import os from pathlib import Path import pytest import numpy as np from numpy.testing import assert_array_almost_equal from ase import units, Atoms import ase.io from ase.calculators.qmmm import ForceConstantCalculator from ase.vibrations import Vibrations, VibrationsData from ase.thermochemistry import IdealGasThermo class TestHarmonicVibrations: """Test the ase.vibrations.Vibrations object using a harmonic calculator """ def setup_method(self): self.logfile = 'vibrations-log.txt' @pytest.fixture def random_dimer(self): rng = np.random.RandomState(42) d = 1 + 0.5 * rng.rand() z_values = rng.randint(1, high=50, size=2) hessian = rng.rand(6, 6) hessian += hessian.T # Ensure the random Hessian is symmetric atoms = Atoms(z_values, [[0, 0, 0], [0, 0, d]]) ref_atoms = atoms.copy() atoms.calc = ForceConstantCalculator(D=hessian, ref=ref_atoms, f0=np.zeros((2, 3))) return atoms def test_harmonic_vibrations(self, testdir): """Check the numerics with a trivial case: one atom in harmonic well""" rng = np.random.RandomState(42) k = rng.rand() ref_atoms = Atoms('H', positions=np.zeros([1, 3])) atoms = ref_atoms.copy() mass = atoms.get_masses()[0] atoms.calc = ForceConstantCalculator(D=np.eye(3) * k, ref=ref_atoms, f0=np.zeros((1, 3))) vib = Vibrations(atoms, name='harmonic') vib.run() vib.read() expected_energy = (units._hbar # In J/s * np.sqrt(k # In eV/A^2 * units._e # eV -> J * units.m**2 # A^-2 -> m^-2 / mass # in amu / units._amu # amu^-1 -> kg^-1 ) ) / units._e # J/s -> eV/s assert np.allclose(vib.get_energies(), expected_energy) def test_consistency_with_vibrationsdata(self, testdir, random_dimer): vib = Vibrations(random_dimer, delta=1e-6, nfree=4) vib.run() vib_data = vib.get_vibrations() assert_array_almost_equal(vib.get_energies(), vib_data.get_energies()) for mode_index in range(3 * len(vib.atoms)): assert_array_almost_equal(vib.get_mode(mode_index), vib_data.get_modes()[mode_index]) # Hessian should be close to the ForceConstantCalculator input assert_array_almost_equal(random_dimer.calc.D, vib_data.get_hessian_2d(), decimal=6) def test_json_manipulation(self, testdir, random_dimer): vib = Vibrations(random_dimer, name='interrupt') vib.run() disp_file = Path('interrupt/cache.1x-.json') comb_file = Path('interrupt/combined.json') assert disp_file.is_file() assert not comb_file.is_file() # Should do nothing harmful as files are already split # (It used to raise an error but this is no longer implemented.) vib.split() # Build a combined file assert vib.combine() == 13 # Individual displacements should be gone, combination should exist assert not disp_file.is_file() assert comb_file.is_file() # Not allowed to run after data has been combined with pytest.raises(RuntimeError): vib.run() # But reading is allowed vib.read() # Splitting should fail if any split file already exists with open(disp_file, 'w') as fd: fd.write("hello") with pytest.raises(AssertionError): vib.split() os.remove(disp_file) # Now split() for real: replace .all.json file with displacements vib.split() assert disp_file.is_file() assert not comb_file.is_file() 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 def test_vibrations_restart_dir(self, testdir, random_dimer): vib = Vibrations(random_dimer) vib.run() freqs = vib.get_frequencies() assert freqs is not None # write/read the data from another working directory atoms = random_dimer.copy() # This copy() removes the Calculator with ase.utils.workdir('run_from_here', mkdir=True): vib = Vibrations(atoms, name=str(Path.cwd().parent / 'vib')) assert_array_almost_equal(freqs, vib.get_frequencies()) assert vib.clean() == 13 class TestVibrationsDataStaticMethods: @pytest.mark.parametrize('mask,expected_indices', [([True, True, False, True], [0, 1, 3]), ([False, False], []), ([], []), (np.array([True, True]), [0, 1]), (np.array([False, True, True]), [1, 2]), (np.array([], dtype=bool), [])]) def test_indices_from_mask(self, mask, expected_indices): assert VibrationsData.indices_from_mask(mask) == expected_indices 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 na2 = Atoms('Na2', cell=[2, 2, 2], positions=[[0, 0, 0], [1, 1, 1]]) na2_image_1 = na2.copy() na2_image_1.info.update({'mode#': '0', 'frequency_cm-1': 8065.5}) na2_image_1.arrays['mode'] = np.array([[1., 1., 1.], [0.5, 0.5, 