def test_load_scan_energies(self):
"""Test loading a PES scan from a TeraCHem log file"""
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethanol_scan_terachem_output.out'))
v_list, angles = log_file.load_scan_energies()
print(angles)
expected_v_list = [
3.31469351e+00, 5.61670297e+02, 2.28894412e+03, 5.02988537e+03,
8.06230147e+03, 1.09146826e+04, 1.31616066e+04, 1.44091777e+04,
1.42173813e+04, 1.28403610e+04, 1.07514495e+04, 7.96656078e+03,
4.81040645e+03, 2.42069223e+03, 7.90256554e+02, 4.20132486e+00,
4.54592173e+02, 2.06279144e+03, 4.67391931e+03, 7.62857835e+03,
1.04970774e+04, 1.27455046e+04, 1.42866289e+04, 1.43930501e+04,
1.31587081e+04, 1.10047441e+04, 8.24254519e+03, 5.10264086e+03,
2.56880350e+03, 7.56736797e+02, 1.30067263e+00, 5.19872864e+02,
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
np.testing.assert_almost_equal(v_list, expected_v_list, 4)
np.testing.assert_almost_equal(angles, expected_angles)
def test_load_zero_point_energy(self):
"""Test loading the ZPE from a TeraChem freq output file"""
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethylamine_freq_output.out'))
zpe = log_file.load_zero_point_energy()
self.assertAlmostEqual(zpe, 243113.46765236984)
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_freq_output.out'))
zpe = log_file.load_zero_point_energy()
self.assertAlmostEqual(zpe, 70663.2091453692)
def test_load_conformer(self):
"""
Test parsing frequencies and spin multiplicity from a TeraChem log file.
Translation and rotation modes are not read from the TeraCHem log, and are instead added in statmech.
"""
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_freq_output.out'))
conformer, unscaled_freqs = log_file.load_conformer()
self.assertIsInstance(conformer, Conformer)
self.assertEqual(len(conformer.modes), 1)
np.testing.assert_almost_equal(conformer.modes[0].frequencies.value_si,
unscaled_freqs)
expected_freqs = [
1198.6352081, 1276.1991058, 1563.6275932, 1893.2440765,
2916.3917533, 2965.8683956
]
np.testing.assert_almost_equal(conformer.modes[0].frequencies.value_si,
expected_freqs)
self.assertEqual(conformer.spin_multiplicity, 1)
failed_log_file = TeraChemLog(
os.path.join(self.data_path, 'failed_freq_job.out'))
with self.assertRaises(LogError):
failed_log_file.load_conformer()
def test_load_force_constant_matrix(self):
"""Test loading the Hessian"""
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethanol_freq_output.out'))
hessian = log_file.load_force_constant_matrix()
self.assertEqual(len(hessian), 27) # 9 atoms * 3 dof = 27
self.assertEqual(len(hessian[0]), 27)
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethylamine_freq_output.out'))
hessian = log_file.load_force_constant_matrix()
expected_hessian = [
[
914.9859609920952, -86.71893487707963, 25.53304366219221,
-229.64170366910673, 9.65273601863364, 122.37178242977485,
-2.4910286499699716, 0.6227571624924929, 14.323414737327337,
-42.347487049489516, -13.389278993588597, 43.90437995572075,
-0.7784464531156161, -3.7365429749549572, 1.8682714874774786,
-0.6227571624924929, -0.15568929062312323, -1.8682714874774786,
3.1137858124624644, -0.46706787186936966, -0.15568929062312323,
2.802407231216218, 0.6227571624924929, -0.31137858124624646,
-99.64114599879886, 27.40131514966969, 10.742561052995502,
-545.6909636340469, 67.10208425856611, -216.40811396614131
],
[
-86.71893487707963, 853.1773126147153, -244.12080769705722,
-20.395297071629145, -150.7072333231833, 73.7967237553604,
16.035996934181693, 13.389278993588597, -12.61083254047298,
9.808425309256764, 4.982057299939943, -11.521007506111118,
-41.5690405963739, -9.497046728010517, 43.74869066509763,
