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Merge pull request #407 from ReactionMechanismGenerator/ndm_fix
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BugFix: Correcly parse normal displacement modes from Gaussian
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@alongd
alongd committed Jul 6, 2020
2 parents 4f3cea0 + 37f1cd4 commit 977a9bf
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Showing 7 changed files with 1,508 additions and 17 deletions.
2 changes: 1 addition & 1 deletion arc/job/trshTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -498,7 +498,7 @@ def test_trsh_ess_job(self):

def test_trsh_negative_freq(self):
"""Test troubleshooting a negative frequency"""
gaussian_neg_freq_path = os.path.join(arc_path, 'arc', 'testing', 'Gaussian_neg_freq.out')
gaussian_neg_freq_path = os.path.join(arc_path, 'arc', 'testing', 'freq', 'Gaussian_neg_freq.out')
current_neg_freqs_trshed, conformers, output_errors, output_warnings = \
trsh.trsh_negative_freq(label='2-methoxy_n-methylaniline', log_file=gaussian_neg_freq_path)
expected_current_neg_freqs_trshed = [-18.07]
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5 changes: 3 additions & 2 deletions arc/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,8 @@ def parse_normal_displacement_modes(path: str,
parse = True
if parse and len(line.split()) in [0, 1, 3]:
parse_normal_disp_modes = False
normal_disp_modes.extend(normal_disp_modes_entries)
normal_disp_modes_entries = list()
if parse and 'Frequencies --' in line:
# e.g.: Frequencies -- -18.0696 127.6948 174.9499
splits = line.split()
Expand All @@ -153,8 +155,7 @@ def parse_normal_displacement_modes(path: str,
if len(normal_disp_modes_entries) < i + 1:
normal_disp_modes_entries.append(list())
normal_disp_modes_entries[i].append(splits[3 * i: 3 * i + 3])
normal_disp_modes.extend(normal_disp_modes_entries)
elif parse and 'Atom AN X Y Z X Y Z X Y Z' in line:
elif parse and 'Atom AN X Y Z' in line:
parse_normal_disp_modes = True
elif parse and not line or '-------------------' in line:
parse = False
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106 changes: 92 additions & 14 deletions arc/parserTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ class TestParser(unittest.TestCase):
"""
Contains unit tests for the parser functions
"""

@classmethod
def setUpClass(cls):
"""
Expand All @@ -33,9 +34,11 @@ def test_parse_frequencies(self):
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', 'orca_example_freq.log')
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')

no3_freqs = parser.parse_frequencies(path=no3_path, software='QChem')
c2h6_freqs = parser.parse_frequencies(path=c2h6_path, software='QChem')
Expand Down Expand Up @@ -75,7 +78,7 @@ def test_parse_frequencies(self):

def test_parse_normal_displacement_modes(self):
"""Test parsing frequencies and normal displacement modes"""
freq_path = os.path.join(arc_path, 'arc', 'testing', 'Gaussian_neg_freq.out')
freq_path = os.path.join(arc_path, 'arc', 'testing', 'freq', 'Gaussian_neg_freq.out')
freqs, normal_disp_modes = parser.parse_normal_displacement_modes(path=freq_path)
expected_freqs = np.array([-18.0696, 127.6948, 174.9499, 207.585, 228.8421, 281.2939, 292.4101,
308.0345, 375.4493, 486.8396, 498.6986, 537.6196, 564.0223, 615.3762,
Expand All @@ -93,20 +96,95 @@ def test_parse_normal_displacement_modes(self):
[0.3, 0.03, 0.41], [0.0, 0.0, -0.15], [0.0, -0.0, 0.01], [0.0, -0.0, 0.21], [0.0, -0.0, 0.19]], np.float64)
np.testing.assert_almost_equal(normal_disp_modes[0], expected_normal_disp_modes_0)

