Merge pull request #570 from ReactionMechanismGenerator/eni_1dhr

Refit Intra R Add Endo/Exocyclic Rate Rules

Author: xiaoruiDong

input/kinetics/families/Intra_R_Add_Endocyclic/groups.py

@@ -0,0 +1,159 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "heavy_oil_ccsdtf12_1dHR"
+shortDesc = "Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann."
+longDesc = """
+This library is made by Kevin Spiekermann and contains the thermochemistry for select species from heavy oil pryolysis mechanisms.
+
+All species were calculated using CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP i.e.
+Optimization and frequency calculations were done at wB97X-D3/def2-TZVP with QChem.
+High level single point calculations were done with CCSD(T)-F12a/cc-pVDZ-F12 with MOLPRO.
+
+A thorough conformer search was done for all species included in this file. 
+Although transition states are not included in this file, a conformer search was done on the TS as well since this is relevant for the kinetics of the training reactions added to the corresponding reaction families.
+1D Hindered Rotors were calculated for steps of 10 degrees up to the full 360 degree cycle, with geometry optimization on each step.
+
+The frequency scaling factor at ωB97X-D3/def2-TZVP was calculated as 0.984 using the method from Alecu et al. (https://pubs.acs.org/doi/abs/10.1021/ct100326h)
+All values include atom energy corrections, which were fit to the single point energies of experimental geometries for 16 small molecules (no geometry optimization was performed).
+All values also include bond additivity corrections.
+BACs were fit using about 400 species from our reference set using the procedure from Petersson et al. 1998 (http://aip.scitation.org/doi/10.1063/1.477794)
+
+Disclaimer: The number of significant figures displayed does not reflect the accuracy of the thermochemistry values.
+After fitting the Petersson BACs, the enthalpy values at the coupled cluster level have an MAE (RMSE) of 0.52 (0.83) kcal/mol relative to our reference set.
+These values are similar to those from other published works:
+- Bischoff, F. A., Wolfsegger, S., Tew, D. P. & Klopper, W. Assessment of basis sets for f12 explicitly-correlated molecular electronic-structure methodfs. Mol. Phys. 107, 963–975 (2009).
+- Knizia, G., Adler, T. B. & Werner, H.-J. Simplified ccsd (t)-f12 methods: Theory and benchmarks. The J. chemical physics 130, 054104 (2009). 
+- Adler, T. B., Knizia, G. & Werner, H.-J. A simple and efficient ccsd(t)-f12 approximation (2007).
+- Pfeiffer, F., Rauhut, G., Feller, D. & Peterson, K. A. Anharmonic zero point vibrational energies: Tipping the scales in accurate thermochemistry calculations? The J. chemical physics 138, 044311 (2013).
+- Shang, Y., Ning, H., Shi, J., Wang, H. & Luo, S.-N. Chemical kinetics of h-abstractions from dimethyl amine by h, ch 3, oh, and ho 2 radicals with multi-structural torsional anharmonicity. Phys. Chem. Chem. Phys. 21, 12685–12696 (2019).
+"""
+entry(
+    index = 0,
+    label = "product0",
+    molecule = 
+"""
+multiplicity 2
+1  C u0 p0 c0 {2,S} {3,S} {6,S} {8,S}
+2  C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
+3  C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
+4  C u0 p0 c0 {2,S} {5,S} {13,S} {14,S}
+5  C u1 p0 c0 {3,S} {4,S} {15,S}
+6  C u0 p0 c0 {1,S} {7,D} {16,S}
+7  C u0 p0 c0 {6,D} {17,S} {18,S}
+8  H u0 p0 c0 {1,S}
+9  H u0 p0 c0 {2,S}
+10 H u0 p0 c0 {2,S}
+11 H u0 p0 c0 {3,S}