0.7784464531156161, 3.1137858124624644, 0.6227571624924929,
-0.6227571624924929, -0.6227571624924929, 1.0898250343618625,
-0.0, -0.46706787186936966, -6.227571624924929,
2.9580965218393414, -620.7332017143923, 60.09606618052557,
119.72506448918175, -94.5033994082358, 95.28184586135141
],
[
25.53304366219221, -244.12080769705722, 432.81622793228263,
54.95831958996249, 23.820461465337853, -210.49192092246258,
48.88643725566069, 14.167725446704214, -49.04212654628382,
-1.5568929062312322, -2.9580965218393414, 11.676696796734241,
16.81444338729731, 9.808425309256764, -15.724618352935446,
-0.6227571624924929, 0.9341357437387393, 4.82636800931682,
0.31137858124624646, 2.179650068723725, 4.982057299939943,
-0.7784464531156161, -6.850328787417422, -11.988075377980488,
11.365318215487996, 143.23414737327337, -40.94628343388141,
-155.06653346063072, 59.784687599279316, -126.88677185784543
],
[
-229.64170366910673, -20.395297071629145, 54.95831958996249,
880.2672491831387, -45.92834073382135, 71.77276297725982,
-131.55745057653914, -13.54496828421172, -26.311490115307823,
-390.1573623015468, 81.1141204146472, -143.3898366638965,
-84.38359551773279, 16.50306480605106, -4.35930013744745,
-0.6227571624924929, 0.6227571624924929, 3.7365429749549572,
-7.4730859499099145, -26.62286869655407, -44.838515699459485,
4.35930013744745, 20.550986362252267, 34.563022518333355,
2.3353393593468486, 0.6227571624924929, 4.514989428070574,
-42.970244211982006, -12.14376466860361, 49.04212654628382
],
[
9.65273601863364, -150.7072333231833, 23.820461465337853,
-45.92834073382135, 917.1656110608188, -66.63501638669673,
-16.191686224804815, -175.15045195101362, -61.80864837737992,
74.57517020847602, -101.50941748627633, 38.455254783911435,
25.377354371569083, -464.4211539287766, 50.59901945251505,
-8.874289565518025, -26.1558008246847, -47.95230151192195,
0.46706787186936966, 6.383260915548052, 10.275493181126134,
3.7365429749549572, 7.7844645311561615, 17.4372005497898,
-48.73074796503757, -17.125821968543555, 47.64092293067571,
5.449125171809313, 4.047921556201204, -11.521007506111118
],
[
122.37178242977485, 73.7967237553604, -210.49192092246258,
71.77276297725982, -66.63501638669673, 700.1347399321851,
-33.00612961210212, -67.41346283981235, -223.8811999160512,
-132.95865419214724, 37.209740458926454, -132.80296490152412,
-7.317396659286792, 58.383483983671205, -85.1620419708484,
2.179650068723725, 3.2694751030855875, 6.071882334301805,
-2.802407231216218, -11.209628924864871, -20.706675652875386,
-3.8922322655780808, -11.521007506111118, -23.353393593468482,
7.628775240533038, -6.850328787417422, -19.616850618513528,
-22.73063643097599, -9.65273601863364, 9.808425309256764
],
[
-2.4910286499699716, 16.035996934181693, 48.88643725566069,
-131.55745057653914, -16.191686224804815, -33.00612961210212,
886.3391315174406, -7.4730859499099145, -21.796500687237252,
-4.35930013744745, -24.910286499699716, -42.03610846824327,
1.7125821968543555, 2.6467179405930947, 2.3353393593468486,
-78.62309176467723, 21.329432815367884, -2.179650068723725,
-394.04959456712487, 80.49136325215471, -137.00657574834844,
-278.68383021539057, -74.57517020847602, 184.64749867902415,
0.15568929062312323, 1.8682714874774786, -2.3353393593468486,
2.6467179405930947, 1.0898250343618625, 2.4910286499699716
],
[
0.6227571624924929, 13.389278993588597, 14.167725446704214,
-13.54496828421172, -175.15045195101362, -67.41346283981235,
-7.4730859499099145, 850.219216092876, -70.37155936165169,
1.2455143249849858, 5.916193043678683, 9.341357437387394,
-8.7186002748949, -25.065975790322838, -46.86247647756009,
