def _test_modes(self):
""" Placeholder """
result = GaussianLogResult(self.logfile)
print("---------- OUT file equivalent ------------")
print(result._compute_modes())
print("---------- HAM file equivalent ------------")
print(result.compute_harmonic_modes(num_modals=3))
def test_compute_modes(self):
""" Test the internal function that is computing modes """
result = GaussianLogResult(self.logfile)
modes = result._compute_modes()
expected = [[352.3005875, 2, 2], [-352.3005875, -2, -2],
[631.6153975, 1, 1], [-631.6153975, -1, -1],
[115.653915, 4, 4], [-115.653915, -4, -4],
[115.653915, 3, 3], [-115.653915, -3, -3],
[-15.341901966295344, 2, 2,
2], [-88.2017421687633, 1, 1, 2],
[42.40478531359112, 4, 4, 2], [26.25167512727164, 4, 3, 2],
[2.2874639206341865, 3, 3, 2],
[0.4207357291666667, 2, 2, 2, 2], [4.9425425, 1, 1, 2, 2],
[1.6122932291666665, 1, 1,
1, 1], [-4.194299375, 4, 4, 2, 2],
[-4.194299375, 3, 3, 2, 2], [-10.20589125, 4, 4, 1, 1],
[-10.20589125, 3, 3, 1, 1], [2.2973803125, 4, 4, 4, 4],
[2.7821204166666664, 4, 4, 4,
3], [7.329224375, 4, 4, 3, 3],
[-2.7821200000000004, 4, 3, 3, 3],
[2.2973803125, 3, 3, 3, 3]]
for i, entry in enumerate(modes):
msg = "mode[{}]={} does not match expected {}".format(
i, entry, expected[i])
self.assertAlmostEqual(entry[0], expected[i][0], msg=msg)
self.assertListEqual(entry[1:], expected[i][1:], msg=msg)
def test_quadratic_force_constants(self):
""" Test quadratic force constants """
result = GaussianLogResult(self.logfile)
qfc = result.quadratic_force_constants
expected = [('1', '1', 1409.20235, 1.17003, 0.07515),
('2', '2', 2526.46159, 3.76076, 0.24156),
('3a', '3a', 462.61566, 0.12609, 0.0081),
('3b', '3b', 462.61566, 0.12609, 0.0081)]
self.assertListEqual(qfc, expected)
def test_cubic_force_constants(self):
""" Test cubic force constants """
result = GaussianLogResult(self.logfile)
cfc = result.cubic_force_constants
expected = [('1', '1', '1', -260.36071, -1.39757, -0.0475),
('2', '2', '1', -498.9444, -4.80163, -0.1632),
('3a', '3a', '1', 239.87769, 0.4227, 0.01437),
('3a', '3b', '1', 74.25095, 0.13084, 0.00445),
('3b', '3b', '1', 12.93985, 0.0228, 0.00078)]
self.assertListEqual(cfc, expected)
def test_gaussian_log_result_file(self):
""" Test result from file """
result = GaussianLogResult(self.logfile)
with open(self.logfile) as file:
lines = file.read().split('\n')
with self.subTest('Check list of lines'):
self.assertListEqual(result.log, lines)
with self.subTest('Check as string'):
line = '\n'.join(lines)
self.assertEqual(str(result), line)
def test_quartic_force_constants(self):
""" Test quartic force constants """
result = GaussianLogResult(self.logfile)
qfc = result.quartic_force_constants
expected = [('1', '1', '1', '1', 40.39063, 1.40169, 0.02521),
