def test_parse_1d_scan_energies(self):
"""Test parsing a 1D scan output file"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'sBuOH.out')
energies, angles = parser.parse_1d_scan_energies(path=path1)
expected_energies = np.array([
1.57530564e-05, 3.98826556e-01, 1.60839959e+00, 3.49030801e+00,
5.74358812e+00, 8.01124810e+00, 9.87649510e+00, 1.10079306e+01,
1.11473788e+01, 1.02373175e+01, 8.49330826e+00, 6.23697731e+00,
3.89294941e+00, 1.87096796e+00, 5.13009545e-01, 1.86410533e-04,
4.16146979e-01, 1.66269755e+00, 3.59565619e+00, 5.90306099e+00,
8.19668453e+00, 1.00329329e+01, 1.10759678e+01, 1.10923247e+01,
1.00763770e+01, 8.28078980e+00, 6.04456755e+00, 3.77500671e+00,
1.83344694e+00, 5.20014378e-01, 2.21067093e-03, 3.70723206e-01,
1.56091218e+00, 3.44323279e+00, 5.73505787e+00, 8.04497265e+00,
9.93330041e+00, 1.10426686e+01, 1.11168469e+01, 1.01271857e+01,
8.32729265e+00, 6.06336876e+00, 3.76108631e+00, 1.80461632e+00,
4.94715062e-01, 0.00000000e+00
], np.float64)
expected_angles = np.array([
0., 8., 16., 24., 32., 40., 48., 56., 64., 72., 80., 88., 96.,
104., 112., 120., 128., 136., 144., 152., 160., 168., 176., 184.,
192., 200., 208., 216., 224., 232., 240., 248., 256., 264., 272.,
280., 288., 296., 304., 312., 320., 328., 336., 344., 352., 360.
], np.float64)
np.testing.assert_almost_equal(energies, expected_energies)
np.testing.assert_almost_equal(angles, expected_angles)
path2 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'scan_1d_curvilinear_error.out')
energies_2, angles_2 = parser.parse_1d_scan_energies(path=path2)
self.assertEqual(energies_2, None)
self.assertEqual(angles_2, None)
def transfer_to_database(spc, database_path, output_file_name='output.out'):
# Create a new folder to store
if 'smiles' not in spc:
spc['smiles'] = xyz_to_mol(spc['geom']).to_smiles()
for i in range(100):
new_dir = os.path.join(database_path, spc['smiles'], str(i))
try:
os.makedirs(new_dir, exist_ok=False)
except:
continue
else:
break
# make sure it is the updated summary
generate_summary(spc)
with open(os.path.join(new_dir, 'info.txt'), 'w') as info:
info.write(spc['summary'])
transfer_species_jobs(spc, new_dir, output_file_name)
spc['directory'] = new_dir
xyz_to_xyz_file(spc)
for rotor in spc['rotors_dict'].values():
try:
energies, angles = parse_1d_scan_energies(rotor['scan_path'])
plot_1d_rotor_scan(angles=angles,
energies=energies,
path=os.path.dirname(rotor['scan_path']),
scan=rotor['scan'])
except:
pass
return spc
def check_scan_quality(spc):
"""
A helper function used to get the status of rotor scans
"""
for rotor in spc['rotors_dict'].values():
path = rotor['scan_path']
if path:
scan_args = parse_scan_args(path)
energies, _ = parse_1d_scan_energies(path)
invalid, reason, _, actions = scan_quality_check(
spc['label'],
pivots=rotor['scan'][1:-1],
energies=energies,
scan_res=scan_args['step_size'],
log_file=path)
else:
rotor['success'] = False
rotor['invalidation_reason'] = 'Unknown'
continue
if not invalid:
rotor['success'] = True
rotor['symmetry'] = determine_rotor_symmetry(
label=spc['label'],
pivots=rotor['scan'][1:3],
energies=energies)[0]
continue
if 'change conformer' in actions:
print(spc['label'] +
': has a bad conformer orientation according to ' +
str(rotor['scan']))
xyz = xyz_to_xyz_file_format(actions['change conformer'])
return {'label': spc['label'], 'change conformer': xyz}
if 'barrier' in reason:
rotor['success'] = False
rotor['invalidation_reason'] = reason
continue
# Otherwise need to come up with troubleshooting methods
species_scan_lists = [rotor['scan']]
scan_trsh, scan_res = trsh_scan_job(spc['label'],
scan_args['step_size'],
rotor['scan'], species_scan_lists,
actions, path)
rotor['trsh_methods'] = [{
'scan_trsh': scan_trsh,
'scan_res': scan_res
}]
rotor['archived'].append(rotor['scan_path'])
spc['scan'].remove(rotor['scan_path'])
return spc
def test_scan_quality_check(self):
"""Test scan quality check for 1D rotor"""
log_file = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'CH2OOH.out')
# Case 1: non-smooth scan which troubleshot once
case1 = {
'label': 'CH2OOH',
'pivots': [1, 2],
'energies': parse_1d_scan_energies(log_file)[0],
'scan_res': 4.0,
'used_methods': None,
'log_file': log_file,
}
invalidate, invalidation_reason, message, actions = trsh.scan_quality_check(
**case1)
self.assertTrue(invalidate)
self.assertEqual(
invalidation_reason,
'Significant difference observed between consecutive conformers')
expect_message = 'Rotor scan of CH2OOH between pivots [1, 2] is inconsistent between ' \
'two consecutive conformers.\nInconsistent consecutive conformers and ' \
'problematic internal coordinates:\nconformer # 63 / # 64 D3, D2' \
'\nconformer # 80 / # 81 D3, D2\nARC will attempt to troubleshoot' \
' this rotor scan.'
self.assertEqual(message, expect_message)
self.assertEqual(len(actions.keys()), 1)
self.assertIn('freeze', actions)
self.assertIn([5, 1, 2, 3], actions['freeze'])
self.assertIn([2, 1, 4, 5], actions['freeze'])
# Case 2: Lower conformer
log_file = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'COCCOO.out')
case2 = {
'label': 'COCCOO',
'pivots': [2, 5],
'energies': parse_1d_scan_energies(log_file)[0],
'scan_res': 8.0,
'used_methods': None,
'log_file': log_file,
}
invalidate, invalidation_reason, message, actions = trsh.scan_quality_check(
**case2)
self.assertTrue(invalidate)
self.assertEqual(
invalidation_reason,
'Another conformer for COCCOO exists which is 4.60 kJ/mol lower.')
expect_message = 'Species COCCOO is not oriented correctly around pivots [2, 5], ' \
'searching for a better conformation...'
self.assertEqual(message, expect_message)
xyz = {
'symbols': ('O', 'O', 'O', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H',
'H', 'H', 'H'),
'isotopes': (16, 16, 16, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1),
'coords':
((1.064082, 0.653765, -0.451343), (-2.342701, 0.031994, 0.662511),
(-2.398473, -1.385822, 0.327886), (0.076296, -0.002042, 0.321439),
(-1.266646, 0.597254, -0.073572), (2.370241, 0.177374, -0.19811),
(0.246556, 0.151577, 1.397399), (0.074611, -1.082893, 0.12612),
(-1.343968, 1.669387, 0.129745), (-1.395784, 0.428829, -1.147694),
(3.049182, 0.738271, -0.841111), (2.661092, 0.333101, 0.85075),
(2.461024, -0.893605, -0.429469), (-3.255509, -1.417186,
-0.119474))
}
self.assertEqual(actions, {'change conformer': xyz})