diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000000..d99f2f30cc --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,6 @@ +{ + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter" + }, + "python.formatting.provider": "none" +} \ No newline at end of file diff --git a/input/thermo/libraries/2BF_thermo.py b/input/thermo/libraries/2BF_thermo.py index 137c1d842b..dbaf360461 100755 --- a/input/thermo/libraries/2BF_thermo.py +++ b/input/thermo/libraries/2BF_thermo.py @@ -2810,57 +2810,6 @@ entry( index = 38, - label = "TB7", - molecule = -""" -multiplicity 2 -1 O u1 p2 c0 {5,S} -2 C u0 p0 c0 {3,S} {4,S} {7,S} {8,S} -3 C u0 p0 c0 {2,S} {5,D} {9,S} -4 C u0 p0 c0 {2,S} {6,D} {10,S} -5 C u0 p0 c0 {1,S} {3,D} {6,S} -6 C u0 p0 c0 {4,D} {5,S} {11,S} -7 H u0 p0 c0 {2,S} -8 H u0 p0 c0 {2,S} -9 H u0 p0 c0 {3,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {6,S} -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[4.0945,-0.00914745,0.000179528,-3.11949e-07,1.72915e-10,7230.53,10.5421], Tmin=(10,'K'), Tmax=(575.423,'K')), - NASAPolynomial(coeffs=[0.211161,0.0442362,-2.8421e-05,8.6726e-09,-1.00923e-12,7240.56,23.3346], Tmin=(575.423,'K'), Tmax=(3000,'K')), - ], - Tmin = (10,'K'), - Tmax = (3000,'K'), - E0 = (60.099,'kJ/mol'), - Cp0 = (33.2579,'J/(mol*K)'), - CpInf = (257.749,'J/(mol*K)'), - ), - shortDesc = """""", - longDesc = -""" -Bond corrections: {'C-C': 3, 'C-H': 5, 'C-O': 1, 'C=C': 2} - -External symmetry: 1, optical isomers: 1 - -Geometry: -O -2.11183600 1.44157200 -0.34260300 -C -1.09179700 0.77674700 -0.18192800 -C -1.00461600 -0.65589200 0.04189600 -C 0.42204500 -1.06270700 0.18675400 -C 1.16236300 0.25104200 0.02907400 -C 0.31953000 1.26955000 -0.17533300 -H -1.86259200 -1.31232300 0.09237900 -H 0.72574600 -1.79975800 -0.57011800 -H 0.62553700 -1.53589300 1.15784600 -H 2.24203400 0.31669200 0.08166200 -H 0.57358500 2.31097000 -0.31962800 -""", -) - -entry( - index = 39, label = "TB8", molecule = """ @@ -2924,7 +2873,7 @@ ) entry( - index = 40, + index = 39, label = "TB9", molecule = """ @@ -2982,7 +2931,7 @@ ) entry( - index = 41, + index = 40, label = "TB10", molecule = """ @@ -3047,48 +2996,7 @@ ) entry( - index = 42, - label = "TB11", - molecule = -""" -multiplicity 2 -1 C u0 p0 c0 {2,D} {4,S} {5,S} -2 C u0 p0 c0 {1,D} {3,D} -3 C u1 p0 c0 {2,D} {6,S} -4 H u0 p0 c0 {1,S} -5 H u0 p0 c0 {1,S} -6 H u0 p0 c0 {3,S} -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[3.94764,0.00319149,5.64828e-05,-1.18956e-07,7.50654e-11,41022.3,5.4829], Tmin=(10,'K'), Tmax=(537.535,'K')), - NASAPolynomial(coeffs=[3.91782,0.0150707,-9.19614e-06,2.84527e-09,-3.46567e-13,40857.1,4.04168], Tmin=(537.535,'K'), Tmax=(3000,'K')), - ], - Tmin = (10,'K'), - Tmax = (3000,'K'), - E0 = (341.061,'kJ/mol'), - Cp0 = (33.2579,'J/(mol*K)'), - CpInf = (133.032,'J/(mol*K)'), - ), - shortDesc = """""", - longDesc = -""" -Bond corrections: {'C-H': 3, 'C=C': 2} - -External symmetry: 2, optical isomers: 1 - -Geometry: -C 1.50226700 -0.00969800 0.11174200 -C 0.28357700 -0.00183100 0.02109300 -C -1.07978000 0.00697100 -0.08031700 -H 2.56148000 -0.01653600 0.19052900 -H -1.62316900 0.93822700 -0.18356100 -H -1.64437500 -0.91713300 -0.05948700 -""", -) - -entry( - index = 43, + index = 41, label = "TB13", molecule = """ @@ -3164,7 +3072,7 @@ ) entry( - index = 44, + index = 42, label = "TB14", molecule = """ @@ -3243,7 +3151,7 @@ ) entry( - index = 45, + index = 43, label = "TB15", molecule = """ @@ -3320,7 +3228,7 @@ ) entry( - index = 46, + index = 44, label = "TB16", molecule = """ @@ -3395,7 +3303,7 @@ ) entry( - index = 47, + index = 45, label = "TB17", molecule = """ @@ -3472,7 +3380,7 @@ ) entry( - index = 48, + index = 46, label = "TB18", molecule = """ @@ -3551,7 +3459,7 @@ ) entry( - index = 49, + index = 47, label = "TB19", molecule = """ @@ -3628,7 +3536,7 @@ ) entry( - index = 50, + index = 48, label = "TB12", molecule = """ @@ -3704,7 +3612,7 @@ ) entry( - index = 51, + index = 49, label = "PBROO15", molecule = """ @@ -3784,7 +3692,7 @@ ) entry( - index = 52, + index = 50, label = "PBROO16", molecule = """ @@ -3864,131 +3772,82 @@ ) entry( - index = 53, - label = "PB20", - molecule = -""" -multiplicity 2 -1 O u0 p2 c0 {3,S} {5,S} -2 C u0 p0 c0 {3,S} {7,S} {8,S} {9,S} -3 C u0 p0 c0 {1,S} {2,S} {4,D} -4 C u0 p0 c0 {3,D} {6,S} {10,S} -5 C u0 p0 c0 {1,S} {6,D} {11,S} -6 C u1 p0 c0 {4,S} {5,D} -7 H u0 p0 c0 {2,S} -8 H u0 p0 c0 {2,S} -9 H u0 p0 c0 {2,S} -10 H u0 p0 c0 {4,S} -11 H u0 p0 c0 {5,S} -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[3.96347,0.00230873,0.000123558,-2.29196e-07,1.37502e-10,22961.8,10.6088], Tmin=(10,'K'), Tmax=(429.631,'K')), - NASAPolynomial(coeffs=[-0.803942,0.0465939,-3.07054e-05,9.63034e-09,-1.15167e-12,23372.4,29.5921], Tmin=(429.631,'K'), Tmax=(3000,'K')), - ], - Tmin = (10,'K'), - Tmax = (3000,'K'), - E0 = (190.906,'kJ/mol'), - Cp0 = (33.2579,'J/(mol*K)'), - CpInf = (257.749,'J/(mol*K)'), - ), - shortDesc = """""", - longDesc = -""" -Bond corrections: {'C-O': 2, 'C=C': 2, 'C-H': 5, 'C-C': 2} - -External symmetry: 1, optical isomers: 1 - -Geometry: -O 0.44861500 -0.42022700 -1.11985500 -C -1.62990300 -0.31077400 0.13113500 -C -0.18317900 0.01263900 0.01464300 -C 0.69240200 0.67580200 0.82641700 -C 1.76903400 -0.02615000 -1.03950300 -C 1.92836400 0.63240800 0.12347300 -H -1.79558700 -1.39235900 0.11153100 -H -2.02620600 0.08057800 1.06894700 -H -2.20018900 0.12750800 -0.69369400 -H 0.47524200 1.12417300 1.78183700 -H 2.40055200 -0.29604900 -1.86625900 -""", -) - -entry( - index = 54, - label = "TB21", + index = 51, + label = "P1", molecule = """ multiplicity 2 -1 O u0 p2 c0 {7,D} -2 C u0 p0 c0 {3,S} {4,S} {12,S} {13,S} -3 C u0 p0 c0 {2,S} {6,S} {10,S} {11,S} -4 C u0 p0 c0 {2,S} {7,S} {14,S} {15,S} -5 C u0 p0 c0 {7,S} {8,S} {16,S} {17,S} -6 C u0 p0 c0 {3,S} {18,S} {19,S} {20,S} -7 C u0 p0 c0 {1,D} {4,S} {5,S} -8 C u0 p0 c0 {5,S} {9,D} {21,S} -9 C u1 p0 c0 {8,D} {22,S} -10 H u0 p0 c0 {3,S} -11 H u0 p0 c0 {3,S} +1 C u0 p0 c0 {2,S} {3,S} {10,S} {11,S} +2 C u0 p0 c0 {1,S} {5,S} {12,S} {13,S} +3 C u0 p0 c0 {1,S} {14,S} {15,S} {16,S} +4 C u0 p0 c0 {5,D} {6,S} {9,S} +5 C u0 p0 c0 {2,S} {4,D} {17,S} +6 C u0 p0 c0 {4,S} {7,D} {18,S} +7 C u0 p0 c0 {6,D} {8,S} {19,S} +8 C u1 p0 c0 {7,S} {9,S} {20,S} +9 O u0 p2 c0 {4,S} {8,S} +10 H u0 p0 c0 {1,S} +11 H u0 p0 c0 {1,S} 12 H u0 p0 c0 {2,S} 13 H u0 p0 c0 {2,S} -14 H u0 p0 c0 {4,S} -15 H u0 p0 c0 {4,S} -16 H u0 p0 c0 {5,S} +14 H u0 p0 c0 {3,S} +15 H u0 p0 c0 {3,S} +16 H u0 p0 c0 {3,S} 17 H u0 p0 c0 {5,S} 18 H u0 p0 c0 {6,S} -19 H u0 p0 c0 {6,S} -20 H u0 p0 c0 {6,S} -21 H u0 p0 c0 {8,S} -22 H u0 p0 c0 {9,S} +19 H u0 p0 c0 {7,S} +20 H u0 p0 c0 {8,S} """, thermo = NASA( polynomials = [ - NASAPolynomial(coeffs=[3.12482,0.0925572,-0.000251538,6.35943e-07,-5.65601e-10,2425.15,15.8297], Tmin=(10,'K'), Tmax=(404.845,'K')), - NASAPolynomial(coeffs=[-1.12152,0.0866053,-5.19839e-05,1.50384e-08,-1.68229e-12,3161.57,37.3249], Tmin=(404.845,'K'), Tmax=(3000,'K')), + NASAPolynomial(coeffs=[3.69874,0.0459091,3.03309e-05,-6.21175e-08,2.42369e-11,-4367.61,15.2042], Tmin=(10,'K'), Tmax=(981.222,'K')), + NASAPolynomial(coeffs=[6.85582,0.0599555,-3.22892e-05,8.38467e-09,-8.48822e-13,-6282.92,-6.5698], Tmin=(981.222,'K'), Tmax=(3000,'K')), ], Tmin = (10,'K'), Tmax = (3000,'K'), - E0 = (20.1364,'kJ/mol'), + E0 = (-36.2446,'kJ/mol'), Cp0 = (33.2579,'J/(mol*K)'), - CpInf = (532.126,'J/(mol*K)'), + CpInf = (469.768,'J/(mol*K)'), ), shortDesc = """""", longDesc = """ -Bond corrections: {'C=O': 1, 'C-H': 13, 'C=C': 1, 'C-C': 6} +Bond corrections: {'C-H': 11, 'C-O': 2, 'C=C': 2, 'C-C': 5} +1D rotors: +pivots: [2, 4], dihedral: [3, 2, 4, 14], rotor symmetry: 3, max scan energy: 11.79 