22.1078792684835, -467.22356115999276, 54.17987313684688,
78.77878105530036, -95.9046030238439, 38.76663336515768,
-74.41948091785291, -107.42561052995504, 66.79070567731986,
0.46706787186936966, 3.2694751030855875, 2.802407231216218,
0.6227571624924929, -1.2455143249849858, -0.9341357437387393
],
[
14.323414737327337, -12.61083254047298, -49.04212654628382,
-26.311490115307823, -61.80864837737992, -223.8811999160512,
-21.796500687237252, -70.37155936165169, 750.2666915128308,
-6.538950206171175, -13.389278993588597, -20.083918490382896,
-0.9341357437387393, 0.46706787186936966, 5.916193043678683,
-3.1137858124624644, 55.26969817120874, -86.09617771458714,
-138.40777936395656, 37.98818691204207, -132.33589702965475,
185.27025584151662, 66.32363780545049, -249.72562215948963,
-0.46706787186936966, -1.7125821968543555, 1.8682714874774786,
-1.8682714874774786, 1.2455143249849858, 3.580853684331834
],
[
-42.347487049489516, 9.808425309256764, -1.5568929062312322,
-390.1573623015468, 74.57517020847602, -132.95865419214724,
-4.35930013744745, 1.2455143249849858, -6.538950206171175,
437.17552806973, -82.82670261150155, 139.34191510769529,
0.31137858124624646, 2.802407231216218, -1.0898250343618625,
0.15568929062312323, -0.46706787186936966, 0.46706787186936966,
1.8682714874774786, -0.6227571624924929, -0.7784464531156161,
0.46706787186936966, -0.15568929062312323, -0.9341357437387393,
0.15568929062312323, -0.46706787186936966, -1.2455143249849858,
-3.580853684331834, -4.514989428070574, 5.2934358811861895
],
[
-13.389278993588597, 4.982057299939943, -2.9580965218393414,
81.1141204146472, -101.50941748627633, 37.209740458926454,
-24.910286499699716, 5.916193043678683, -13.389278993588597,
-82.82670261150155, 97.46149593007515, -36.58698329643396,
46.239719315067596, -9.18566814676427, 18.83840416539791,
-0.46706787186936966, 1.401203615608109, 1.5568929062312322,
-1.5568929062312322, -1.2455143249849858, -5.449125171809313,
0.6227571624924929, 0.7784464531156161, 0.7784464531156161,
-0.46706787186936966, 0.6227571624924929, -1.401203615608109,
-4.047921556201204, 0.9341357437387393, 1.0898250343618625
],
[
43.90437995572075, -11.521007506111118, 11.676696796734241,
-143.3898366638965, 38.455254783911435, -132.80296490152412,
-42.03610846824327, 9.341357437387394, -20.083918490382896,
139.34191510769529, -36.58698329643396, 150.39585474193703,
-7.006018078040545, 1.7125821968543555, -2.6467179405930947,
0.9341357437387393, 0.15568929062312323, 2.3353393593468486,
-0.46706787186936966, -5.760503753055559, -7.4730859499099145,
0.46706787186936966, 0.7784464531156161, 1.5568929062312322,
-0.6227571624924929, -0.0, 1.2455143249849858,
8.25153240302553, 3.2694751030855875, -4.047921556201204
],
[
-0.7784464531156161, -41.5690405963739, 16.81444338729731,
-84.38359551773279, 25.377354371569083, -7.317396659286792,
1.7125821968543555, -8.7186002748949, -0.9341357437387393,
0.31137858124624646, 46.239719315067596, -7.006018078040545,
85.47342055209465, -14.323414737327337, -4.982057299939943,
1.401203615608109, -1.5568929062312322, -0.9341357437387393,
0.31137858124624646, -0.46706787186936966, 1.2455143249849858,
0.31137858124624646, 0.31137858124624646, -0.31137858124624646,
-5.760503753055559, -4.35930013744745, 5.2934358811861895,
1.2455143249849858, -1.0898250343618625, -1.8682714874774786
],
[
-3.7365429749549572, -9.497046728010517, 9.808425309256764,
16.50306480605106, -464.4211539287766, 58.383483983671205,
2.6467179405930947, -25.065975790322838, 0.46706787186936966,
2.802407231216218, -9.18566814676427, 1.7125821968543555,
-14.323414737327337, 503.8105444564267, -65.54519135233488,