('2', '2', '1', '1', 79.08068, 4.92017, 0.0885),
('2', '2', '2', '2', 154.78015, 17.26491, 0.31053),
('3a', '3a', '1', '1', -67.10879, -0.76453, -0.01375),
('3b', '3b', '1', '1', -67.10879, -0.76453, -0.01375),
('3a', '3a', '2', '2', -163.29426, -3.33524, -0.05999),
('3b', '3b', '2', '2', -163.29426, -3.33524, -0.05999),
('3a', '3a', '3a', '3a', 220.54851, 0.82484, 0.01484),
('3a', '3a', '3a', '3b', 66.77089, 0.24972, 0.00449),
('3a', '3a', '3b', '3b', 117.26759, 0.43857, 0.00789),
('3a', '3b', '3b', '3b', -66.77088, -0.24972, -0.00449),
('3b', '3b', '3b', '3b', 220.54851, 0.82484, 0.01484)]
self.assertListEqual(qfc, expected)
def test_gaussian_log_result_string(self):
""" Test result from string """
with open(self.logfile) as file:
line = file.read()
result = GaussianLogResult(line)
self.assertListEqual(result.log, line.split('\n'))
def test_gaussian_log_result_list(self):
""" Test result from list of strings """
with open(self.logfile) as file:
lines = file.read().split('\n')
result = GaussianLogResult(lines)
self.assertListEqual(result.log, lines)
def test_harmonic_modes(self):
""" Test harmonic modes """
result = GaussianLogResult(self.logfile)
hmodes = result.compute_harmonic_modes(num_modals=3)
expected = [[([[0, 0, 0]], 1268.0676746875001),
([[0, 0, 2]], 13.68076170725888),
([[0, 1, 1]], 3813.8767834375008),
([[0, 2, 0]], 13.68076170725888),
([[0, 2, 2]], 6379.033410937501),
([[1, 0, 0]], 705.8633821875002),
([[1, 0, 1]], -46.025705898886045),
([[1, 0, 2]], 3.5700610461746014),
([[1, 1, 0]], -46.025705898886045),
([[1, 1, 1]], 2120.1145609375008),
([[1, 1, 2]], -130.180355),
([[1, 2, 0]], 3.5700610461746014),
([[1, 2, 1]], -130.180355),
([[1, 2, 2]], 3539.4145684375007),
([[2, 0, 0]], 238.19997093750004),
([[2, 0, 2]], 19.493918375198643),
([[2, 1, 1]], 728.3841946875002),
([[2, 2, 0]], 19.493918375198643),
([[2, 2, 2]], 1246.1369821875003),
([[3, 0, 0]], 238.19997093750004),
([[3, 0, 2]], 19.493918375198643),
([[3, 1, 1]], 728.3841946875002),
([[3, 2, 0]], 19.493918375198643),
([[3, 2, 2]], 1246.1369821875003)],
[([[0, 0, 0], [1, 0, 0]], 4.942542500000002),
([[0, 0, 0], [1, 0, 1]], -88.20174216876333),
([[0, 0, 0], [1, 0, 2]], 6.989810636105426),
([[0, 0, 0], [1, 1, 0]], -88.20174216876333),
([[0, 0, 0], [1, 1, 1]], 14.827627500000007),
([[0, 0, 0], [1, 1, 2]], -124.73610000000002),
([[0, 0, 0], [1, 2, 0]], 6.989810636105426),
([[0, 0, 0], [1, 2, 1]], -124.73610000000002),
([[0, 0, 0], [1, 2, 2]], 24.71271250000001),
([[0, 0, 2], [1, 0, 0]], 6.989810636105426),
([[0, 0, 2], [1, 0, 1]], -124.73610000000005),
([[0, 0, 2], [1, 0, 2]], 9.885085000000004),
([[0, 0, 2], [1, 1, 0]], -124.73610000000005),
([[0, 0, 2], [1, 1, 1]], 20.96943190831628),
([[0, 0, 2], [1, 1, 2]], -176.40348433752666),
([[0, 0, 2], [1, 2, 0]], 9.885085000000004),
