def test_loading_different_versions_of_yaml(self):
"""Test loading a YAML file generated by RMG v 2.4.1 and by a more recent version"""
arkane_spc_v_241 = ArkaneSpecies.__new__(ArkaneSpecies)
arkane_spc_v_241.load_yaml(
path=os.path.join(self.data_path, 'vinoxy_v_2.4.1.yml'))
self.assertIsInstance(arkane_spc_v_241,
ArkaneSpecies) # checks make_object
self.assertEqual(arkane_spc_v_241.conformer.spin_multiplicity, 2)
arkane_current = ArkaneSpecies.__new__(ArkaneSpecies)
arkane_current.load_yaml(
path=os.path.join(self.data_path, 'vinoxy_current.yml'))
self.assertIsInstance(arkane_current,
ArkaneSpecies) # checks make_object
self.assertEqual(arkane_current.conformer.spin_multiplicity, 2)
def test_load_existing_yaml(self):
"""
Test that existing Arkane YAML files can still be loaded
"""
# Load in YAML file
arkane_spc = ArkaneSpecies.__new__(ArkaneSpecies)
arkane_spc.load_yaml(path=os.path.join(self.load_path, 'C2H6.yml'))
self.assertIsInstance(arkane_spc, ArkaneSpecies) # checks make_object
self.assertIsInstance(arkane_spc.molecular_weight, ScalarQuantity)
self.assertIsInstance(arkane_spc.thermo, NASA)
self.assertNotEqual(arkane_spc.author, '')
self.assertEqual(arkane_spc.inchi, 'InChI=1S/C2H6/c1-2/h1-2H3')
self.assertEqual(arkane_spc.inchi_key, 'OTMSDBZUPAUEDD-UHFFFAOYSA-N')
self.assertEqual(arkane_spc.smiles, 'CC')
self.assertTrue('8 H u0 p0 c0 {2,S}' in arkane_spc.adjacency_list)
self.assertEqual(arkane_spc.label, 'C2H6')
self.assertEqual(arkane_spc.frequency_scale_factor,
0.99) # checks float conversion
self.assertFalse(arkane_spc.use_bond_corrections)
self.assertAlmostEqual(
arkane_spc.conformer.modes[2].frequencies.value_si[0], 818.91718,
4) # HarmonicOsc.
self.assertIsInstance(arkane_spc.energy_transfer_model,
SingleExponentialDown)
self.assertFalse(arkane_spc.is_ts)
self.assertTrue(arkane_spc.use_hindered_rotors)
self.assertTrue('C 7.54e-14 1.193e-13 5.52e-14' in arkane_spc.xyz)
self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)
def test_create_and_load_yaml(self):
"""
Test properly loading the ArkaneSpecies object and respective sub-objects
"""
# Create YAML file by running Arkane
job_list = self.arkane.load_input_file(self.dump_input_path)
for job in job_list:
job.execute(output_directory=self.dump_path)
# Load in newly created YAML file
arkane_spc_old = job_list[0].arkane_species
arkane_spc = ArkaneSpecies.__new__(ArkaneSpecies)
arkane_spc.load_yaml(
path=os.path.join(self.dump_path, 'species', arkane_spc_old.label +
'.yml'))
self.assertIsInstance(arkane_spc, ArkaneSpecies) # checks make_object
self.assertIsInstance(arkane_spc.molecular_weight, ScalarQuantity)
self.assertIsInstance(arkane_spc.thermo, NASA)
self.assertNotEqual(arkane_spc.author, '')
self.assertEqual(arkane_spc.inchi, 'InChI=1S/C2H6/c1-2/h1-2H3')
self.assertEqual(arkane_spc.inchi_key, 'OTMSDBZUPAUEDD-UHFFFAOYSA-N')
self.assertEqual(arkane_spc.smiles, 'CC')
self.assertTrue('8 H u0 p0 c0 {2,S}' in arkane_spc.adjacency_list)
self.assertEqual(arkane_spc.label, 'C2H6')
self.assertEqual(arkane_spc.frequency_scale_factor,
0.99 * 1.014) # checks float conversion
self.assertFalse(arkane_spc.use_bond_corrections)
self.assertAlmostEqual(
arkane_spc.conformer.modes[2].frequencies.value_si[0], 830.38202,
4) # HarmonicOsc.
self.assertIsInstance(arkane_spc.energy_transfer_model,
SingleExponentialDown)
self.assertFalse(arkane_spc.is_ts)
self.assertEqual(arkane_spc.level_of_theory, 'cbs-qb3')
self.assertIsInstance(arkane_spc.thermo_data, ThermoData)
self.assertTrue(arkane_spc.use_hindered_rotors)
self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)
expected_xyz = """8
C2H6
C 0.00075400 0.00119300 0.00055200
H 0.00074000 0.00117100 1.09413800
H 1.04376600 0.00117100 -0.32820200
H -0.44760300 0.94289500 -0.32825300
C -0.76014200 -1.20389600 -0.55748300
H -0.76012800 -1.20387400 -1.65106900
H -0.31178500 -2.14559800 -0.22867800
H -1.80315400 -1.20387400 -0.22872900"""
self.assertEqual(arkane_spc.xyz, expected_xyz)
def test_create_and_load_yaml(self):
"""
Test properly loading the ArkaneSpecies object and respective sub-objects
"""
# Create YAML file by running Arkane
jobList = self.arkane.loadInputFile(self.dump_input_path)
for job in jobList:
job.execute(output_directory=self.dump_path)
# Load in newly created YAML file
arkane_spc_old = jobList[0].arkane_species
arkane_spc = ArkaneSpecies.__new__(ArkaneSpecies)
arkane_spc.load_yaml(
path=os.path.join(self.dump_path, 'species', arkane_spc_old.label +
'.yml'))
self.assertIsInstance(arkane_spc, ArkaneSpecies) # checks make_object
self.assertIsInstance(arkane_spc.molecular_weight, ScalarQuantity)
self.assertIsInstance(arkane_spc.thermo, NASA)
self.assertNotEqual(arkane_spc.author, '')
self.assertEqual(arkane_spc.inchi, 'InChI=1S/C2H6/c1-2/h1-2H3')
self.assertEqual(arkane_spc.inchi_key, 'OTMSDBZUPAUEDD-UHFFFAOYSA-N')
self.assertEqual(arkane_spc.smiles, 'CC')
self.assertTrue('8 H u0 p0 c0 {2,S}' in arkane_spc.adjacency_list)
self.assertEqual(arkane_spc.label, 'C2H6')
self.assertEqual(arkane_spc.frequency_scale_factor,
0.99 * 1.014) # checks float conversion
self.assertFalse(arkane_spc.use_bond_corrections)
self.assertAlmostEqual(
arkane_spc.conformer.modes[2].frequencies.value_si[0], 830.38202,
4) # HarmonicOsc.
self.assertIsInstance(arkane_spc.energy_transfer_model,
SingleExponentialDown)
self.assertFalse(arkane_spc.is_ts)
self.assertEqual(arkane_spc.level_of_theory, 'cbs-qb3')
self.assertIsInstance(arkane_spc.thermo_data, ThermoData)
self.assertTrue(arkane_spc.use_hindered_rotors)
self.assertTrue('C 7.54e-14 1.193e-13 5.52e-14' in arkane_spc.xyz)
self.assertIsInstance(arkane_spc.chemkin_thermo_string, str)