Determine the rotor symmetry number from the potential scan

arkane/commonTest.py

@@ -56,13 +56,13 @@ def test_check_conformer_energy(self):
         """
         test the check_conformer_energy function with an list of energies.
         """
-        Vlist = [-272.2779012225, -272.2774933703, -272.2768397635, -272.2778432059, -272.278645477, -272.2789602654,
+        v_list = [-272.2779012225, -272.2774933703, -272.2768397635, -272.2778432059, -272.278645477, -272.2789602654,
                  -272.2788749196, -272.278496709, -272.2779350675, -272.2777008843, -272.2777167286, -272.2780937643,
                  -272.2784838846, -272.2788050464, -272.2787865352, -272.2785091607, -272.2779977452, -272.2777957743,
                  -272.2779134906, -272.2781827547, -272.278443339, -272.2788244214, -272.2787748749]
-        Vlist = numpy.array(Vlist, numpy.float64)
-        Vdiff = (Vlist[0] - numpy.min(Vlist)) * constants.E_h * constants.Na / 1000
-        self.assertAlmostEqual(Vdiff / 2.7805169838282797, 1, 5)
+        v_list = numpy.array(v_list, numpy.float64)
+        v_diff = (v_list[0] - numpy.min(v_list)) * constants.E_h * constants.Na / 1000
+        self.assertAlmostEqual(v_diff / 2.7805169838282797, 1, 5)
 
 
 class TestArkaneJob(unittest.TestCase):
@@ -270,24 +270,6 @@ def testTransitionStateStatmech(self):
         job.load()
 
 
-class TestStatmech(unittest.TestCase):
-    """
-    Contains unit tests of statmech.py
-    """
-    @classmethod
-    def setUp(self):
-        arkane = Arkane()
-        self.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
-                                                         'data', 'Benzyl', 'input.py'))
-
-    def test_gaussian_log_file_error(self):
-        """Test that the proper error is raised if gaussian geometry and frequency file paths are the same"""
-        job = self.job_list[-2]
-        self.assertTrue(isinstance(job, StatMechJob))
-        with self.assertRaises(InputError):
-            job.load()
-
-
 class TestGetMass(unittest.TestCase):
     """
     Contains unit tests of common.py

arkane/gaussian.py

@@ -382,7 +382,7 @@ def loadScanEnergies(self):
         check_conformer_energy(Vlist, self.path)
 
         # Adjust energies to be relative to minimum energy conformer
-        # Also convert units from Hartree/particle to kJ/mol
+        # Also convert units from Hartree/particle to J/mol
         Vlist -= numpy.min(Vlist)
         Vlist *= constants.E_h * constants.Na
 

arkane/statmechTest.py

@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),           #
+# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
+#                                                                             #
+# Permission is hereby granted, free of charge, to any person obtaining a     #
+# copy of this software and associated documentation files (the 'Software'),  #
+# to deal in the Software without restriction, including without limitation   #
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,    #
+# and/or sell copies of the Software, and to permit persons to whom the       #
+# Software is furnished to do so, subject to the following conditions:        #
+#                                                                             #
+# The above copyright notice and this permission notice shall be included in  #
+# all copies or substantial portions of the Software.                         #
+#                                                                             #
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,    #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER      #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING     #
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER         #
+# DEALINGS IN THE SOFTWARE.                                                   #
+#                                                                             #
+###############################################################################
+
+"""
+This script contains unit tests of the :mod:`arkane.main` module.
+"""
+
+import unittest
+import os
+
+from rmgpy.exceptions import InputError
+
+from arkane import Arkane
+from arkane.statmech import StatMechJob, determine_rotor_symmetry
+from arkane.qchem import QChemLog
+
+################################################################################
+
+
+class TestStatmech(unittest.TestCase):
+    """
+    Contains unit tests of the StatmechJob class.
+    """
+    @classmethod
+    def setUp(self):
+        arkane = Arkane()
+        self.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                                          'data', 'Benzyl', 'input.py'))
+
+    def test_gaussian_log_file_error(self):
+        """Test that the proper error is raised if gaussian geometry and frequency file paths are not the same"""
+        job = self.job_list[-2]
+        self.assertTrue(isinstance(job, StatMechJob))
+        with self.assertRaises(InputError):
+            job.load()
+
+    def test_rotor_symmetry_determination(self):
+        """
+        Test that the correct symmetry number is determined for rotor potential scans.
+        """
+        path1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_NRotor.out')
+        path2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'NCC_CRotor.out')
+        scan_log1 = QChemLog(path1)
+        scan_log2 = QChemLog(path2)
+        v_list1, angle = scan_log1.loadScanEnergies()
+        v_list2, angle = scan_log2.loadScanEnergies()
+        symmetry1 = determine_rotor_symmetry(energies=v_list1, label='NCC', pivots=[])
+        symmetry2 = determine_rotor_symmetry(energies=v_list2, label='NCC', pivots=[])
+        self.assertEqual(symmetry1, 1)
+        self.assertEqual(symmetry2, 3)
+
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

documentation/source/users/arkane/input.rst

@@ -306,8 +306,10 @@ scan in the following format::
 
 The ``Energy`` can be in units of ``kJ/mol``, ``J/mol``, ``cal/mol``, ``kcal/mol``, ``cm^-1`` or ``hartree``.
 