([[0, 0, 2], [1, 2, 1]], -176.40348433752666),
([[0, 0, 2], [1, 2, 2]], 34.94905318052713),
([[0, 1, 1], [1, 0, 0]], 14.827627500000007),
([[0, 1, 1], [1, 0, 1]], -264.60522650629),
([[0, 1, 1], [1, 0, 2]], 20.96943190831628),
([[0, 1, 1], [1, 1, 0]], -264.60522650629),
([[0, 1, 1], [1, 1, 1]], 44.482882500000024),
([[0, 1, 1], [1, 1, 2]], -374.20830000000007),
([[0, 1, 1], [1, 2, 0]], 20.96943190831628),
([[0, 1, 1], [1, 2, 1]], -374.20830000000007),
([[0, 1, 1], [1, 2, 2]], 74.13813750000003),
([[0, 2, 0], [1, 0, 0]], 6.989810636105426),
([[0, 2, 0], [1, 0, 1]], -124.73610000000005),
([[0, 2, 0], [1, 0, 2]], 9.885085000000004),
([[0, 2, 0], [1, 1, 0]], -124.73610000000005),
([[0, 2, 0], [1, 1, 1]], 20.96943190831628),
([[0, 2, 0], [1, 1, 2]], -176.40348433752666),
([[0, 2, 0], [1, 2, 0]], 9.885085000000004),
([[0, 2, 0], [1, 2, 1]], -176.40348433752666),
([[0, 2, 0], [1, 2, 2]], 34.94905318052713),
([[0, 2, 2], [1, 0, 0]], 24.712712500000013),
([[0, 2, 2], [1, 0, 1]], -441.0087108438167),
([[0, 2, 2], [1, 0, 2]], 34.94905318052713),
([[0, 2, 2], [1, 1, 0]], -441.0087108438167),
([[0, 2, 2], [1, 1, 1]], 74.13813750000004),
([[0, 2, 2], [1, 1, 2]], -623.6805),
([[0, 2, 2], [1, 2, 0]], 34.94905318052713),
([[0, 2, 2], [1, 2, 1]], -623.6805),
([[0, 2, 2], [1, 2, 2]], 123.56356250000005),
([[2, 0, 0], [0, 0, 0]], -10.205891250000004),
([[2, 0, 0], [0, 0, 2]], -14.433309821854907),
([[2, 0, 0], [0, 1, 1]], -30.617673750000016),
([[2, 0, 0], [0, 2, 0]], -14.433309821854907),
([[2, 0, 0], [0, 2, 2]], -51.029456250000024),
([[2, 0, 0], [1, 0, 0]], -4.194299375000002),
([[2, 0, 0], [1, 0, 1]], 2.2874639206341874),
([[2, 0, 0], [1, 0, 2]], -5.931635060777999),
([[2, 0, 0], [1, 1, 0]], 2.2874639206341874),
([[2, 0, 0], [1, 1, 1]], -12.582898125000007),
([[2, 0, 0], [1, 1, 2]], 3.2349625000000004),
([[2, 0, 0], [1, 2, 0]], -5.931635060777999),
([[2, 0, 0], [1, 2, 1]], 3.2349625000000004),
([[2, 0, 0], [1, 2, 2]], -20.971496875000007),
([[2, 0, 2], [0, 0, 0]], -14.433309821854907),
([[2, 0, 2], [0, 0, 2]], -20.411782500000008),
([[2, 0, 2], [0, 1, 1]], -43.29992946556472),
([[2, 0, 2], [0, 2, 0]], -20.411782500000008),
([[2, 0, 2], [0, 2, 2]], -72.16654910927453),
([[2, 0, 2], [1, 0, 0]], -5.931635060777999),
([[2, 0, 2], [1, 0, 1]], 3.2349625000000013),
([[2, 0, 2], [1, 0, 2]], -8.388598750000003),
([[2, 0, 2], [1, 1, 0]], 3.2349625000000013),
([[2, 0, 2], [1, 1, 1]], -17.794905182334),
([[2, 0, 2], [1, 1, 2]], 4.574927841268375),
([[2, 0, 2], [1, 2, 0]], -8.388598750000003),
([[2, 0, 2], [1, 2, 1]], 4.574927841268375),
([[2, 0, 2], [1, 2, 2]], -29.658175303889994),
([[2, 1, 1], [0, 0, 0]], -30.61767375000002),
([[2, 1, 1], [0, 0, 2]], -43.29992946556473),
([[2, 1, 1], [0, 1, 1]], -91.85302125000007),