+12 H u0 p0 c0 {3,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {4,S}
+15 H u0 p0 c0 {5,S}
+16 H u0 p0 c0 {6,S}
+17 H u0 p0 c0 {7,S}
+18 H u0 p0 c0 {7,S}
+""",
+    thermo = NASA(
+        polynomials = [
+            NASAPolynomial(coeffs=[3.9257,0.00488388,0.000218528,-4.34102e-07,2.83245e-10,19471.1,12.6608], Tmin=(10,'K'), Tmax=(392.75,'K')),
+            NASAPolynomial(coeffs=[-2.84849,0.0738789,-4.49891e-05,1.32176e-08,-1.50109e-12,20003.2,39.011], Tmin=(392.75,'K'), Tmax=(3000,'K')),
+        ],
+        Tmin = (10,'K'),
+        Tmax = (3000,'K'),
+        E0 = (161.878,'kJ/mol'),
+        Cp0 = (33.2579,'J/(mol*K)'),
+        CpInf = (432.353,'J/(mol*K)'),
+    ),
+    shortDesc = """Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.""",
+    longDesc = 
+"""
+Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.
+""",
+)
+
+entry(
+    index = 1,
+    label = "product1",
+    molecule = 
+"""
+multiplicity 2
+1  C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
+2  C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
+3  C u0 p0 c0 {1,S} {6,S} {13,S} {14,S}
+4  C u0 p0 c0 {2,S} {5,S} {11,S} {12,S}
+5  C u0 p0 c0 {4,S} {6,D} {15,S}
+6  C u0 p0 c0 {3,S} {5,D} {16,S}
+7  C u1 p0 c0 {1,S} {17,S} {18,S}
+8  H u0 p0 c0 {1,S}
+9  H u0 p0 c0 {2,S}
+10 H u0 p0 c0 {2,S}
+11 H u0 p0 c0 {4,S}
+12 H u0 p0 c0 {4,S}
+13 H u0 p0 c0 {3,S}
+14 H u0 p0 c0 {3,S}
+15 H u0 p0 c0 {5,S}
+16 H u0 p0 c0 {6,S}
+17 H u0 p0 c0 {7,S}
+18 H u0 p0 c0 {7,S}
+""",
+    thermo = NASA(
+        polynomials = [
+            NASAPolynomial(coeffs=[3.93148,0.00443778,0.000214765,-4.15326e-07,2.62941e-10,18256.3,11.7966], Tmin=(10,'K'), Tmax=(408.605,'K')),
+            NASAPolynomial(coeffs=[-3.22181,0.0750039,-4.62666e-05,1.37976e-08,-1.59062e-12,18836.4,39.8497], Tmin=(408.605,'K'), Tmax=(3000,'K')),
+        ],
+        Tmin = (10,'K'),
+        Tmax = (3000,'K'),
+        E0 = (151.777,'kJ/mol'),
+        Cp0 = (33.2579,'J/(mol*K)'),
+        CpInf = (432.353,'J/(mol*K)'),
+    ),
+    shortDesc = """Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.""",
+    longDesc = 
+"""
+Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.
+""",
+)
+
+entry(
+    index = 2,
+    label = "reactant0",
+    molecule = 
+"""
+multiplicity 2
+1  C u0 p0 c0 {2,S} {4,S} {10,S} {11,S}
+2  C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
+3  C u0 p0 c0 {2,S} {5,D} {12,S}
+4  C u0 p0 c0 {1,S} {6,D} {13,S}
+5  C u0 p0 c0 {3,D} {7,S} {14,S}
+6  C u0 p0 c0 {4,D} {17,S} {18,S}
+7  C u1 p0 c0 {5,S} {15,S} {16,S}
+8  H u0 p0 c0 {2,S}
+9  H u0 p0 c0 {2,S}
+10 H u0 p0 c0 {1,S}
+11 H u0 p0 c0 {1,S}
+12 H u0 p0 c0 {3,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {5,S}
+15 H u0 p0 c0 {7,S}
+16 H u0 p0 c0 {7,S}
+17 H u0 p0 c0 {6,S}
+18 H u0 p0 c0 {6,S}
+""",
+    thermo = NASA(
+        polynomials = [
+            NASAPolynomial(coeffs=[3.71953,0.0393074,2.68863e-05,-5.10858e-08,1.9113e-11,21097.9,12.6025], Tmin=(10,'K'), Tmax=(1008.73,'K')),
+            NASAPolynomial(coeffs=[5.44059,0.0545486,-2.85895e-05,7.26324e-09,-7.22401e-13,19628.1,-1.28013], Tmin=(1008.73,'K'), Tmax=(3000,'K')),
+        ],
+        Tmin = (10,'K'),
+        Tmax = (3000,'K'),
+        E0 = (175.467,'kJ/mol'),
+        Cp0 = (33.2579,'J/(mol*K)'),
+        CpInf = (432.353,'J/(mol*K)'),
+    ),
+    shortDesc = """Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.""",
+    longDesc = 
+"""
+Calculated at CCSD(T)-F12a/cc-pVDZ-F12//wB97X-D3/def2-TZVP by Kevin Spiekermann.
+""",
+)
+