def test_energies_and_modes(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
energies, modes = vib_data.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'],
vib_data.get_energies() / units.invcm,
decimal=5)
assert_array_almost_equal(n2_data['ref_frequencies'],
vib_data.get_frequencies(),
decimal=5)
assert (vib_data.get_zero_point_energy() == pytest.approx(
n2_data['ref_zpe']))
assert vib_data.tabulate() == vibrations_n2_log
atoms_with_forces = vib_data.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_bad_hessian(self, n2_data):
bad_hessians = (None, 'fish', 1, np.array([1, 2, 3]), np.eye(6),
np.array([[[1, 0, 0]], [[0, 0, 1]]]))
for bad_hessian in bad_hessians:
with pytest.raises(ValueError):
VibrationsData(n2_data['atoms'], bad_hessian)
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_todict(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
vib_data_dict = vib_data.todict()
assert vib_data_dict['indices'] is None
assert_array_almost_equal(vib_data_dict['atoms'].positions,
n2_data['atoms'].positions)
assert_array_almost_equal(vib_data_dict['hessian'], n2_data['hessian'])
def test_pdos(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
with pytest.warns(np.ComplexWarning):
pdos = vib_data.get_pdos()
assert_array_almost_equal(pdos[0].get_energies(),
vib_data.get_energies())
assert_array_almost_equal(pdos[1].get_energies(),
vib_data.get_energies())
assert sum(pdos[0].get_weights()) == pytest.approx(3.0)
def test_new_mass(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
original_masses = vib_data.get_atoms().get_masses()
new_masses = original_masses * 3
new_vib_data = vib_data.with_new_masses(new_masses)
assert_array_almost_equal(new_vib_data.get_atoms().get_masses(),
new_masses)
assert_array_almost_equal(vib_data.get_energies() / np.sqrt(3),
new_vib_data.get_energies())
def test_fixed_atoms(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'],
n2_data['hessian'][1:, :, 1:, :],
indices=[
1,
])
assert vib_data.get_indices() == [
1,
]
assert vib_data.get_mask().tolist() == [False, True]
def test_dict_indices(self, n2_data, indices, expected_mask):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
vib_data_dict = vib_data.todict()
vib_data_dict['indices'] = indices
# Reduce size of Hessian if necessary
if indices is not None:
n_active = len(indices)
vib_data_dict['hessian'] = (np.asarray(
vib_data_dict['hessian'])[:n_active, :, :n_active, :].tolist())
vib_data_fromdict = VibrationsData.fromdict(vib_data_dict)
assert_array_almost_equal(vib_data_fromdict.get_mask(), expected_mask)
def test_dict_roundtrip(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
vib_data_dict = vib_data.todict()
vib_data_roundtrip = VibrationsData.fromdict(vib_data_dict)
for getter in ('get_atoms', ):
assert (getattr(vib_data,
getter)() == getattr(vib_data_roundtrip, getter)())
for array_getter in ('get_hessian', 'get_hessian_2d', 'get_mask',
'get_indices'):
assert_array_almost_equal(
getattr(vib_data, array_getter)(),
getattr(vib_data_roundtrip, array_getter)())
def test_jmol_roundtrip(self, testdir, n2_data):
ir_intensities = np.random.random(6)
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
vib_data.write_jmol(self.jmol_file, ir_intensities=ir_intensities)
images = ase.io.read(self.jmol_file, index=':')
for i, image in enumerate(images):
assert_array_almost_equal(image.positions,
vib_data.get_atoms().positions)
assert (image.info['IR_intensity'] == pytest.approx(
ir_intensities[i]))
assert_array_almost_equal(image.arrays['mode'],
vib_data.get_modes()[i])
def test_dos(self, n2_data):
vib_data = VibrationsData(n2_data['atoms'], n2_data['hessian'])
with pytest.warns(np.ComplexWarning):
dos = vib_data.get_dos()
assert_array_almost_equal(dos.get_energies(), vib_data.get_energies())
def test_zero_mass(self, n2_data):
atoms = n2_data['atoms']
atoms.set_masses([0., 1.])
vib_data = VibrationsData(atoms, n2_data['hessian'])
with pytest.raises(ValueError):
vib_data.get_energies_and_modes()
def test_imaginary_energies(self, n2_unstable_data):
vib_data = VibrationsData(n2_unstable_data['atoms'],
n2_unstable_data['hessian'])
assert vib_data.tabulate() == unstable_n2_log
def test_init(self, n2_data):
# Check that init runs without error; properties are checked in other
# methods using the (identical) n2_vibdata fixture
VibrationsData(n2_data['atoms'], n2_data['hessian'])
def n2_vibdata(self, n2_data):
return VibrationsData(n2_data['atoms'], n2_data['hessian'])