-0.7784464531156161, -0.15568929062312323, -5.137746590563067,
-0.6227571624924929, 1.2455143249849858, 0.46706787186936966,
0.31137858124624646, 0.7784464531156161, -0.15568929062312323,
-2.4910286499699716, 2.4910286499699716, 0.31137858124624646,
-0.15568929062312323, 0.15568929062312323, -0.6227571624924929
],
[
1.8682714874774786, 43.74869066509763, -15.724618352935446,
-4.35930013744745, 50.59901945251505, -85.1620419708484,
2.3353393593468486, -46.86247647756009, 5.916193043678683,
-1.0898250343618625, 18.83840416539791, -2.6467179405930947,
-4.982057299939943, -65.54519135233488, 103.84475684562318,
-1.5568929062312322, -5.2934358811861895, -8.25153240302553,
0.15568929062312323, 1.401203615608109, 2.023960778100602,
0.15568929062312323, 1.5568929062312322, 2.3353393593468486,
7.7844645311561615, 2.179650068723725, -3.580853684331834,
-0.31137858124624646, -0.6227571624924929, 1.0898250343618625
],
[
-0.6227571624924929, 0.7784464531156161, -0.6227571624924929,
-0.6227571624924929, -8.874289565518025, 2.179650068723725,
-78.62309176467723, 22.1078792684835, -3.1137858124624644,
0.15568929062312323, -0.46706787186936966, 0.9341357437387393,
1.401203615608109, -0.7784464531156161, -1.5568929062312322,
75.50930595221476, -22.73063643097599, 4.514989428070574,
-0.9341357437387393, 47.018165768183216, -6.071882334301805,
2.802407231216218, -37.67680833079582, 3.425164393708711,
0.6227571624924929, 0.15568929062312323, 0.6227571624924929,
0.0, 0.31137858124624646, 0.0
],
[
-0.15568929062312323, 3.1137858124624644, 0.9341357437387393,
0.6227571624924929, -26.1558008246847, 3.2694751030855875,
21.329432815367884, -467.22356115999276, 55.26969817120874,
-0.46706787186936966, 1.401203615608109, 0.15568929062312323,
-1.5568929062312322, -0.15568929062312323, -5.2934358811861895,
-22.73063643097599, 508.4812231751205, -57.760726821178714,
1.2455143249849858, -9.18566814676427, 2.023960778100602,
0.31137858124624646, -11.05393963424175, 2.179650068723725,
1.0898250343618625, 0.6227571624924929, -1.0898250343618625,
0.31137858124624646, -0.0, 0.15568929062312323
],
[
-1.8682714874774786, 0.6227571624924929, 4.82636800931682,
3.7365429749549572, -47.95230151192195, 6.071882334301805,
-2.179650068723725, 54.17987313684688, -86.09617771458714,
0.46706787186936966, 1.5568929062312322, 2.3353393593468486,
-0.9341357437387393, -5.137746590563067, -8.25153240302553,
4.514989428070574, -57.760726821178714, 89.8327206895421,
0.46706787186936966, 19.77253990913665, -3.7365429749549572,
-4.670678718693697, 33.31750819334837, -4.514989428070574,
0.31137858124624646, 1.401203615608109, -0.31137858124624646,
0.31137858124624646, -0.15568929062312323, -0.15568929062312323
],
[
3.1137858124624644, -0.6227571624924929, 0.31137858124624646,
-7.4730859499099145, 0.46706787186936966, -2.802407231216218,
-394.04959456712487, 78.77878105530036, -138.40777936395656,
1.8682714874774786, -1.5568929062312322, -0.46706787186936966,
0.31137858124624646, -0.6227571624924929, 0.15568929062312323,
-0.9341357437387393, 1.2455143249849858, 0.46706787186936966,
426.4329670167345, -87.18600274894901, 155.37791204187698,
-30.670790252755275, 8.7186002748949, -14.167725446704214,
0.15568929062312323, 0.31137858124624646, 0.15568929062312323,
0.7784464531156161, 0.31137858124624646, -0.6227571624924929
],
[
-0.46706787186936966, -0.6227571624924929, 2.179650068723725,
-26.62286869655407, 6.383260915548052, -11.209628924864871,
80.49136325215471, -95.9046030238439, 37.98818691204207,
-0.6227571624924929, -1.2455143249849858, -5.760503753055559,
-0.46706787186936966, 1.2455143249849858, 1.401203615608109,