([[2, 1, 1], [0, 2, 0]], -43.29992946556473),
([[2, 1, 1], [0, 2, 2]], -153.0883687500001),
([[2, 1, 1], [1, 0, 0]], -12.582898125000007),
([[2, 1, 1], [1, 0, 1]], 6.862391761902563),
([[2, 1, 1], [1, 0, 2]], -17.794905182334),
([[2, 1, 1], [1, 1, 0]], 6.862391761902563),
([[2, 1, 1], [1, 1, 1]], -37.74869437500002),
([[2, 1, 1], [1, 1, 2]], 9.704887500000002),
([[2, 1, 1], [1, 2, 0]], -17.794905182334),
([[2, 1, 1], [1, 2, 1]], 9.704887500000002),
([[2, 1, 1], [1, 2, 2]], -62.91449062500003),
([[2, 2, 0], [0, 0, 0]], -14.433309821854907),
([[2, 2, 0], [0, 0, 2]], -20.411782500000008),
([[2, 2, 0], [0, 1, 1]], -43.29992946556472),
([[2, 2, 0], [0, 2, 0]], -20.411782500000008),
([[2, 2, 0], [0, 2, 2]], -72.16654910927453),
([[2, 2, 0], [1, 0, 0]], -5.931635060777999),
([[2, 2, 0], [1, 0, 1]], 3.2349625000000013),
([[2, 2, 0], [1, 0, 2]], -8.388598750000003),
([[2, 2, 0], [1, 1, 0]], 3.2349625000000013),
([[2, 2, 0], [1, 1, 1]], -17.794905182334),
([[2, 2, 0], [1, 1, 2]], 4.574927841268375),
([[2, 2, 0], [1, 2, 0]], -8.388598750000003),
([[2, 2, 0], [1, 2, 1]], 4.574927841268375),
([[2, 2, 0], [1, 2, 2]], -29.658175303889994),
([[2, 2, 2], [0, 0, 0]], -51.029456250000024),
([[2, 2, 2], [0, 0, 2]], -72.16654910927453),
([[2, 2, 2], [0, 1, 1]], -153.0883687500001),
([[2, 2, 2], [0, 2, 0]], -72.16654910927453),
([[2, 2, 2], [0, 2, 2]], -255.1472812500001),
([[2, 2, 2], [1, 0, 0]], -20.971496875000007),
([[2, 2, 2], [1, 0, 1]], 11.437319603170936),
([[2, 2, 2], [1, 0, 2]], -29.65817530388999),
([[2, 2, 2], [1, 1, 0]], 11.437319603170936),
([[2, 2, 2], [1, 1, 1]], -62.91449062500003),
([[2, 2, 2], [1, 1, 2]], 16.1748125),
([[2, 2, 2], [1, 2, 0]], -29.65817530388999),
([[2, 2, 2], [1, 2, 1]], 16.1748125),
([[2, 2, 2], [1, 2, 2]], -104.85748437500004),
([[3, 0, 0], [0, 0, 0]], -10.205891250000004),
([[3, 0, 0], [0, 0, 2]], -14.433309821854907),
([[3, 0, 0], [0, 1, 1]], -30.617673750000016),
([[3, 0, 0], [0, 2, 0]], -14.433309821854907),
([[3, 0, 0], [0, 2, 2]], -51.029456250000024),
([[3, 0, 0], [1, 0, 0]], -4.194299375000002),
([[3, 0, 0], [1, 0, 1]], 42.404785313591134),
([[3, 0, 0], [1, 0, 2]], -5.931635060777999),
([[3, 0, 0], [1, 1, 0]], 42.404785313591134),
([[3, 0, 0], [1, 1, 1]], -12.582898125000007),
([[3, 0, 0], [1, 1, 2]], 59.969422500000015),
([[3, 0, 0], [1, 2, 0]], -5.931635060777999),
([[3, 0, 0], [1, 2, 1]], 59.969422500000015),
([[3, 0, 0], [1, 2, 2]], -20.971496875000007),
([[3, 0, 0], [2, 0, 0]], 7.3292243750000035),
([[3, 0, 0], [2, 0, 2]], 10.365088512800476),
([[3, 0, 0], [2, 1, 1]], 21.98767312500001),
([[3, 0, 0], [2, 2, 0]], 10.365088512800476),
([[3, 0, 0], [2, 2, 2]], 36.64612187500001),
([[3, 0, 1], [2, 0, 1]], 1.2499999986204102e-06),
([[3, 0, 1], [2, 1, 0]], 1.2499999986204102e-06),
