def test_parse_frequencies(self):
"""Test frequency parsing"""
no3_path = os.path.join(arc_path, 'arc', 'testing',
'NO3_freq_QChem_fails_on_cclib.out')
c2h6_path = os.path.join(arc_path, 'arc', 'testing',
'C2H6_freq_Qchem.out')
so2oo_path = os.path.join(arc_path, 'arc', 'testing',
'SO2OO_CBS-QB3.log')
no3_freqs = parser.parse_frequencies(path=no3_path, software='QChem')
c2h6_freqs = parser.parse_frequencies(path=c2h6_path, software='QChem')
so2oo_freqs = parser.parse_frequencies(path=so2oo_path,
software='Gaussian')
self.assertTrue(
np.array_equal(
no3_freqs,
np.array([-390.08, -389.96, 822.75, 1113.23, 1115.24, 1195.35],
np.float64)))
self.assertTrue(
np.array_equal(
c2h6_freqs,
np.array([
352.37, 847.01, 861.68, 1023.23, 1232.66, 1235.04, 1425.48,
1455.31, 1513.67, 1518.02, 1526.18, 1526.56, 3049.78,
3053.32, 3111.61, 3114.2, 3134.14, 3136.8
], np.float64)))
self.assertTrue(
np.array_equal(
so2oo_freqs,
np.array([
302.51, 468.1488, 469.024, 484.198, 641.0067, 658.6316,
902.2888, 1236.9268, 1419.0826
], np.float64)))
def test_parse_frequencies(self):
"""Test frequency parsing"""
no3_path = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'NO3_freq_QChem_fails_on_cclib.out')
c2h6_path = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'C2H6_freq_QChem.out')
so2oo_path = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'SO2OO_CBS-QB3.log')
ch2o_path_molpro = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'CH2O_freq_molpro.out')
ch2o_path_terachem = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'CH2O_freq_terachem.dat')
ch2o_path_terachem_output = os.path.join(ARC_PATH, 'arc', 'testing', 'freq',
'formaldehyde_freq_terachem_output.out')
ncc_path_terachem_output = os.path.join(ARC_PATH, 'arc', 'testing', 'freq',
'ethylamine_freq_terachem_output.out')
orca_path = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'orca_example_freq.log')
dual_freq_path = os.path.join(ARC_PATH, 'arc', 'testing', 'freq', 'dual_freq_output.out')
no3_freqs = parser.parse_frequencies(path=no3_path, software='QChem')
c2h6_freqs = parser.parse_frequencies(path=c2h6_path, software='QChem')
so2oo_freqs = parser.parse_frequencies(path=so2oo_path, software='Gaussian')
ch2o_molpro_freqs = parser.parse_frequencies(path=ch2o_path_molpro, software='Molpro')
ch2o_terachem_freqs = parser.parse_frequencies(path=ch2o_path_terachem, software='TeraChem')
ch2o_terachem_output_freqs = parser.parse_frequencies(path=ch2o_path_terachem_output, software='TeraChem')
ncc_terachem_output_freqs = parser.parse_frequencies(path=ncc_path_terachem_output, software='TeraChem')
orca_freqs = parser.parse_frequencies(path=orca_path, software='Orca')
dual_freqs = parser.parse_frequencies(path=dual_freq_path, software='Gaussian')
np.testing.assert_almost_equal(no3_freqs,
np.array([-390.08, -389.96, 822.75, 1113.23, 1115.24, 1195.35], np.float64))
np.testing.assert_almost_equal(c2h6_freqs,
np.array([352.37, 847.01, 861.68, 1023.23, 1232.66, 1235.04, 1425.48, 1455.31,
1513.67, 1518.02, 1526.18, 1526.56, 3049.78, 3053.32, 3111.61, 3114.2,
3134.14, 3136.8], np.float64))
np.testing.assert_almost_equal(so2oo_freqs,
np.array([302.51, 468.1488, 469.024, 484.198, 641.0067, 658.6316,