47.018165768183216, -9.18566814676427, 19.77253990913665,
-87.18600274894901, 96.06029231446702, -37.67680833079582,
-13.07790041234235, 2.179650068723725, -7.161707368663668,
0.31137858124624646, 0.15568929062312323, -0.15568929062312323,
0.9341357437387393, 0.6227571624924929, 0.46706787186936966
],
[
-0.15568929062312323, 1.0898250343618625, 4.982057299939943,
-44.838515699459485, 10.275493181126134, -20.706675652875386,
-137.00657574834844, 38.76663336515768, -132.33589702965475,
-0.7784464531156161, -5.449125171809313, -7.4730859499099145,
1.2455143249849858, 0.46706787186936966, 2.023960778100602,
-6.071882334301805, 2.023960778100602, -3.7365429749549572,
155.37791204187698, -37.67680833079582, 143.23414737327337,
30.048033090262784, -9.497046728010517, 15.724618352935446,
-0.15568929062312323, 0.31137858124624646,
-0.31137858124624646, 1.8682714874774786, -0.46706787186936966,
-1.7125821968543555
],
[
2.802407231216218, -0.0, -0.7784464531156161, 4.35930013744745,
3.7365429749549572, -3.8922322655780808, -278.68383021539057,
-74.41948091785291, 185.27025584151662, 0.46706787186936966,
0.6227571624924929, 0.46706787186936966, 0.31137858124624646,
0.31137858124624646, 0.15568929062312323, 2.802407231216218,
0.31137858124624646, -4.670678718693697, -30.670790252755275,
-13.07790041234235, 30.048033090262784, 297.67792367141163,
82.98239190212468, -205.50986362252266, 0.0,
-0.15568929062312323, -0.15568929062312323, 0.7784464531156161,
-0.6227571624924929, -0.9341357437387393
],
[
0.6227571624924929, -0.46706787186936966, -6.850328787417422,
20.550986362252267, 7.7844645311561615, -11.521007506111118,
-74.57517020847602, -107.42561052995504, 66.32363780545049,
-0.15568929062312323, 0.7784464531156161, 0.7784464531156161,
0.31137858124624646, 0.7784464531156161, 1.5568929062312322,
-37.67680833079582, -11.05393963424175, 33.31750819334837,
8.7186002748949, 2.179650068723725, -9.497046728010517,
82.98239190212468, 107.58129982057814, -73.32965588349104, 0.0,
-0.15568929062312323, -1.0898250343618625, -0.7784464531156161,
0.0, 0.31137858124624646
],
[
-0.31137858124624646, -6.227571624924929, -11.988075377980488,
34.563022518333355, 17.4372005497898, -23.353393593468482,
184.64749867902415, 66.79070567731986, -249.72562215948963,
-0.9341357437387393, 0.7784464531156161, 1.5568929062312322,
-0.31137858124624646, -0.15568929062312323, 2.3353393593468486,
3.425164393708711, 2.179650068723725, -4.514989428070574,
-14.167725446704214, -7.161707368663668, 15.724618352935446,
-205.50986362252266, -73.32965588349104, 268.40833703426443,
-0.6227571624924929, -0.6227571624924929, 1.2455143249849858,
-0.7784464531156161, 0.0, 0.31137858124624646
],
[
-99.64114599879886, 2.9580965218393414, 11.365318215487996,
2.3353393593468486, -48.73074796503757, 7.628775240533038,
0.15568929062312323, 0.46706787186936966, -0.46706787186936966,
0.15568929062312323, -0.46706787186936966, -0.6227571624924929,
-5.760503753055559, -2.4910286499699716, 7.7844645311561615,
0.6227571624924929, 1.0898250343618625, 0.31137858124624646,
0.15568929062312323, 0.31137858124624646, -0.15568929062312323,
0.0, 0.0, -0.6227571624924929, 103.06631039250756,
-18.83840416539791, -13.389278993588597, -0.9341357437387393,
65.38950206171175, -11.676696796734241
],
[
27.40131514966969, -620.7332017143923, 143.23414737327337,
0.6227571624924929, -17.125821968543555, -6.850328787417422,
1.8682714874774786, 3.2694751030855875, -1.7125821968543555,
-0.46706787186936966, 0.6227571624924929, -0.0,
-4.35930013744745, 2.4910286499699716, 2.179650068723725,
0.15568929062312323, 0.6227571624924929, 1.401203615608109,