([[3, 0, 1], [2, 1, 2]], -11.803533740681361),
([[3, 0, 1], [2, 2, 1]], -11.803533740681361),
([[3, 0, 2], [0, 0, 0]], -14.433309821854907),
([[3, 0, 2], [0, 0, 2]], -20.411782500000008),
([[3, 0, 2], [0, 1, 1]], -43.29992946556472),
([[3, 0, 2], [0, 2, 0]], -20.411782500000008),
([[3, 0, 2], [0, 2, 2]], -72.16654910927453),
([[3, 0, 2], [1, 0, 0]], -5.931635060777999),
([[3, 0, 2], [1, 0, 1]], 59.96942250000003),
([[3, 0, 2], [1, 0, 2]], -8.388598750000003),
([[3, 0, 2], [1, 1, 0]], 59.96942250000003),
([[3, 0, 2], [1, 1, 1]], -17.794905182334),
([[3, 0, 2], [1, 1, 2]], 84.80957062718227),
([[3, 0, 2], [1, 2, 0]], -8.388598750000003),
([[3, 0, 2], [1, 2, 1]], 84.80957062718227),
([[3, 0, 2], [1, 2, 2]], -29.658175303889994),
([[3, 0, 2], [2, 0, 0]], 10.365088512800474),
([[3, 0, 2], [2, 0, 2]], 14.658448750000005),
([[3, 0, 2], [2, 1, 1]], 31.095265538401428),
([[3, 0, 2], [2, 2, 0]], 14.658448750000005),
([[3, 0, 2], [2, 2, 2]], 51.82544256400237),
([[3, 1, 0], [2, 0, 1]], 1.2499999986204102e-06),
([[3, 1, 0], [2, 1, 0]], 1.2499999986204102e-06),
([[3, 1, 0], [2, 1, 2]], -11.803533740681361),
([[3, 1, 0], [2, 2, 1]], -11.803533740681361),
([[3, 1, 1], [0, 0, 0]], -30.61767375000002),
([[3, 1, 1], [0, 0, 2]], -43.29992946556473),
([[3, 1, 1], [0, 1, 1]], -91.85302125000007),
([[3, 1, 1], [0, 2, 0]], -43.29992946556473),
([[3, 1, 1], [0, 2, 2]], -153.0883687500001),
([[3, 1, 1], [1, 0, 0]], -12.582898125000007),
([[3, 1, 1], [1, 0, 1]], 127.21435594077343),
([[3, 1, 1], [1, 0, 2]], -17.794905182334),
([[3, 1, 1], [1, 1, 0]], 127.21435594077343),
([[3, 1, 1], [1, 1, 1]], -37.74869437500002),
([[3, 1, 1], [1, 1, 2]], 179.90826750000008),
([[3, 1, 1], [1, 2, 0]], -17.794905182334),
([[3, 1, 1], [1, 2, 1]], 179.90826750000008),
([[3, 1, 1], [1, 2, 2]], -62.91449062500003),
([[3, 1, 1], [2, 0, 0]], 21.98767312500001),
([[3, 1, 1], [2, 0, 2]], 31.09526553840143),
([[3, 1, 1], [2, 1, 1]], 65.96301937500004),
([[3, 1, 1], [2, 2, 0]], 31.09526553840143),
([[3, 1, 1], [2, 2, 2]], 109.93836562500006),
([[3, 1, 2], [2, 0, 1]], 11.80353904398221),
([[3, 1, 2], [2, 1, 0]], 11.80353904398221),
([[3, 1, 2], [2, 1, 2]], 4.999999994481641e-06),
([[3, 1, 2], [2, 2, 1]], 4.999999994481641e-06),
([[3, 2, 0], [0, 0, 0]], -14.433309821854907),
([[3, 2, 0], [0, 0, 2]], -20.411782500000008),
([[3, 2, 0], [0, 1, 1]], -43.29992946556472),
([[3, 2, 0], [0, 2, 0]], -20.411782500000008),
([[3, 2, 0], [0, 2, 2]], -72.16654910927453),
([[3, 2, 0], [1, 0, 0]], -5.931635060777999),
([[3, 2, 0], [1, 0, 1]], 59.96942250000003),
([[3, 2, 0], [1, 0, 2]], -8.388598750000003),
([[3, 2, 0], [1, 1, 0]], 59.96942250000003),
([[3, 2, 0], [1, 1, 1]], -17.794905182334),
([[3, 2, 0], [1, 1, 2]], 84.80957062718227),
([[3, 2, 0], [1, 2, 0]], -8.388598750000003),
