Revert "Merge branch 'master' into recipe"

This reverts commit fa87c39, reversing
changes made to 95dc1ed.

arkane/ess/gaussian.py → arkane/logs/gaussian.py

@@ -43,7 +43,7 @@
 
 from arkane.common import check_conformer_energy, get_element_mass
 from arkane.exceptions import LogError
-from arkane.ess.log import Log
+from arkane.logs.log import Log
 
 
 ################################################################################

arkane/ess/gaussianTest.py → arkane/logs/gaussianTest.py

@@ -28,7 +28,7 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.gaussian` module.
+This module contains unit tests of the :mod:`arkane.logs.gaussian` module.
 """
 
 import os
@@ -40,10 +40,11 @@
 from external.wip import work_in_progress
 from rmgpy.statmech import IdealGasTranslation, LinearRotor, NonlinearRotor, HarmonicOscillator, HinderedRotor
 
-from arkane.ess.gaussian import GaussianLog
+from arkane.logs.gaussian import GaussianLog
 from arkane.statmech import determine_qm_software
 from arkane.exceptions import LogError
 
+
 ################################################################################
 
 
@@ -90,12 +91,11 @@ def test_gaussian_energies(self):
         """
         test parsing double hydride, MP2, CCSD, CCSD(T) form Gaussian log
         """
-        log_doublehybrid = GaussianLog(os.path.join(self.data_path, 'B2PLYP.LOG'))
-        log_mp2 = GaussianLog(os.path.join(self.data_path, 'UMP2_C_ATOM.LOG'))
-        log_ccsd = GaussianLog(os.path.join(self.data_path, 'UCCSD_C_ATOM.LOG'))
-        log_ccsdt = GaussianLog(os.path.join(self.data_path, 'UCCSDT_C_ATOM.LOG'))
-        log_qb3 = GaussianLog(os.path.join(os.path.dirname(os.path.dirname(__file__)),
-                                           '../examples/arkane/species/C2H5/', 'ethyl_cbsqb3.log'))
+        log_doublehybrid = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'B2PLYP.LOG'))
+        log_mp2 = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'UMP2_C_ATOM.LOG'))
+        log_ccsd = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'UCCSD_C_ATOM.LOG'))
+        log_ccsdt = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'UCCSDT_C_ATOM.LOG'))
+        log_qb3 = GaussianLog(os.path.join(os.path.dirname(__file__), '../examples/arkane/species/C2H5/', 'ethyl_cbsqb3.log'))
 
         self.assertAlmostEqual(log_doublehybrid.load_energy() / constants.Na / constants.E_h, -0.40217794572194e+02,
                                delta=1e-6)
@@ -188,28 +188,28 @@ def test_load_scan_angle(self):
         """
         Ensures proper scan angle found in Gaussian scan job
         """
-        log = GaussianLog(os.path.join(self.data_path, 'isobutanolQOOH_scan.log'))
+        log = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'isobutanolQOOH_scan.log'))
         self.assertAlmostEqual(log._load_scan_angle(), 10.0)
 
     def test_load_number_scans(self):
         """
         Ensures proper scan angle found in Gaussian scan job
         """
-        log = GaussianLog(os.path.join(self.data_path, 'isobutanolQOOH_scan.log'))
+        log = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'isobutanolQOOH_scan.log'))
         self.assertAlmostEqual(log._load_number_scans(), 36)
 
     def test_determine_qm_software(self):
         """
         Ensures that determine_qm_software returns a GaussianLog object
         """
-        log = determine_qm_software(os.path.join(self.data_path, 'oxygen.log'))
+        log = determine_qm_software(os.path.join(os.path.dirname(__file__), 'data', 'oxygen.log'))
         self.assertIsInstance(log, GaussianLog)
 