0.31137858124624646, 0.15568929062312323, 0.31137858124624646,
-0.15568929062312323, -0.15568929062312323,
-0.6227571624924929, -18.83840416539791, 647.5117597015695,
-131.86882915778537, -6.383260915548052, -14.946171899819829,
-6.227571624924929
],
[
10.742561052995502, 60.09606618052557, -40.94628343388141,
4.514989428070574, 47.64092293067571, -19.616850618513528,
-2.3353393593468486, 2.802407231216218, 1.8682714874774786,
-1.2455143249849858, -1.401203615608109, 1.2455143249849858,
5.2934358811861895, 0.31137858124624646, -3.580853684331834,
0.6227571624924929, -1.0898250343618625, -0.31137858124624646,
0.15568929062312323, -0.15568929062312323,
-0.31137858124624646, -0.15568929062312323,
-1.0898250343618625, 1.2455143249849858, -13.389278993588597,
-131.86882915778537, 68.03622000230486, -4.047921556201204,
24.754597209076593, -7.628775240533038
],
[
-545.6909636340469, 119.72506448918175, -155.06653346063072,
-42.970244211982006, 5.449125171809313, -22.73063643097599,
2.6467179405930947, 0.6227571624924929, -1.8682714874774786,
-3.580853684331834, -4.047921556201204, 8.25153240302553,
1.2455143249849858, -0.15568929062312323, -0.31137858124624646,
0.0, 0.31137858124624646, 0.31137858124624646,
0.7784464531156161, 0.9341357437387393, 1.8682714874774786,
0.7784464531156161, -0.7784464531156161, -0.7784464531156161,
-0.9341357437387393, -6.383260915548052, -4.047921556201204,
587.8827613929133, -116.14421080484992, 174.68338407914425
],
[
67.10208425856611, -94.5033994082358, 59.784687599279316,
-12.14376466860361, 4.047921556201204, -9.65273601863364,
1.0898250343618625, -1.2455143249849858, 1.2455143249849858,
-4.514989428070574, 0.9341357437387393, 3.2694751030855875,
-1.0898250343618625, 0.15568929062312323, -0.6227571624924929,
0.31137858124624646, -0.0, -0.15568929062312323,
0.31137858124624646, 0.6227571624924929, -0.46706787186936966,
-0.6227571624924929, 0.0, 0.0, 65.38950206171175,
-14.946171899819829, 24.754597209076593, -116.14421080484992,
105.09027117060819, -78.15602389280787
],
[
-216.40811396614131, 95.28184586135141, -126.88677185784543,
49.04212654628382, -11.521007506111118, 9.808425309256764,
2.4910286499699716, -0.9341357437387393, 3.580853684331834,
5.2934358811861895, 1.0898250343618625, -4.047921556201204,
-1.8682714874774786, -0.6227571624924929, 1.0898250343618625,
0.0, 0.15568929062312323, -0.15568929062312323,
-0.6227571624924929, 0.46706787186936966, -1.7125821968543555,
-0.9341357437387393, 0.31137858124624646, 0.31137858124624646,
-11.676696796734241, -6.227571624924929, -7.628775240533038,
174.68338407914425, -78.15602389280787, 125.95263611410668
]
]
np.testing.assert_almost_equal(hessian,
np.array(expected_hessian, np.float64))
def test_load_energy(self):
"""Test loading the energy in J/mol from a TeraChem output.out or results.dat file"""
output_file = TeraChemLog(
os.path.join(self.data_path,
'formaldehyde_sp_terachem_output.out'))
results_file = TeraChemLog(
os.path.join(self.data_path,
'formaldehyde_sp_terachem_results.dat'))
freq_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_freq_output.out'))
opt_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_minimize_output.out'))
e_elect_1 = output_file.load_energy()
e_elect_2 = results_file.load_energy()
e_elect_3 = freq_file.load_energy()
e_elect_4 = opt_file.load_energy()
self.assertEqual(e_elect_1, e_elect_2)
self.assertEqual(e_elect_1, e_elect_3)
self.assertAlmostEqual(e_elect_1, -300621953.7863082)
self.assertAlmostEqual(e_elect_4, -206346606.4271929)
def test_get_number_of_atoms(self):
"""Uses various TeraChem log files to test that number of atoms can be properly read."""
