Tests: Test scaling factors in utilities

arc/utils/scaleTest.py

@@ -0,0 +1,143 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+This module contains unit tests for the arc.utils.scale module
+"""
+
+from __future__ import (absolute_import, division, print_function, unicode_literals)
+import unittest
+import os
+import shutil
+import time
+
+from rmgpy import settings
+
+from arc.utils.scale import calculate_truhlar_scaling_factors, summarize_results, get_species_list, get_zpe,\
+    rename_level
+from arc.species.species import ARCSpecies
+from arc.settings import arc_path
+from arc.arc_exceptions import InputError
+
+################################################################################
+
+
+class TestScale(unittest.TestCase):
+    """
+    Contains unit tests for the arc.utils.scale module
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        """
+        A method that is run before all unit tests in this class.
+        """
+        cls.zpe_dicts = [{'C2H2': 16 * 4184,
+                          'CH4': 27 * 4184,
+                          'CO2': 7 * 4184,
+                          'CO': 3 * 4184,
+                          'F2': 1 * 4184,
+                          'CH2O': 16 * 4184,
+                          'H2O': 13 * 4184,
+                          'H2': 6 * 4184,
+                          'HCN': 10 * 4184,
+                          'HF': 5 * 4184,
+                          'N2O': 6 * 4184,
+                          'N2': 3 * 4184,
+                          'NH3':21 * 4184,
+                          'OH': 5 * 4184,
+                          'Cl2': 0 * 4184},
+                         {'C2H2': 15 * 4184,
+                          'CH4': 27 * 4184,
+                          'CO2': None,
+                          'CO': 3 * 4184,
+                          'F2': 1 * 4184,
+                          'CH2O': 16 * 4184,
+                          'H2O': 13 * 4184,
+                          'H2': 6 * 4184,
+                          'HCN': 10 * 4184,
+                          'HF': 5 * 4184,
+                          'N2O': 6 * 4184,
+                          'N2': 3 * 4184,
+                          'NH3': 21 * 4184,
+                          'OH': 5 * 4184}]
+
+    def test_calculate_truhlar_scaling_factors(self):
+        """Test the scale calculate_truhlar_scaling_factors() function"""
+        lambda_zpe = calculate_truhlar_scaling_factors(zpe_dict=self.zpe_dicts[0], level_of_theory='test')
+        self.assertAlmostEqual(lambda_zpe, 1.0241661, 5)
+
+    def test_summarize_results(self):
+        """Test the scale summarize_results() function"""
+        lambda_zpes = [0.95, 0.98]
+        levels_of_theory = ['level1', 'level2']
+        times = ['3', '5']
+        overall_time = '8.5'
+        base_path = os.path.join(arc_path, 'Projects', 'scaling_factors_arc_testing_delete_after_usage')
+
+        summarize_results(lambda_zpes, levels_of_theory, self.zpe_dicts, times, overall_time, base_path)
+
+        info_file_path = os.path.join(base_path, 'scaling_factors_0.info')
+        self.assertTrue(os.path.isfile(info_file_path))
+        with open(info_file_path, 'r') as f:
+            lines = f.readlines()
+        self.assertIn('CITATIONS:\n', lines)
+        self.assertIn('Level of theory: level1\n', lines)
+        self.assertIn('Level of theory: level2\n', lines)
+        self.assertIn('The following species from the standard set did not converge at this level:\n', lines)
+        self.assertIn(" [u'CO2']\n", lines)
+        self.assertIn('Scale Factor for Fundamental Frequencies = 0.95452\n', lines)
+        self.assertIn('Scale Factor for Harmonic Frequencies    = 0.99372\n', lines)
+        self.assertIn('Scaling factors calculation for 2 levels of theory completed (elapsed time: 8.5).\n', lines)
+        self.assertIn('You may copy-paste the following harmonic frequencies scaling factor/s to Arkane\n', lines)
+        self.assertIn("                 'level2': 0.99372,  # [4]\n", lines)
+
+    def test_get_species_list(self):
+        """Test the scale get_species_list() function"""
+        species_list = get_species_list()
+        self.assertEqual(len(species_list), 15)
+        labels = ['C2H2', 'CH4', 'CO2', 'CO', 'F2', 'CH2O', 'H2O', 'H2', 'HCN', 'HF', 'N2O', 'N2', 'NH3', 'OH',  'Cl2']
+        for spc in species_list:
+            self.assertIn(spc.label, labels)
+            self.assertTrue(spc.initial_xyz)
+        c2h2_xyz = """    C                  0.00000000    0.00000000    0.00000000
+     C                  0.00000000    0.00000000    1.20314200
+     H                  0.00000000   -0.00000000    2.26574700
+     H                 -0.00000000   -0.00000000   -1.06260500"""
+        self.assertEqual(species_list[0].initial_xyz, c2h2_xyz)
+
+    def test_get_zpe(self):
+        """Test the scale get_zpe() function"""
+        path1 = os.path.join(arc_path, 'arc', 'testing', 'C2H6_freq_Qchem.out')
+        path2 = os.path.join(arc_path, 'arc', 'testing', 'CH2O_freq_molpro.out')
+        path3 = os.path.join(arc_path, 'arc', 'testing', 'NO3_freq_QChem_fails_on_cclib.out')
+        path4 = os.path.join(arc_path, 'arc', 'testing', 'SO2OO_CBS-QB3.log')
+        zpe1, zpe2, zpe3, zpe4 = get_zpe(path1), get_zpe(path2), get_zpe(path3), get_zpe(path4)
+        self.assertAlmostEqual(zpe1, 198083.11200000, 5)
+        self.assertAlmostEqual(zpe2, 69793.662734869, 5)
+        self.assertAlmostEqual(zpe3, 25401.064000000, 5)
+        self.assertAlmostEqual(zpe4, 39368.057626223, 5)
+
+    def test_rename_level(self):
+        """Test the scale rename_level() function"""
+        level1 = 'b3lyp/6-311+G**'
+        level2 = 'wb97xd/6-311+G(2d,2p)'
+        renamed_level1 = rename_level(level1)
+        renamed_level2 = rename_level(level2)
+        self.assertEqual(renamed_level1, 'b3lyp_6-311pGss')
+        self.assertEqual(renamed_level2, 'wb97xd_6-311pGb2d,2pb')
+
+    @classmethod
+    def tearDownClass(cls):
+        """
+        A function that is run ONCE after all unit tests in this class.
+        Delete all directories created during these unit tests
+        """
+        path = os.path.join(arc_path, 'Projects', 'scaling_factors_arc_testing_delete_after_usage')
+        shutil.rmtree(path)
+
+################################################################################
+
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))