ND Hindered Rotor Improvements

arkane/input.py

@@ -58,6 +58,7 @@
 from rmgpy.thermo.nasa import NASAPolynomial, NASA
 from rmgpy.thermo.thermodata import ThermoData
 from rmgpy.thermo.wilhoit import Wilhoit
+from rmgpy.kinetics.uncertainties import RateUncertainty
 from rmgpy.transport import TransportData
 from rmgpy.util import as_list
 
@@ -567,6 +568,7 @@ def load_input_file(path):
         'SingleExponentialDown': SingleExponentialDown,
         # Kinetics
         'Arrhenius': Arrhenius,
+        'RateUncertainty' : RateUncertainty,
         # Statistical mechanics
         'IdealGasTranslation': IdealGasTranslation,
         'LinearRotor': LinearRotor,

examples/arkane/species/Toulene_Hindered_Rotor_SemiClassicalND/toluene_HinderedRotor.py

@@ -1,5 +1,16 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+bonds = {
+    'C-C': 4,
+    'C-H': 8,
+    'C=C': 3,
+}
+
+externalSymmetry = 1
+
+spinMultiplicity = 1
+
+opticalIsomers = 1
 
 energy = {
     'CBS-QB3': Log('TolueneEnergy.log')

rmgpy/statmech/conformer.pyx

@@ -384,7 +384,8 @@ cdef class Conformer(RMGObject):
         elif pivots[0] in top1 and pivots[1] in top1:
             raise ValueError('Both pivot atoms included in top; you must specify only one pivot atom that belongs'
                              ' with the specified top.')
-
+        elif 0 in top1:
+            raise ValueError('Top must be one indexed, top1: {}'.format(top1))
         # Enumerate atoms in other top
         top2 = [i + 1 for i in range(n_atoms) if i + 1 not in top1]
 

rmgpy/statmech/ndTorsions.py

@@ -31,6 +31,7 @@
 import os
 import os.path
 import subprocess
+import itertools
 
 import numdifftools as nd
 import numpy as np
@@ -576,12 +577,9 @@ def fit(self):
         generate splines for the first and second derivatives of the partition function
         """
         N = len(self.pivots)
-        if N > 2:
+        if N > 1:
             self.V = interpolate.LinearNDInterpolator(self.phis, self.Es)
             self.rootD = interpolate.LinearNDInterpolator(self.phis, self.rootDs)
-        elif N == 2:
-            self.V = interpolate.SmoothBivariateSpline(self.phis[:, 0], self.phis[:, 1], self.Es)
-            self.rootD = interpolate.SmoothBivariateSpline(self.phis[:, 0], self.phis[:, 1], self.rootDs)
         else:
             self.V = interpolate.CubicSpline(self.phis, self.Es)
             self.rootD = interpolate.CubicSpline(self.phis, self.rootDs)
@@ -600,12 +598,22 @@ def calc_partition_function(self, T):
         """
         calculate the classical/semiclassical partition function at a given temperature
         """
-        rngs = [(0.0, 2.0 * np.pi) for x in range(len(self.pivots))]
 
         def f(*phis):
             return self.rootD(*phis) * np.exp(-self.V(*phis) / (constants.R * T))
-
-        intg = inte.nquad(f, ranges=rngs)[0]
+
+        rphis = np.linspace(0, 2.0*np.pi, 30)
+        Imat = np.zeros([len(rphis) for i in range(len(self.pivots))])
+        it = itertools.product(*[list(range(len(rphis))) for i in range(len(self.pivots))])
+
+        for coords in it:
+            Imat[coords] = f(*rphis[np.array(coords)])
+
+        for i in range(len(self.pivots)):
+            Imat = inte.simps(Imat, rphis)
+
+        intg = Imat
+
         Q = intg * (2.0 * np.pi * constants.kB * T / constants.h**2) ** (len(self.pivots) / 2.0) / np.prod(self.sigmas)
 
         if self.semiclassical:
@@ -615,7 +623,6 @@ def f(*phis):
             x = constants.h * freqs / (constants.kB * T)
             out = x / (1.0 - np.exp(-x))
             Q *= np.prod(out)
-
         return Q
 
     def get_partition_function(self, T):

rmgpy/statmech/ndTorsionsTest.py

@@ -114,7 +114,7 @@ def test_hindered_rotor_nd(self):
         self.hdnd.read_scan()
         self.assertAlmostEqual(self.hdnd.Es[0], 20.048316823666962, 4)
         self.hdnd.fit()
-        self.assertAlmostEqual(self.hdnd.calc_partition_function(300.0), 2.85254214434672, 5)
+        self.assertAlmostEqual(self.hdnd.calc_partition_function(300.0), 2.8524691948593133, 5)
 
 
 if __name__ == '__main__':