kJ/mol +pivots: [2, 3], dihedral: [4, 2, 3, 6], rotor symmetry: 1, max scan energy: 21.03 kJ/mol +pivots: [3, 6], dihedral: [2, 3, 6, 5], rotor symmetry: 1, max scan energy: 11.52 kJ/mol +* Invalidated! pivots: [5, 6], dihedral: [1, 5, 6, 3], invalidation reason: Another conformer for P1 exists which is 2.28 kJ/mol lower. + External symmetry: 1, optical isomers: 2 Geometry: -O 1.94167600 1.33598800 2.23521600 -C 1.37012100 3.89237700 1.12608200 -C 2.33843300 4.54888200 2.11847300 -C 0.29470800 3.02662200 1.78765800 -C -0.28671900 0.76803200 2.90716300 -C 3.39420100 5.41745900 1.42959800 -C 0.78601600 1.68562300 2.31414900 -C 0.27648100 -0.28042000 3.83398800 -C -0.25717200 -0.64383900 4.96970000 -H 1.76615700 5.16240900 2.82598600 -H 2.83182800 3.76897700 2.70443700 -H 1.93825500 3.27527900 0.42264300 -H 0.87653700 4.67250400 0.53527100 -H -0.17888400 3.55911600 2.62345600 -H -0.52460900 2.81417100 1.08788300 -H -1.06829500 1.35238800 3.39840800 -H -0.76678300 0.27983000 2.04530800 -H 2.93158800 6.22173700 0.84828000 -H 4.06628700 5.87887600 2.15806700 -H 4.00625600 4.82302700 0.74446400 -H 1.21403800 -0.73312600 3.49712100 -H -0.04833700 -1.34234400 5.76596700 +O 0.64234900 -0.45457200 -3.06055100 +C -2.07694600 0.75863300 -0.35312500 +C -1.89342300 -0.07189700 -1.64092800 +C -2.60848700 -0.07363700 0.81666700 +C -0.22101800 0.55457800 -3.46655900 +C -1.41915300 0.73634800 -2.80650300 +C 0.37355400 1.21893700 -4.55567700 +C 1.61301400 0.59120500 -4.79895000 +C 1.73365600 -0.41104000 -3.87483600 +H -1.11643700 1.21021000 -0.08351800 +H -2.76160400 1.59056000 -0.55529700 +H -2.85901700 -0.53679000 -1.88827400 +H -1.19410100 -0.88975300 -1.44954800 +H -1.92715300 -0.89522500 1.05839300 +H -2.72680700 0.53557000 1.71681800 +H -3.58350100 -0.51152000 0.58059400 +H -2.04870700 1.54334700 -3.16695800 +H -0.05913400 2.05072000 -5.08824100 +H 2.33563600 0.84016500 -5.56028200 +H 2.49779800 -1.14371800 -3.67694000 """, ) entry( - index = 55, + index = 52, label = "PBROO14", molecule = """ @@ -4067,78 +3926,5 @@ """, ) -entry( - index = 56, - label = "P1", - molecule = -""" -multiplicity 2 -1 C u0 p0 c0 {2,S} {3,S} {10,S} {11,S} -2 C u0 p0 c0 {1,S} {5,S} {12,S} {13,S} -3 C u0 p0 c0 {1,S} {14,S} {15,S} {16,S} -4 C u0 p0 c0 {5,D} {6,S} {9,S} -5 C u0 p0 c0 {2,S} {4,D} {17,S} -6 C u0 p0 c0 {4,S} {7,D} {18,S} -7 C u0 p0 c0 {6,D} {8,S} {19,S} -8 C u1 p0 c0 {7,S} {9,S} {20,S} -9 O u0 p2 c0 {4,S} {8,S} -10 H u0 p0 c0 {1,S} -11 H u0 p0 c0 {1,S} -12 H u0 p0 c0 {2,S} -13 H u0 p0 c0 {2,S} -14 H u0 p0 c0 {3,S} -15 H u0 p0 c0 {3,S} -16 H u0 p0 c0 {3,S} -17 H u0 p0 c0 {5,S} -18 H u0 p0 c0 {6,S} -19 H u0 p0 c0 {7,S} -20 H u0 p0 c0 {8,S} -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[3.69874,0.0459091,3.03309e-05,-6.21175e-08,2.42369e-11,-4367.61,15.2042], Tmin=(10,'K'), Tmax=(981.222,'K')), - NASAPolynomial(coeffs=[6.85582,0.0599555,-3.22892e-05,8.38467e-09,-8.48822e-13,-6282.92,-6.5698], Tmin=(981.222,'K'), Tmax=(3000,'K')), - ], - Tmin = (10,'K'), - Tmax = (3000,'K'), - E0 = (-36.2446,'kJ/mol'), - Cp0 = (33.2579,'J/(mol*K)'), - CpInf = (469.768,'J/(mol*K)'), - ), - shortDesc = """""", - longDesc = -""" -Bond corrections: {'C-H': 11, 'C-O': 2, 'C=C': 2, 'C-C': 5} -1D rotors: -pivots: [2, 4], dihedral: [3, 2, 4, 14], rotor symmetry: 3, max scan energy: 11.79 kJ/mol -pivots: [2, 3], dihedral: [4, 2, 3, 6], rotor symmetry: 1, max scan energy: 21.03 kJ/mol -pivots: [3, 6], dihedral: [2, 3, 6, 5], rotor symmetry: 1, max scan energy: 11.52 kJ/mol -* Invalidated! pivots: [5, 6], dihedral: [1, 5, 6, 3], invalidation reason: Another conformer for P1 exists which is 2.28 kJ/mol lower. - -External symmetry: 1, optical isomers: 2 - -Geometry: -O 0.64234900 -0.45457200 -3.06055100 -C -2.07694600 0.75863300 -0.35312500 -C -1.89342300 -0.07189700 -1.64092800 -C -2.60848700 -0.07363700 0.81666700 -C -0.22101800 0.55457800 -3.46655900 -C -1.41915300 0.73634800 -2.80650300 -C 0.37355400 1.21893700 -4.55567700 -C 1.61301400 0.59120500 -4.79895000 -C 1.73365600 -0.41104000 -3.87483600 -H -1.11643700 1.21021000 -0.08351800 -H -2.76160400 1.59056000 -0.55529700 -H -2.85901700 -0.53679000 -1.88827400 -H -1.19410100 -0.88975300 -1.44954800 -H -1.92715300 -0.89522500 1.05839300 -H -2.72680700 0.53557000 1.71681800 -H -3.58350100 -0.51152000 0.58059400 -H -2.04870700 1.54334700 -3.16695800 -H -0.05913400 2.05072000 -5.08824100 -H 2.33563600 0.84016500 -5.56028200 -H 2.49779800 -1.14371800 -3.67694000 -""", -) diff --git a/input/thermo/libraries/2BF_thermo_wo_rotors.py b/input/thermo/libraries/2BF_thermo_wo_rotors.py new file mode 100755 index 0000000000..41118fdb5f --- /dev/null +++ b/input/thermo/libraries/2BF_thermo_wo_rotors.py @@ -0,0 +1,111 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "2BF_thermo_wo_rotors" +shortDesc = "" +longDesc = """ +ARC v1.1.0 +ARC projects 2BF_thermo_1, 2BF_thermo_2, 2BF_thermo_3, 2BF_thermo_4 + +Levels of theory used: + +Conformers: wb97xd/def2svp, software: gaussian (dft) +TS guesses: None +Composite method: cbs-qb3, software: gaussian (composite) (using a fine grid) +Frequencies: b3lyp/cbsb7, software: gaussian (dft) +Rotor scans: b3lyp/cbsb7, software: gaussian (dft) +Using p-type bond additivity corrections for thermo + +Using the following ESS settings: {'gaussian': ['local'], 'molpro': ['local']} +""" +entry( + index = 0, + label = "TB7", + molecule = +""" +multiplicity 2 +1 O u1 p2 c0 {5,S} +2 C u0 p0 c0 {3,S} {4,S} {7,S} {8,S} +3 C u0 p0 c0 {2,S} {5,D} {9,S} +4 C u0 p0 c0 {2,S} {6,D} {10,S} +5 C u0 p0 c0 {1,S} {3,D} {6,S} +6 C u0 p0 c0 {4,D} {5,S} {11,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {4,S} +11 H u0 p0 c0 {6,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[4.0945,-0.00914745,0.000179528,-3.11949e-07,1.72915e-10,7230.53,10.5421], Tmin=(10,'K'), Tmax=(575.423,'K')), + NASAPolynomial(coeffs=[0.211161,0.0442362,-2.8421e-05,8.6726e-09,-1.00923e-12,7240.56,23.3346], Tmin=(575.423,'K'), Tmax=(3000,'K')), + ], + Tmin = (10,'K'), + Tmax = (3000,'K'), + E0 = (60.099,'kJ/mol'), + Cp0 = (33.2579,'J/(mol*K)'), + CpInf = (257.749,'J/(mol*K)'), + ), + shortDesc = """""", + longDesc = +""" +Bond corrections: {'C-C': 3, 'C-H': 5, 'C-O': 1, 'C=C': 2} + +External symmetry: 1, optical isomers: 1 + +Geometry: +O -2.11183600 1.44157200 -0.34260300 +C -1.09179700 0.77674700 -0.18192800 +C -1.00461600 -0.65589200 0.04189600 +C 0.42204500 -1.06270700 0.18675400 +C 1.16236300 0.25104200 0.02907400 +C 0.31953000 1.26955000 -0.17533300 +H -1.86259200 -1.31232300 0.09237900 +H 0.72574600 -1.79975800 -0.57011800 +H 0.62553700 -1.53589300 1.15784600 +H 2.24203400 0.31669200 0.08166200 +H 0.57358500 2.31097000 -0.31962800 +""", +) + +entry( + index = 1, + label = "TB11", + molecule = +""" +multiplicity 2 +1 C u0 p0 c0 {2,D} {4,S} {5,S} +2 C u0 p0 c0 {1,D} {3,D} +3 C u1 p0 c0 {2,D} {6,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[3.94764,0.00319149,5.64828e-05,-1.18956e-07,7.50654e-11,41022.3,5.4829], Tmin=(10,'K'), Tmax=(537.535,'K')), + NASAPolynomial(coeffs=[3.91782,0.0150707,-9.19614e-06,2.84527e-09,-3.46567e-13,40857.1,4.04168], Tmin=(537.535,'K'), Tmax=(3000,'K')), + ], + Tmin = (10,'K'), + Tmax = (3000,'K'), + E0 = (341.061,'kJ/mol'), + Cp0 = (33.2579,'J/(mol*K)'), + CpInf = (133.032,'J/(mol*K)'), + ), + shortDesc = """""", + longDesc = +""" +Bond corrections: {'C-H': 3, 'C=C': 2} + +External symmetry: 2, optical isomers: 1 + +Geometry: +C 1.50226700 -0.00969800 0.11174200 +C 0.28357700 -0.00183100 0.02109300 +C -1.07978000 0.00697100 -0.08031700 +H 2.56148000 -0.01653600 0.19052900 +H -1.62316900 0.93822700 -0.18356100 +H -1.64437500 -0.91713300 -0.05948700 +""", +) \ No newline at end of file