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'])