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