Merge pull request #256 from connie/qchem

Qchem Module for Cantherm.

Author: connie

examples/cantherm/reactions/23dimethylpropoxy/cantherm_dimetpropoxy.out

@@ -0,0 +1,96 @@
+# Coordinates for dimetpropoxy (angstroms):
+#   C    0.0000    0.0000    0.0000
+#   C    0.5847    1.3498   -0.4247
+#   C   -0.3680    2.4927   -0.0596
+#   C    1.9489    1.6005    0.2416
+#   C    3.0151    0.5519   -0.1732
+#   O    2.5011    2.7974   -0.1357
+#   H   -1.0250   -0.1099   -0.3763
+#   H   -0.0415   -0.0712    1.0976
+#   H    0.5865   -0.8473   -0.3756
+#   H    0.7553    1.3572   -1.5131
+#   H   -0.5498    2.5044    1.0255
+#   H   -1.3364    2.3739   -0.5615
+#   H    0.0563    3.4630   -0.3459
+#   H    1.8443    1.5532    1.3464
+#   H    3.0942    0.5186   -1.2657
+#   H    2.7067   -0.4294    0.2034
+#   H    3.9893    0.8093    0.2531
+conformer(
+    label = 'dimetpropoxy',
+    E0 = (-714283, 'kJ/mol'),
+    modes = [
+        IdealGasTranslation(mass=(87.081, 'amu')),
+        NonlinearRotor(
+            inertia = ([109.585, 168.42, 254.532], 'amu*angstrom^2'),
+            symmetry = 1,
+        ),
+        HarmonicOscillator(
+            frequencies = ([76.6052, 186.455, 191.636, 234.446, 247.313, 318.777, 329.629, 372.351, 442.006, 468.193, 763.781, 879.235, 893.4, 898.659, 936.032, 956.026, 988.249, 1075.39, 1115.92, 1140.49, 1157.11, 1230.46, 1254.14, 1307.33, 1331.07, 1339.86, 1360.26, 1375.36, 1432.51, 1439.04, 1446.46, 1451.11, 1456.22, 1466.11, 2852.38, 2916.49, 2919.41, 2929.98, 2947.12, 2983.89, 2989.25, 2999.98, 3005.72, 3030.24, 3037.25], 'cm^-1'),
+        ),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+)
+
+# Coordinates for dimetpropoxy_betasci (angstroms):
+#   C    0.0000    0.0000    0.0000
+#   C    0.3933    1.3553   -0.5133
+#   C   -0.3992    2.5309   -0.0252
+#   C    2.2646    1.7438    0.2725
+#   C    3.0582    0.5248   -0.1747
+#   O    2.5003    2.8638   -0.2091
+#   H   -1.0613   -0.1878   -0.2340
+#   H    0.0978   -0.0527    1.0945
+#   H    0.5868   -0.8082   -0.4482
+#   H    0.7200    1.4038   -1.5543
+#   H   -0.5221    2.4933    1.0667
+#   H   -1.4078    2.5152   -0.4695
+#   H    0.0890    3.4732   -0.2927
+#   H    1.8198    1.6748    1.2927
+#   H    3.0712    0.4600   -1.2691
+#   H    2.6659   -0.4039    0.2536
+#   H    4.0935    0.6524    0.1687
+conformer(
+    label = 'dimetpropoxy_betasci',
+    E0 = (-714248, 'kJ/mol'),
+    modes = [
+        IdealGasTranslation(mass=(87.081, 'amu')),
+        NonlinearRotor(
+            inertia = ([116.366, 182.943, 273.434], 'amu*angstrom^2'),
+            symmetry = 1,
+        ),
+        HarmonicOscillator(
+            frequencies = ([54.586, 137.512, 160.544, 179.574, 244.433, 258.588, 295.637, 332.49, 390.674, 481.247, 817.355, 846.53, 864.952, 898.01, 908.371, 910.897, 1000.4, 1077.97, 1114.11, 1121.38, 1158.79, 1317.47, 1327.16, 1351.9, 1369.23, 1374.51, 1425.6, 1428.19, 1429.34, 1435.69, 1447.31, 1451, 1543.93, 2831.47, 2900.98, 2910.98, 2935.27, 2955.13, 2968.69, 3003.86, 3016.14, 3025.87, 3029.75, 3054.65], 'cm^-1'),
+        ),
+    ],
+    spinMultiplicity = 2,
+    opticalIsomers = 1,
+    frequency = (-383.861, 'cm^-1'),
+)
+
+#   ======= =========== =========== =========== ===============
+#   Temp.   k (TST)     Tunneling   k (TST+T)   Units
+#   ======= =========== =========== =========== ===============
+#     300 K   1.677e+07           1   1.677e+07 s^-1
+#     400 K   8.206e+08           1   8.206e+08 s^-1
+#     500 K   8.867e+09           1   8.867e+09 s^-1
+#     600 K   4.433e+10           1   4.433e+10 s^-1
+#     800 K   3.408e+11           1   3.408e+11 s^-1
+#    1000 K   1.177e+12           1   1.177e+12 s^-1
+#    1500 K   6.267e+12           1   6.267e+12 s^-1
+#    2000 K   1.458e+13           1   1.458e+13 s^-1
+#   ======= =========== =========== =========== ===============
+kinetics(
+    label = 'dimetpropoxy = dimetpropoxy_betasci',
+    kinetics = Arrhenius(
+        A = (9.43418e+12, 's^-1'),
+        n = 0.361953,
+        Ea = (38.2618, 'kJ/mol'),
+        T0 = (1, 'K'),
+        Tmin = (303.03, 'K'),
+        Tmax = (2500, 'K'),
+        comment = 'Fitted to 59 data points; dA = *|/ 1.11869, dn = +|- 0.0147204, dEa = +|- 0.0809767 kJ/mol',
+    ),
+)
+

examples/cantherm/reactions/23dimethylpropoxy/cantherm_dimetpropoxy.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+title = 'dimetpropoxy intra-H migrations and decomposition pathways'
+
+description = \
+"""
+NONE
+"""
+
+modelChemistry = "M08SO"
+frequencyScaleFactor = 0.983
+useHinderedRotors = True
+useBondCorrections = False
+
+species('dimetpropoxy', './dimetpropoxy.py')
+transitionState('dimetpropoxy_betasci', './dimetpropoxy_betasci.py')
+
+reaction(
+    label = 'dimetpropoxy = dimetpropoxy_betasci',
+    reactants = ['dimetpropoxy'],
+    products = ['dimetpropoxy'],
+    transitionState = 'dimetpropoxy_betasci',
+#    tunneling='Eckart',
+)
+
+kinetics('dimetpropoxy = dimetpropoxy_betasci') 
+
+statmech('dimetpropoxy_betasci')
+statmech('dimetpropoxy')