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_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_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_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_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())