([[3, 2, 0], [1, 2, 1]], 84.80957062718227),
([[3, 2, 0], [1, 2, 2]], -29.658175303889994),
([[3, 2, 0], [2, 0, 0]], 10.365088512800474),
([[3, 2, 0], [2, 0, 2]], 14.658448750000005),
([[3, 2, 0], [2, 1, 1]], 31.095265538401428),
([[3, 2, 0], [2, 2, 0]], 14.658448750000005),
([[3, 2, 0], [2, 2, 2]], 51.82544256400237),
([[3, 2, 1], [2, 0, 1]], 11.80353904398221),
([[3, 2, 1], [2, 1, 0]], 11.80353904398221),
([[3, 2, 1], [2, 1, 2]], 4.999999994481641e-06),
([[3, 2, 1], [2, 2, 1]], 4.999999994481641e-06),
([[3, 2, 2], [0, 0, 0]], -51.029456250000024),
([[3, 2, 2], [0, 0, 2]], -72.16654910927453),
([[3, 2, 2], [0, 1, 1]], -153.0883687500001),
([[3, 2, 2], [0, 2, 0]], -72.16654910927453),
([[3, 2, 2], [0, 2, 2]], -255.1472812500001),
([[3, 2, 2], [1, 0, 0]], -20.971496875000007),
([[3, 2, 2], [1, 0, 1]], 212.0239265679557),
([[3, 2, 2], [1, 0, 2]], -29.65817530388999),
([[3, 2, 2], [1, 1, 0]], 212.0239265679557),
([[3, 2, 2], [1, 1, 1]], -62.91449062500003),
([[3, 2, 2], [1, 1, 2]], 299.8471125000001),
([[3, 2, 2], [1, 2, 0]], -29.65817530388999),
([[3, 2, 2], [1, 2, 1]], 299.8471125000001),
([[3, 2, 2], [1, 2, 2]], -104.85748437500004),
([[3, 2, 2], [2, 0, 0]], 36.64612187500001),
([[3, 2, 2], [2, 0, 2]], 51.82544256400237),
([[3, 2, 2], [2, 1, 1]], 109.93836562500005),
([[3, 2, 2], [2, 2, 0]], 51.82544256400237),
([[3, 2, 2], [2, 2, 2]], 183.23060937500006)],
[([[3, 0, 1], [2, 0, 1], [1, 0, 1]], 26.25167512727166),
([[3, 0, 1], [2, 0, 1], [1, 1, 0]], 26.25167512727166),
([[3, 0, 1], [2, 0, 1], [1, 1, 2]], 37.12547500000002),
([[3, 0, 1], [2, 0, 1], [1, 2, 1]], 37.12547500000002),
([[3, 0, 1], [2, 1, 0], [1, 0, 1]], 26.25167512727166),
([[3, 0, 1], [2, 1, 0], [1, 1, 0]], 26.25167512727166),
([[3, 0, 1], [2, 1, 0], [1, 1, 2]], 37.12547500000002),
([[3, 0, 1], [2, 1, 0], [1, 2, 1]], 37.12547500000002),
([[3, 0, 1], [2, 1, 2], [1, 0, 1]], 37.125475000000016),
([[3, 0, 1], [2, 1, 2], [1, 1, 0]], 37.125475000000016),
([[3, 0, 1], [2, 1, 2], [1, 1, 2]], 52.5033502545433),
([[3, 0, 1], [2, 1, 2], [1, 2, 1]], 52.5033502545433),
([[3, 0, 1], [2, 2, 1], [1, 0, 1]], 37.125475000000016),
([[3, 0, 1], [2, 2, 1], [1, 1, 0]], 37.125475000000016),
([[3, 0, 1], [2, 2, 1], [1, 1, 2]], 52.5033502545433),
([[3, 0, 1], [2, 2, 1], [1, 2, 1]], 52.5033502545433),
([[3, 1, 0], [2, 0, 1], [1, 0, 1]], 26.25167512727166),
([[3, 1, 0], [2, 0, 1], [1, 1, 0]], 26.25167512727166),
([[3, 1, 0], [2, 0, 1], [1, 1, 2]], 37.12547500000002),
([[3, 1, 0], [2, 0, 1], [1, 2, 1]], 37.12547500000002),
([[3, 1, 0], [2, 1, 0], [1, 0, 1]], 26.25167512727166),
([[3, 1, 0], [2, 1, 0], [1, 1, 0]], 26.25167512727166),
([[3, 1, 0], [2, 1, 0], [1, 1, 2]], 37.12547500000002),
([[3, 1, 0], [2, 1, 0], [1, 2, 1]], 37.12547500000002),