-The ``symmetry`` parameter will usually equal either 1, 2 or 3. Below are examples of internal rotor scans with these
-commonly encountered symmetry numbers. First, ``symmetry = 3``:
+The ``symmetry`` parameter will usually equal either 1, 2 or 3. It could be determined automatically by Arkane
+(by simply not specifying it altogether), however it is always better to explicitly specify it if it is known. If it is
+determined by Arkane, the log file will specify the determined value and what it was based on. Below are examples of
+internal rotor scans with these commonly encountered symmetry numbers. First, ``symmetry = 3``:
 
 .. image:: symmetry_3_example.png
 

documentation/source/users/arkane/input_pdep.rst

@@ -351,8 +351,10 @@ scan in the following format::
 
 The ``Energy`` can be in units of ``kJ/mol``, ``J/mol``, ``cal/mol``, ``kcal/mol``, ``cm^-1`` or ``hartree``.
 
-The ``symmetry`` parameter will usually equal either 1, 2 or 3. Below are examples of internal rotor scans with these
-commonly encountered symmetry numbers. First, ``symmetry = 3``:
+The ``symmetry`` parameter will usually equal either 1, 2 or 3. It could be determined automatically by Arkane
+(by simply not specifying it altogether), however it is always better to explicitly specify it if it is known. If it is
+determined by Arkane, the log file will specify the determined value and what it was based on. Below are examples of
+internal rotor scans with these commonly encountered symmetry numbers. First, ``symmetry = 3``:
 
 .. image:: symmetry_3_example.png
 

examples/arkane/species/Benzyl/benzyl.py

@@ -23,6 +23,4 @@
 
 frequencies = Log('BenzylFreq.log')
 
-rotors = [ 
-    HinderedRotor(scanLog=Log('BenzylRot1.log'), pivots=[12,4], top=[12,13,14], symmetry=2, fit='best'),
-    ]
+rotors = [HinderedRotor(scanLog=Log('BenzylRot1.log'), pivots=[12,4], top=[12,13,14])]

examples/arkane/species/C2H5/ethyl.py

@@ -19,14 +19,15 @@
     'Klip_2': -78.98344186,
 }
 
-geometry = Log('ethyl_cbsqb3.log')
+geometry = Log('ethyl_b3lyp.log')
 
-frequencies = Log('ethyl_cbsqb3.log')
+frequencies = Log('ethyl_b3lyp.log')
 
 """pivot are the two atoms that are attached to the rotor
 top contains the atoms that are being rotated including one of the atoms from pivots
 symmetry is the symmetry number of the scan
-fit is fit of the scan data. It defaults to 'best', but can also be assigned as 'cosine' or 'fourier'"""
-rotors = [
-    HinderedRotor(scanLog=Log('ethyl_scan_72.log'), pivots=[1,2], top=[1,3,4], symmetry=6, fit='best')
-]
+fit is fit of the scan data. It defaults to 'best', but can also be assigned as 'cosine' or 'fourier'
+Principally, the rotor symmetry can be automatically determined by Arkane, but could also be given by the user
+(then the user's input overrides Arkane's determination):
+rotors = [HinderedRotor(scanLog=Log('ethyl_scan_72.log'), pivots=[1,2], top=[1,3,4], symmetry=6, fit='best')]"""
+rotors = [HinderedRotor(scanLog=Log('ethyl_scan_72.log'), pivots=[1,2], top=[1,3,4])]

examples/arkane/species/C2H5/input.py

@@ -7,5 +7,4 @@
 
 species('C2H5', 'ethyl.py')
 
-statmech('C2H5')
 thermo('C2H5', 'Wilhoit')

examples/arkane/species/C2H6/C2H6.py

@@ -28,7 +28,8 @@
 """pivot are the two atoms that are attached to the rotor
 top contains the atoms that are being rotated including one of the atoms from pivots
 symmetry is the symmetry number of the scan
-fit is fit of the scan data. It defaults to 'best', but can also be assigned as 'cosine' or 'fourier'"""
-rotors = [
-    HinderedRotor(scanLog=Log('ethane_scan_1.log'), pivots=[1,5], top=[1,2,3,4], symmetry=3, fit='best'),
-]
+fit is fit of the scan data. It defaults to 'best', but can also be assigned as 'cosine' or 'fourier'
+Principally, the rotor symmetry can be automatically determined by Arkane, but could also be given by the user
+(then the user's input overrides Arkane's determination):
+rotors = [HinderedRotor(scanLog=Log('ethane_scan_1.log'), pivots=[1,5], top=[1,2,3,4], symmetry=3, fit='best')]"""
+rotors = [HinderedRotor(scanLog=Log('ethane_scan_1.log'), pivots=[1,5], top=[1,2,3,4], fit='best')]