     def test_gaussian_log_error_termination(self):
         """
         Ensures that error termination gaussian log file raises an logError
         """
-        file_path = os.path.join(self.data_path, 'error_termination.out')
+        file_path = os.path.join(os.path.dirname(__file__), 'data', 'error_termination.out')
         log = GaussianLog(file_path)
         with self.assertRaises(LogError) as log_error:
             log.load_conformer()
@@ -219,7 +219,7 @@ def test_load_scan_with_freq(self):
         """
         Ensures that the length of enegies with hr scans and freq calc is correct
         """
-        log = GaussianLog(os.path.join(self.data_path, 'hr_scan_with_freq.log'))
+        log = GaussianLog(os.path.join(os.path.dirname(__file__), 'data', 'hr_scan_with_freq.log'))
         self.assertAlmostEqual(log._load_number_scans(), 36)
         self.assertAlmostEqual(log._load_scan_angle(), 10.0)
         vlist, _ = log.load_scan_energies()

arkane/ess/molpro.py → arkane/logs/molpro.py

@@ -42,7 +42,7 @@
 
 from arkane.common import get_element_mass
 from arkane.exceptions import LogError
-from arkane.ess.log import Log
+from arkane.logs.log import Log
 
 ################################################################################
 

arkane/ess/molproTest.py → arkane/logs/molproTest.py

@@ -28,7 +28,7 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.molpro` module.
+This module contains unit tests of the :mod:`arkane.logs.molpro` module.
 """
 
 import unittest
@@ -39,7 +39,7 @@
 import rmgpy.constants as constants
 from rmgpy.statmech import IdealGasTranslation, NonlinearRotor, HarmonicOscillator, HinderedRotor
 
-from arkane.ess.molpro import MolproLog
+from arkane.logs.molpro import MolproLog
 
 ################################################################################
 

arkane/ess/orca.py → arkane/logs/orca.py

@@ -38,7 +38,7 @@
 import rmgpy.constants as constants
 
 from arkane.common import get_element_mass
-from arkane.ess.log import Log
+from arkane.logs.log import Log
 from arkane.exceptions import LogError
 
 ################################################################################

arkane/ess/orcaTest.py → arkane/logs/orcaTest.py

@@ -29,13 +29,13 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.orca` module.
+This module contains unit tests of the :mod:`arkane.logs.orca` module.
 """
 
 import os
 import unittest
 
-from arkane.ess.orca import OrcaLog
+from arkane.logs.orca import OrcaLog
 
 ################################################################################
 
@@ -44,32 +44,26 @@ class OrcaTest(unittest.TestCase):
     """
     Contains unit tests for the orca module, used for parsing Orca log files.
     """
-    @classmethod
-    def setUpClass(cls):
-        """
-        A method that is run before all unit tests in this class.
-        """
-        cls.data_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data', 'orca')
 
     def test_number_of_atoms_from_orca_log(self):
         """
         Uses a Orca log files to test that
         number of atoms can be properly read.
         """
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_opt_freq_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_opt_freq_test.log'))
         self.assertEqual(log.get_number_of_atoms(), 3)
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_dlpno_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_dlpno_test.log'))
         self.assertEqual(log.get_number_of_atoms(), 30)
 
     def test_read_coordinates_from_orca_log(self):
         """
         Uses a Orca log files to test that
         coordinate can be properly read.
         """
-        log1 = OrcaLog(os.path.join(self.data_path, 'Orca_opt_freq_test.log'))
+        log1 = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_opt_freq_test.log'))
         coord, number, mass = log1.load_geometry()
         self.assertEqual(len(coord), 3)
-        log2 = OrcaLog(os.path.join(self.data_path, 'Orca_dlpno_test.log'))
+        log2 = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_dlpno_test.log'))
         coord, number, mass = log2.load_geometry()
         self.assertEqual(len(coord), 30)
 