([[3, 1, 0], [2, 1, 2], [1, 0, 1]], 37.125475000000016),
([[3, 1, 0], [2, 1, 2], [1, 1, 0]], 37.125475000000016),
([[3, 1, 0], [2, 1, 2], [1, 1, 2]], 52.5033502545433),
([[3, 1, 0], [2, 1, 2], [1, 2, 1]], 52.5033502545433),
([[3, 1, 0], [2, 2, 1], [1, 0, 1]], 37.125475000000016),
([[3, 1, 0], [2, 2, 1], [1, 1, 0]], 37.125475000000016),
([[3, 1, 0], [2, 2, 1], [1, 1, 2]], 52.5033502545433),
([[3, 1, 0], [2, 2, 1], [1, 2, 1]], 52.5033502545433),
([[3, 1, 2], [2, 0, 1], [1, 0, 1]], 37.125475000000016),
([[3, 1, 2], [2, 0, 1], [1, 1, 0]], 37.125475000000016),
([[3, 1, 2], [2, 0, 1], [1, 1, 2]], 52.5033502545433),
([[3, 1, 2], [2, 0, 1], [1, 2, 1]], 52.5033502545433),
([[3, 1, 2], [2, 1, 0], [1, 0, 1]], 37.125475000000016),
([[3, 1, 2], [2, 1, 0], [1, 1, 0]], 37.125475000000016),
([[3, 1, 2], [2, 1, 0], [1, 1, 2]], 52.5033502545433),
([[3, 1, 2], [2, 1, 0], [1, 2, 1]], 52.5033502545433),
([[3, 1, 2], [2, 1, 2], [1, 0, 1]], 52.5033502545433),
([[3, 1, 2], [2, 1, 2], [1, 1, 0]], 52.5033502545433),
([[3, 1, 2], [2, 1, 2], [1, 1, 2]], 74.25095000000002),
([[3, 1, 2], [2, 1, 2], [1, 2, 1]], 74.25095000000002),
([[3, 1, 2], [2, 2, 1], [1, 0, 1]], 52.5033502545433),
([[3, 1, 2], [2, 2, 1], [1, 1, 0]], 52.5033502545433),
([[3, 1, 2], [2, 2, 1], [1, 1, 2]], 74.25095000000002),
([[3, 1, 2], [2, 2, 1], [1, 2, 1]], 74.25095000000002),
([[3, 2, 1], [2, 0, 1], [1, 0, 1]], 37.125475000000016),
([[3, 2, 1], [2, 0, 1], [1, 1, 0]], 37.125475000000016),
([[3, 2, 1], [2, 0, 1], [1, 1, 2]], 52.5033502545433),
([[3, 2, 1], [2, 0, 1], [1, 2, 1]], 52.5033502545433),
([[3, 2, 1], [2, 1, 0], [1, 0, 1]], 37.125475000000016),
([[3, 2, 1], [2, 1, 0], [1, 1, 0]], 37.125475000000016),
([[3, 2, 1], [2, 1, 0], [1, 1, 2]], 52.5033502545433),
([[3, 2, 1], [2, 1, 0], [1, 2, 1]], 52.5033502545433),
([[3, 2, 1], [2, 1, 2], [1, 0, 1]], 52.5033502545433),
([[3, 2, 1], [2, 1, 2], [1, 1, 0]], 52.5033502545433),
([[3, 2, 1], [2, 1, 2], [1, 1, 2]], 74.25095000000002),
([[3, 2, 1], [2, 1, 2], [1, 2, 1]], 74.25095000000002),
([[3, 2, 1], [2, 2, 1], [1, 0, 1]], 52.5033502545433),
([[3, 2, 1], [2, 2, 1], [1, 1, 0]], 52.5033502545433),
([[3, 2, 1], [2, 2, 1], [1, 1, 2]], 74.25095000000002),
([[3, 2, 1], [2, 2, 1], [1, 2, 1]], 74.25095000000002)]]
for i, hmode in enumerate(hmodes):
for j, entry in enumerate(hmode):
msg = "mode[{}][{}]={} does not match expected {}".format(
i, j, entry, expected[i][j])
self.assertListEqual(entry[0], expected[i][j][0], msg=msg)
self.assertAlmostEqual(entry[1], expected[i][j][1], msg=msg)
def setUp(self):
super().setUp()
self.reference_energy = 2539.259482550559
self.gaussian_log_data = GaussianLogResult(
self.get_resource_path('CO2_freq_B3LYP_ccpVDZ.log'))
class TestHarmonicIntegrals(QiskitChemistryTestCase):
"""Hamiltonian in harmonic basis tests."""
