231,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS15 in [Li]O[O] + CCC <=> [Li]OO + C[CH]C: @@ -351,7 +351,7 @@ label = "[Li]O[O] + CC <=> [Li]OO + C[CH2]", degeneracy = 1.0, kinetics = Arrhenius(A=(0.023197,'cm^3/(mol*s)'), n=4.65665, Ea=(125.28,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS16 in [Li]O[O] + CC <=> [Li]OO + C[CH2]: @@ -385,7 +385,7 @@ label = "[Li]O[O] + CC[C]C <=> [Li]OO + C[C][C]C", degeneracy = 1.0, kinetics = Arrhenius(A=(0.19477,'cm^3/(mol*s)'), n=4.27128, Ea=(104.632,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS17 in [Li]O[O] + CC[C]C <=> [Li]OO + C[C][C]C: @@ -424,10 +424,10 @@ entry( index = 11, - label = "[Li]O[C]1OCCO1 + [Li] <=> C=C + [Li]OC[=O]O[Li]", + label = "[Li]O[C]1OCCO1 + [Li] <=> C=C + [Li]OC(=O)O[Li]", degeneracy = 1.0, kinetics = Arrhenius(A=(265439,'cm^3/(mol*s)'), n=1.96819, Ea=(-156.013,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS19 in [Li]O[C]1OCCO1 + [Li] <=> C=C + [Li]OC[=O]O[Li]: @@ -461,7 +461,7 @@ label = "[Li]OC(=O)OCC[Li] <=> C=C + [Li]OC(=O)O[Li]", degeneracy = 1.0, kinetics = Arrhenius(A=(9.75697e+10,'s^-1'), n=0.20961, Ea=(-32.9662,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS1 in [Li]OC(=O)OCC[Li] <=> C=C + [Li]OC(=O)O[Li]: @@ -485,9 +485,9 @@ Li -2.49325448 -1.14082524 -0.15038278 1D rotors: -* Invalidated! pivots: [3, 9], dihedral: [2, 3, 9, 12], invalidation reason: -* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: -* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: +* Invalidated! pivots: [3, 9], dihedral: [2, 3, 9, 12], invalidation reason: +* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: +* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: * Invalidated! pivots: [5, 6], dihedral: [4, 5, 6, 7], invalidation reason: ccsd(t)-f12/cc-pvdz-f12//wb97x-d3/def2-tzvp """, @@ -498,7 +498,7 @@ label = "O=CCOC[Li] <=> O=C + [Li]OC=C", degeneracy = 1.0, kinetics = Arrhenius(A=(2.61629e+10,'s^-1'), n=0.571031, Ea=(48.5744,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS2 in O=CCOC[Li] <=> O=C + [Li]OC=C: @@ -521,8 +521,8 @@ H -0.25873063 2.12146356 0.23345536 1D rotors: -* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: -* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: +* Invalidated! pivots: [3, 4], dihedral: [2, 3, 4, 5], invalidation reason: +* Invalidated! pivots: [4, 5], dihedral: [3, 4, 5, 6], invalidation reason: * Invalidated! pivots: [5, 6], dihedral: [4, 5, 6, 7], invalidation reason: ccsd(t)-f12/cc-pvdz-f12//wb97x-d3/def2-tzvp """, @@ -533,7 +533,7 @@ label = "N=CCNC[Li] <=> N=C + [Li]NC=C", degeneracy = 1.0, kinetics = Arrhenius(A=(4.58931e+10,'s^-1'), n=0.578655, Ea=(18.0231,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(3000,'K')), - longDesc = + longDesc = """ TS method summary for TS3 in N=CCNC[Li] <=> N=C + [Li]NC=C: Methods that successfully generated a TS guess: @@ -559,10 +559,9 @@ H 1.14454041 0.94268226 1.13275931 1D rotors: -* Invalidated! pivots: [1, 5], dihedral: [6, 1, 5, 3], invalidation reason: -* Invalidated! pivots: [2, 3], dihedral: [4, 2, 3, 5], invalidation reason: +* Invalidated! pivots: [1, 5], dihedral: [6, 1, 5, 3], invalidation reason: +* Invalidated! pivots: [2, 3], dihedral: [4, 2, 3, 5], invalidation reason: * Invalidated! pivots: [3, 5], dihedral: [2, 3, 5, 1], invalidation reason: ccsd(t)-f12/cc-pvdz-f12//wb97x-d3/def2-tzvp """, ) -