@@ -78,37 +72,37 @@ def test_energy_from_orca_log(self):
         Uses a Orca log files to test that
         molecular energies can be properly read.
         """
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_opt_freq_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_opt_freq_test.log'))
         self.assertAlmostEqual(log.load_energy(), -200656222.56292167, delta=1e-3)
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_TS_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_TS_test.log'))
         self.assertAlmostEqual(log.load_energy(), -88913623.10592663, delta=1e-3)
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_dlpno_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_dlpno_test.log'))
         self.assertAlmostEqual(log.load_energy(), -1816470909.1153, delta=1e-3)
 
     def test_load_zero_point_energy_from_orca_log(self):
         """
         Uses a Orca log files to test that
         molecular zero point_energy can be properly read.
         """
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_opt_freq_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_opt_freq_test.log'))
         self.assertAlmostEqual(log.load_zero_point_energy(), 55502.673180815, delta=1e-3)
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_TS_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_TS_test.log'))
         self.assertAlmostEqual(log.load_zero_point_energy(), 93500.08860598055, delta=1e-3)
 
     def test_load_negative_frequency_from_orca_log(self):
         """
         Uses a orca log file for npropyl to test that its
         negative frequency can be properly read.
         """
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_TS_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_TS_test.log'))
         self.assertAlmostEqual(log.load_negative_frequency(), -503.24, delta=1e-1)
 
     def test_T1_diagnostic_from_orca_log(self):
         """
         Uses a Orca log file for npropyl to test that its
         T1_diagnostic of freedom can be properly read.
         """
-        log = OrcaLog(os.path.join(self.data_path, 'Orca_dlpno_test.log'))
+        log = OrcaLog(os.path.join(os.path.dirname(__file__), 'data', 'Orca_dlpno_test.log'))
         self.assertAlmostEqual(log.get_T1_diagnostic(), 0.009872238, delta=1e-3)
 
 ################################################################################

arkane/ess/qchem.py → arkane/logs/qchem.py

@@ -43,7 +43,7 @@
 
 from arkane.common import check_conformer_energy, get_element_mass
 from arkane.exceptions import LogError
-from arkane.ess.log import Log
+from arkane.logs.log import Log
 
 ################################################################################
 

arkane/ess/qchemTest.py → arkane/logs/qchemTest.py

@@ -28,15 +28,15 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.qchem` module.
+This module contains unit tests of the :mod:`arkane.logs.qchem` module.
 """
 
 import os
 import unittest
 
 from rmgpy.statmech import IdealGasTranslation, LinearRotor, NonlinearRotor, HarmonicOscillator, HinderedRotor
 
-from arkane.ess.qchem import QChemLog
+from arkane.logs.qchem import QChemLog
 
 ################################################################################
 

arkane/ess/terachem.py → arkane/logs/terachem.py

@@ -43,7 +43,7 @@
 
 from arkane.common import check_conformer_energy, get_element_mass, symbol_by_number
 from arkane.exceptions import LogError
-from arkane.ess.log import Log
+from arkane.logs.log import Log
 
 ################################################################################
 

arkane/ess/terachemTest.py → arkane/logs/terachemTest.py

@@ -28,7 +28,7 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.terachem` module.
+This module contains unit tests of the :mod:`arkane.logs.terachem` module.
 """
 
 import os
@@ -39,7 +39,7 @@
 from rmgpy.statmech.conformer import Conformer
 
 from arkane.exceptions import LogError
-from arkane.ess.terachem import TeraChemLog
+from arkane.logs.terachem import TeraChemLog
 
