def test_imaginary_energies(self, n2_unstable_data):
vib_data = VibrationsData(n2_unstable_data['atoms'],
n2_unstable_data['hessian'])
assert vib_data.tabulate() == ('\n'.join(
VibrationsData._tabulate_from_energies(vib_data.get_energies())) +
'\n')
def test_tabulate_energies(self):
# Test the private classmethod _tabulate_from_energies
# used by public tabulate() method
energies = np.array([1., complex(2., 1.), complex(1., 1e-3)])
table = VibrationsData._tabulate_from_energies(energies, im_tol=1e-2)
for sep_row in 0, 2, 6:
assert table[sep_row] == '-' * 21
assert tuple(table[1].strip().split()) == ('#', 'meV', 'cm^-1')
expected_rows = [
# energy in eV should be converted to meV and cm-1
('0', '1000.0', '8065.5'),
# Imaginary component over threshold detected
('1', '1000.0i', '8065.5i'),
# Small imaginary component ignored
('2', '1000.0', '8065.5')
]
for row, expected in zip(table[3:6], expected_rows):
assert tuple(row.split()) == expected
# ZPE = (1 + 2 + 1) / 2 - currently we keep all real parts
assert table[7].split()[2] == '2.000'
assert len(table) == 8
def test_energies_and_modes(self, n2_data, n2_vibdata):
energies, modes = n2_vibdata.get_energies_and_modes()
assert_array_almost_equal(n2_data['ref_frequencies'],
energies / units.invcm,
decimal=5)
assert_array_almost_equal(n2_data['ref_frequencies'],
n2_vibdata.get_energies() / units.invcm,
decimal=5)
assert_array_almost_equal(n2_data['ref_frequencies'],
n2_vibdata.get_frequencies(),
decimal=5)
assert (n2_vibdata.get_zero_point_energy() == pytest.approx(
n2_data['ref_zpe']))
assert n2_vibdata.tabulate() == (
'\n'.join(VibrationsData._tabulate_from_energies(energies)) + '\n')
atoms_with_forces = n2_vibdata.show_as_force(-1, show=False)
try:
assert_array_almost_equal(atoms_with_forces.get_forces(),
n2_data['ref_forces'])
except AssertionError:
# Eigenvectors may be off by a sign change, which is allowed
assert_array_almost_equal(atoms_with_forces.get_forces(),
-n2_data['ref_forces'])
def test_vibrations_methods(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=vib.atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
with open(self.logfile, 'w') as fd:
vib.summary(log=fd)
with open(self.logfile, 'rt') as fd:
log_txt = fd.read()
assert log_txt == '\n'.join(
VibrationsData._tabulate_from_energies(vib_energies)) + '\n'
last_mode = vib.get_mode(-1)
scale = 0.5
assert_array_almost_equal(
vib.show_as_force(-1, scale=scale, show=False).get_forces(),
last_mode * 3 * len(vib.atoms) * scale)
vib.write_mode(n=3, nimages=5)
for i in range(3):
assert not Path('vib.{}.traj'.format(i)).is_file()
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
random_dimer.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
random_dimer.get_all_distances())
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, image in vib.iterdisplace(inplace=True):
assert d[name] == random_dimer