freq_path = os.path.join(arc_path, 'arc', 'testing', 'CHO_neg_freq.out')
freq_path = os.path.join(arc_path, 'arc', 'testing', 'freq', 'CHO_neg_freq.out')
freqs, normal_disp_modes = parser.parse_normal_displacement_modes(path=freq_path)
expected_freqs = np.array([-1612.8294, 840.8655, 1883.4822, 3498.091], np.float64)
np.testing.assert_almost_equal(freqs, expected_freqs)
expected_normal_disp_modes = np.array(
[[[0.05, 0.03, 0.], [-0.13, -0.09, 0.], [0.8, 0.57, 0.]],
[[-0.03, 0.05, 0.], [0.09, -0.13, 0.], [-0.57, 0.8, 0.]],
[[0., 0., -0.41], [-0., 0., 0.49], [0., 0., 0.77]],
[[0.05, 0.03, 0.], [-0.13, -0.09, 0.], [0.8, 0.57, 0.]],
[[-0.03, 0.05, 0.], [0.09, -0.13, 0.], [-0.57, 0.8, 0.]],
[[0., 0., -0.41], [0., 0., 0.49], [0., 0., 0.77]],
[[0.05, 0.03, 0.], [-0.13, -0.09, 0.], [0.8, 0.57, 0.]],
[[-0.03, 0.05, 0.], [0.09, -0.13, 0.], [-0.57, 0.8, 0.]],
[[0., 0., -0.41], [-0., 0., 0.49], [0., 0., 0.77]]], np.float64)
[[[0.05, 0.03, -0.0], [-0.13, -0.09, 0.0], [0.8, 0.57, -0.0]],
[[-0.03, 0.05, -0.0], [0.09, -0.13, 0.0], [-0.57, 0.8, 0.0]],
[[0.0, -0.0, -0.41], [-0.0, 0.0, 0.49], [0.0, -0.0, 0.77]],
[[0.0, -0.0, 0.02], [-0.0, 0.0, -0.11], [0.0, -0.0, 0.99]]], np.float64)
np.testing.assert_almost_equal(normal_disp_modes, expected_normal_disp_modes)

freq_path = os.path.join(arc_path, 'arc', 'testing', 'freq', 'CH3OO_freq_gaussian.out')
freqs, normal_disp_modes = parser.parse_normal_displacement_modes(path=freq_path)
expected_freqs = np.array([136.4446, 494.1267, 915.7812, 1131.4603, 1159.9315, 1225.148, 1446.5652,
1474.8065, 1485.6423, 3046.2186, 3134.8026, 3147.5619], np.float64)
np.testing.assert_almost_equal(freqs, expected_freqs)
expected_normal_disp_modes = np.array(
[[[-0.0, -0.0, 0.02],
[0.0, 0.0, -0.11],
[0.0, -0.0, 0.09],
[0.32, 0.39, -0.23],
[0.0, 0.0, 0.61],
[-0.32, -0.39, -0.23]],
[[-0.24, -0.06, -0.0],
[-0.02, 0.22, 0.0],
[0.26, -0.13, -0.0],
[-0.54, -0.11, 0.01],
[0.12, -0.43, -0.0],
[-0.54, -0.11, -0.01]],
[[0.41, -0.16, -0.0],
[-0.25, 0.25, 0.0],
[-0.1, -0.09, 0.0],
[-0.03, -0.16, -0.0],
[0.66, -0.42, -0.0],
[-0.03, -0.16, 0.0]],
[[0.0, 0.0, 0.13],
[0.0, 0.0, -0.06],
[-0.0, -0.0, -0.0],
[-0.52, 0.38, -0.16],
[-0.0, 0.0, -0.29],
[0.52, -0.38, -0.16]],
[[-0.01, 0.17, -0.0],
[0.21, 0.02, 0.0],
[-0.2, -0.12, 0.0],
[-0.35, -0.01, 0.1],
[0.62, -0.46, 0.0],
[-0.35, -0.01, -0.1]],
[[-0.07, -0.14, -0.0],
[0.13, 0.2, 0.0],
[-0.11, -0.12, -0.0],
[0.52, 0.06, -0.1],
[-0.48, 0.3, 0.0],
[0.52, 0.06, 0.1]],
[[-0.09, 0.05, 0.0],
[-0.04, -0.0, 0.0],
[0.02, 0.02, -0.0],
[0.52, -0.16, 0.17],
[0.39, -0.44, -0.0],
[0.52, -0.16, -0.17]],
[[-0.0, 0.0, -0.06],
[-0.0, 0.0, -0.01],
[0.0, -0.0, 0.0],
[-0.44, -0.19, 0.07],
[0.0, 0.0, 0.73],
[0.44, 0.19, 0.07]],
[[-0.03, -0.05, -0.0],
[-0.01, -0.02, -0.0],
[0.0, 0.01, 0.0],
[0.06, 0.53, -0.37],
[0.24, -0.29, 0.0],
[0.06, 0.53, 0.37]],
[[-0.03, 0.02, -0.0],
[-0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[0.02, -0.33, -0.5],
[0.37, 0.37, -0.0],
[0.02, -0.33, 0.5]],
[[0.0, 0.0, -0.1],
[0.0, 0.0, 0.0],
[-0.0, -0.0, 0.0],
[-0.02, 0.4, 0.58],
[-0.0, -0.0, -0.02],
[0.02, -0.4, 0.58]],
[[-0.05, -0.08, -0.0],
[-0.0, -0.0, -0.0],
[0.0, 0.0, 0.0],
[-0.02, 0.19, 0.31],
[0.61, 0.6, -0.0],
[-0.02, 0.19, -0.31]]], np.float64)
np.testing.assert_almost_equal(normal_disp_modes, expected_normal_disp_modes)

def test_parse_xyz_from_file(self):
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