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_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()