902.2888, 1236.9268, 1419.0826], np.float64))
np.testing.assert_almost_equal(ch2o_molpro_freqs,
np.array([1181.01, 1261.34, 1529.25, 1764.47, 2932.15, 3000.10], np.float64))
np.testing.assert_almost_equal(ch2o_terachem_freqs,
np.array([1198.228, 1271.913, 1562.435, 1900.334, 2918.771, 2966.569],
np.float64))
np.testing.assert_almost_equal(ch2o_terachem_output_freqs,
np.array([1198.63520807, 1276.19910582, 1563.62759321, 1893.24407646,
2916.39175334, 2965.86839559], np.float64))
np.testing.assert_almost_equal(ncc_terachem_output_freqs,
np.array([170.56668709, 278.52007409, 406.49102131, 765.91960508, 861.6118189,
910.16404036, 1010.63529045, 1052.86795614, 1160.15911873,
1275.00946008, 1386.75755192, 1406.08828477, 1425.90872097,
1506.47789418, 1522.65901736, 1527.41841768, 1710.89393731,
3020.79869151, 3035.66348773, 3061.21808688, 3085.3062489,
3087.60678739, 3447.41720077, 3529.23879182], np.float64))
np.testing.assert_almost_equal(orca_freqs,
np.array([1151.03, 1250.19, 1526.12, 1846.4, 3010.49, 3070.82], np.float64))
np.testing.assert_almost_equal(dual_freqs,
np.array([-1617.8276, 56.9527, 76.681, 121.4038, 182.1572, 194.9796,
202.4056, 209.9621, 273.506, 342.468, 431.985, 464.0768,
577.758, 594.4119, 615.5216, 764.1286, 962.2969, 968.0013,
1004.7852, 1098.0136, 1129.3888, 1137.0454, 1150.7824, 1185.4531,
1249.0746, 1387.4803, 1401.5073, 1413.8079, 1420.6471, 1453.6296,
1481.9425, 1487.0125, 1496.0713, 1498.382, 1507.7379, 2280.9881,
3015.0638, 3018.8871, 3030.1281, 3074.8208, 3079.5256, 3103.8434,
3109.1728, 3156.4352, 3783.7315], np.float64))
def test_check_negative_freq(self):
"""Test the check_negative_freq() method"""
label = 'C2H6'
self.job3.local_path_to_output_file = os.path.join(arc_path, 'arc', 'testing', 'C2H6_freq_Qchem.out')
self.job3.job_status = ['done', 'done']
vibfreqs = parser.parse_frequencies(path=str(self.job3.local_path_to_output_file), software=self.job3.software)
self.assertTrue(self.sched1.check_negative_freq(label=label, job=self.job3, vibfreqs=vibfreqs))
def determine_convergence(path, job_type, ts=False):
try:
log = ess_factory(path)
except:
return False
else:
for log_type in [GaussianLog, MolproLog, OrcaLog, QChemLog, TeraChemLog]:
if isinstance(log, log_type):
software = log_type.__name__.replace('Log', '').lower()
break
try:
done = determine_ess_status(path,
species_label='',
job_type=job_type,
software=software,
)[0] == 'done'
except:
return False
if done and job_type in ['optfreq', 'freq', 'composite']:
freqs = parse_frequencies(path=path, software=software)
if not len(freqs):
# Single atom without freq
return done
neg_freqs = [freq for freq in freqs if freq < 0]
if not ts:
return done and not len(neg_freqs)
return done and len(neg_freqs) == 1
def test_check_negative_freq(self):
"""Test the check_negative_freq() method"""
label = 'C2H6'
self.job3.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'freq', 'C2H6_freq_QChem.out')
self.job3.job_status = [
'done', {
'status': 'done',
'keywords': list(),
'error': '',
'line': ''
}
]
vibfreqs = parser.parse_frequencies(
path=self.job3.local_path_to_output_file,
software=self.job3.software)
self.assertTrue(
self.sched1.check_negative_freq(label=label,
job=self.job3,
vibfreqs=vibfreqs))