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_minimize_output.out'))
self.assertEqual(log_file.get_number_of_atoms(), 6)
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_coords.xyz'))
self.assertEqual(log_file.get_number_of_atoms(), 6)
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_coords.xyz'))
self.assertEqual(log_file.get_number_of_atoms(), 4)
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_output.geometry'))
self.assertEqual(log_file.get_number_of_atoms(), 6)
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_output.geometry'))
self.assertEqual(log_file.get_number_of_atoms(), 4)
def test_load_geometry(self):
"""Test loading the geometry from a TeraChem xyz output file"""
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_coords.xyz'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([[0.66409651, 0.00395265, 0.07100793],
[-0.66409647, -0.00395253, -0.0710079],
[1.24675866, 0.88983869, -0.1613784],
[1.19483972, -0.8753068, 0.42244414],
[-1.19483975, 0.87530673, -0.42244421],
[-1.24675868, -0.88983873, 0.16137844]], np.float64))
np.testing.assert_almost_equal(
numbers, np.array([6, 6, 1, 1, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array(
[12., 12., 1.00782503, 1.00782503, 1.00782503, 1.00782503],
np.float64))
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_coords.xyz'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([[-4.23756410e-03, 4.24348000e-05, -5.28516700e-04],
[1.19165823e+00, -1.75471911e-02, 1.58030931e-01],
[-5.96146428e-01, 9.38505681e-01, 4.33255558e-02],
[-5.91274235e-01, -9.21000915e-01, -2.00827970e-01]],
np.float64))
np.testing.assert_almost_equal(numbers,
np.array([6, 8, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array([12., 15.99491462, 1.00782503, 1.00782503], np.float64))
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethane_output.geometry'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([[0.66409651, 0.00395265, 0.07100793],
[-0.66409647, -0.00395253, -0.0710079],
[1.24675866, 0.88983869, -0.1613784],
[1.19483972, -0.8753068, 0.42244414],
[-1.19483975, 0.87530673, -0.42244421],
[-1.24675868, -0.88983873, 0.16137844]], np.float64))
np.testing.assert_almost_equal(
numbers, np.array([6, 6, 1, 1, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array(
[12., 12., 1.00782504, 1.00782504, 1.00782504, 1.00782504],
np.float64))
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_output.geometry'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([[-1.2224100e-02, 1.8041000e-04, -1.6211600e-03],
[1.2016482e+00, -1.7734170e-02, 1.5936241e-01],
[-5.9716440e-01, 9.3272817e-01, 4.2440100e-02],
[-5.9225970e-01, -9.1517440e-01, -2.0018135e-01]],
np.float64))
np.testing.assert_almost_equal(numbers,
np.array([6, 8, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array([12., 15.99491464, 1.00782504, 1.00782504], np.float64))
log_file = TeraChemLog(
os.path.join(self.data_path, 'ethylamine_freq_output.out'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([
[2.370236, 0.065481, -1.194536],
[0.512276, -0.516064, 0.779232], [0.859257, 0.87292, 3.300986],
[-1.367578, -0.100279, 0.008089],
[0.56292, -2.564216, 1.100445], [0.755566, 2.927958, 3.038153],
[2.705598, 0.43874, 4.141338], [-0.600934, 0.336582, 4.672435],
[2.352825, 1.959707, -1.552162],
[4.141389, -0.322693, -0.540207]
], np.float64))
np.testing.assert_almost_equal(
numbers, np.array([7, 6, 6, 1, 1, 1, 1, 1, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array([
14.003074, 12., 12., 1.00782503, 1.00782503, 1.00782503,
1.00782503, 1.00782503, 1.00782503, 1.00782503
], np.float64))
log_file = TeraChemLog(
os.path.join(self.data_path, 'formaldehyde_freq_output.out'))
coords, numbers, masses = log_file.load_geometry()
np.testing.assert_almost_equal(
coords,
np.array([[2.261989e+00, -1.149050e-01, 1.783170e-01],
[-8.108000e-03, 2.710000e-04, -6.880000e-04],
[-1.038653e+00, 1.827038e+00, -6.398200e-02],
[-1.215229e+00, -1.712404e+00, -1.136470e-01]],
np.float64))
np.testing.assert_almost_equal(numbers,
np.array([8, 6, 1, 1], np.float64))
np.testing.assert_almost_equal(
masses,
np.array([15.99491462, 12., 1.00782503, 1.00782503], np.float64))