 ################################################################################
 
@@ -399,15 +399,15 @@ def test_load_scan_energies(self):
                            2.30963595e+03, 5.02046166e+03, 7.97285489e+03, 1.06923710e+04,
                            1.29244615e+04, 1.43422341e+04, 1.43905580e+04, 1.32047110e+04,
                            1.12088126e+04, 8.31162367e+03, 5.06568695e+03, 2.54966151e+03,
-                           8.50076205e+02, 0.00000000e+00]
-        expected_angles = [0., 0.13962634, 0.27925268, 0.41887902, 0.55850536, 0.6981317,
-                           0.83775804, 0.97738438, 1.11701072, 1.25663706, 1.3962634, 1.53588974,
-                           1.67551608, 1.81514242, 1.95476876, 2.0943951, 2.23402144, 2.37364778,
-                           2.51327412, 2.65290046, 2.7925268, 2.93215314, 3.07177948, 3.21140582,
-                           3.35103216, 3.4906585, 3.63028484, 3.76991118, 3.90953752, 4.04916386,
-                           4.1887902, 4.32841654, 4.46804289, 4.60766923, 4.74729557, 4.88692191,
-                           5.02654825, 5.16617459, 5.30580093, 5.44542727, 5.58505361, 5.72467995,
-                           5.86430629, 6.00393263, 6.14355897, 6.28318531]  # radians
+                           8.50076205e+02, 0.00000000e+00, 3.31469351e+00]
+        expected_angles = [0., 0.13659098, 0.27318197, 0.40977295, 0.54636394, 0.68295492,
+                           0.81954591, 0.95613689, 1.09272788, 1.22931886, 1.36590985, 1.50250083,
+                           1.63909182, 1.7756828, 1.91227379, 2.04886477, 2.18545576, 2.32204674,
+                           2.45863773, 2.59522871, 2.7318197, 2.86841068, 3.00500167, 3.14159265,
+                           3.27818364, 3.41477462, 3.55136561, 3.68795659, 3.82454758, 3.96113856,
+                           4.09772955, 4.23432053, 4.37091152, 4.5075025, 4.64409349, 4.78068447,
+                           4.91727546, 5.05386644, 5.19045743, 5.32704841, 5.4636394, 5.60023038,
+                           5.73682137, 5.87341235, 6.01000334, 6.14659432, 6.28318531]  # radians
         np.testing.assert_almost_equal(v_list, expected_v_list, 4)
         np.testing.assert_almost_equal(angles, expected_angles)
 

arkane/outputTest.py

@@ -29,7 +29,7 @@
 ###############################################################################
 
 """
-This module contains unit tests of the :mod:`arkane.ess.gaussian` module.
+This module contains unit tests of the :mod:`arkane.logs.gaussian` module.
 """
 
 import os
@@ -40,7 +40,7 @@
 
 import rmgpy
 
-from arkane.ess.gaussian import GaussianLog
+from arkane.logs.gaussian import GaussianLog
 from arkane.main import Arkane
 from arkane.output import prettify, get_str_xyz
 from rmgpy.species import Species

arkane/statmech.py

@@ -53,7 +53,12 @@
 
 from arkane.common import ArkaneSpecies, symbol_by_number, get_principal_moments_of_inertia
 from arkane.encorr.corr import get_atom_correction, get_bac
-from arkane.ess import GaussianLog, Log, MolproLog, OrcaLog, QChemLog, TeraChemLog
+from arkane.logs.gaussian import GaussianLog
+from arkane.logs.log import Log
+from arkane.logs.molpro import MolproLog
+from arkane.logs.orca import OrcaLog
+from arkane.logs.qchem import QChemLog
+from arkane.logs.terachem import TeraChemLog
 from arkane.output import prettify
 from arkane.util import determine_qm_software
 

arkane/statmechTest.py

@@ -40,7 +40,7 @@
 from rmgpy.exceptions import InputError
 
 from arkane import Arkane
-from arkane.ess.qchem import QChemLog
+from arkane.logs.qchem import QChemLog
 from arkane.statmech import StatMechJob, determine_rotor_symmetry, is_linear
 
 ################################################################################

arkane/thermoTest.py

@@ -36,7 +36,7 @@
 
 from rmgpy.species import Species
 
-from arkane.ess.gaussian import GaussianLog
+from arkane.logs.gaussian import GaussianLog
 from arkane.thermo import ThermoJob
 
 ################################################################################