def setUp(self):
super().setUp()
self.reference_energy = 2539.259482550559
self.gaussian_log_data = GaussianLogResult(
self.get_resource_path('CO2_freq_B3LYP_ccpVDZ.log'))
def test_compute_modes(self):
""" test for computing the general hamiltonian from the gaussian log data"""
reference = [[605.3643675, 1, 1], [-605.3643675, -1, -1],
[340.5950575, 2, 2], [-340.5950575, -2, -2],
[163.7595125, 3, 3], [-163.7595125, -3, -3],
[163.7595125, 4, 4], [-163.7595125, -4, -4],
[-89.09086530649508, 2, 1, 1],
[-15.590557244410897, 2, 2, 2],
[44.01468537435673, 3, 2, 1],
[21.644966371722838, 3, 3, 2],
[-78.71701132125833, 4, 2,
1], [17.15529085952822, 4, 3, 2],
[6.412754934114705, 4, 4, 2],
[1.6512647916666667, 1, 1, 1,
1], [5.03965375, 2, 2, 1, 1],
[0.43840625000000005, 2, 2, 2, 2],
[-2.4473854166666666, 3, 1, 1, 1],
[-3.73513125, 3, 2, 2, 1], [-6.3850425, 3, 3, 1, 1],
[-2.565723125, 3, 3, 2, 2],
[1.7778641666666666, 3, 3, 3, 1],
[0.6310235416666666, 3, 3, 3, 3],
[4.376968333333333, 4, 1, 1, 1], [6.68000625, 4, 2, 2, 1],
[-5.82197125, 4, 3, 1, 1], [-2.86914875, 4, 3, 2, 2],
[-9.53873625, 4, 3, 3,
1], [1.3534904166666666, 4, 3, 3, 3],
[-4.595841875, 4, 4, 1, 1], [-1.683979375, 4, 4, 2, 2],
[5.3335925, 4, 4, 3, 1], [-0.551021875, 4, 4, 3, 3],
[-3.1795791666666666, 4, 4, 4, 1], [1.29536, 4, 4, 4, 3],
[0.20048104166666667, 4, 4, 4, 4]]
result = self.gaussian_log_data._compute_modes()
check_indices = np.random.randint(0, high=len(reference), size=10)
for idx in check_indices:
for i in range(len(reference[idx])):
self.assertAlmostEqual(reference[idx][i],
result[idx][i],
places=6)
def test_harmonic_basis(self):
"""test for obtaining the hamiltonian in the harmonic basis"""
num_modals = 2
hamiltonian_in_harmonic_basis = \
self.gaussian_log_data.compute_harmonic_modes(num_modals, truncation_order=2)
basis = [num_modals, num_modals, num_modals,
num_modals] # 4 modes and 2 modals per mode
bos_op = BosonicOperator(hamiltonian_in_harmonic_basis, basis)
qubit_op = bos_op.mapping('direct', threshold=1e-5)
algo = NumPyEigensolver(qubit_op, k=100)
result = algo.run()
vecs = result['eigenstates']
energies = result['eigenvalues']
gs_energy = bos_op.ground_state_energy(vecs, energies)
self.assertAlmostEqual(gs_energy, self.reference_energy, places=6)