0.5]]) @pytest.mark.parametrize('kwargs,expected', [(dict(atoms=na2, energies=[1.], modes=np.array([[[1., 1., 1.], [0.5, 0.5, 0.5]]])), [na2_image_1]) ]) def test_get_jmol_images(self, kwargs, expected): # Test the private staticmethod _get_jmol_images # used by the public write_jmol_images() method from ase.calculators.calculator import compare_atoms jmol_images = list(VibrationsData._get_jmol_images(**kwargs)) assert len(jmol_images) == len(expected) for image, reference in zip(jmol_images, expected): assert compare_atoms(image, reference) == [] for key, value in reference.info.items(): if key == 'frequency_cm-1': assert float(image.info[key]) == pytest.approx(value, abs=0.1) else: assert image.info[key] == value class TestVibrationsData: @pytest.fixture def random_dimer(self): rng = np.random.RandomState(42) d = 1 + 0.5 * rng.rand() z_values = rng.randint(1, high=50, size=2) hessian = rng.rand(6, 6) hessian += hessian.T # Ensure the random Hessian is symmetric atoms = Atoms(z_values, [[0, 0, 0], [0, 0, d]]) ref_atoms = atoms.copy() atoms.calc = ForceConstantCalculator(D=hessian, ref=ref_atoms, f0=np.zeros((2, 3))) return atoms @pytest.fixture def n2_data(self): return{'atoms': Atoms('N2', positions=[[0., 0., 0.05095057], [0., 0., 1.04904943]]), 'hessian': np.array([[[[4.67554672e-03, 0.0, 0.0], [-4.67554672e-03, 0.0, 0.0]], [[0.0, 4.67554672e-03, 0.0], [0.0, -4.67554672e-03, 0.0]], [[0.0, 0.0, 3.90392599e+01], [0.0, 0.0, -3.90392599e+01]]], [[[-4.67554672e-03, 0.0, 0.0], [4.67554672e-03, 0.0, 0.0]], [[0.0, -4.67554672e-03, 0.0], [0.0, 4.67554672e-03, 0.0]], [[0.0, 0.0, -3.90392599e+01], [0.0, 0.0, 3.90392599e+01]]]]), 'ref_frequencies': [0.00000000e+00 + 0.j, 6.06775530e-08 + 0.j, 3.62010442e-06 + 0.j, 1.34737571e+01 + 0.j, 1.34737571e+01 + 0.j, 1.23118496e+03 + 0.j], 'ref_zpe': 0.07799427233401508, 'ref_forces': np.array([[0., 0., -2.26722e-1], [0., 0., 2.26722e-1]]) } @pytest.fixture def n2_unstable_data(self): return{'atoms': Atoms('N2', positions=[[0., 0., 0.45], [0., 0., -0.45]]), 'hessian': np.array( [-5.150829928323684, 0.0, -0.6867385017096544, 5.150829928323684, 0.0, 0.6867385017096544, 0.0, -5.158454318599951, 0.0, 0.0, 5.158454318599951, 0.0, -0.6867385017096544, 0.0, 56.65107699250456, 0.6867385017096544, 0.0, -56.65107699250456, 5.150829928323684, 0.0, 0.6867385017096544, -5.150829928323684, 0.0, -0.6867385017096544, 0.0, 5.158454318599951, 0.0, 0.0, -5.158454318599951, 0.0, 0.6867385017096544, 0.0, -56.65107699250456, -0.6867385017096544, 0.0, 56.65107699250456 ]).reshape((2, 3, 2, 3)) } @pytest.fixture def n2_vibdata(self, n2_data): return VibrationsData(n2_data['atoms'], n2_data['hessian']) def setup_method(self): self.jmol_file = 'vib-data.xyz' 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 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_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_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_new_mass(self, n2_data, n2_vibdata): original_masses = n2_vibdata.get_atoms().get_masses() new_masses = original_masses * 3 new_vib_data = n2_vibdata.with_new_masses(new_masses) assert_array_almost_equal(new_vib_data.get_atoms().get_masses(), new_masses) assert_array_almost_equal(n2_vibdata.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_dos(self, n2_vibdata): with pytest.warns(np.ComplexWarning): dos = n2_vibdata.get_dos() assert_array_almost_equal(dos.get_energies(), n2_vibdata.get_energies()) def test_pdos(self, n2_vibdata): with pytest.warns(np.ComplexWarning): pdos = n2_vibdata.get_pdos() assert_array_almost_equal(pdos[0].get_energies(), n2_vibdata.get_energies()) assert_array_almost_equal(pdos[1].get_energies(), n2_vibdata.get_energies()) # 3N states = 6, divided equally over two N atoms = 3.0 assert sum(pdos[0].get_weights()) == pytest.approx(3.0) def test_todict(self, n2_data, n2_vibdata): vib_data_dict = n2_vibdata.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_dict_roundtrip(self, n2_vibdata): vib_data_dict = n2_vibdata.todict() vib_data_roundtrip = VibrationsData.fromdict(vib_data_dict) for getter in ('get_atoms',): assert (getattr(n2_vibdata, getter)() == getattr(vib_data_roundtrip, getter)()) for array_getter in ('get_hessian', 'get_hessian_2d', 'get_mask', 'get_indices'): assert_array_almost_equal( getattr(n2_vibdata, array_getter)(), getattr(vib_data_roundtrip, array_getter)()) @pytest.mark.parametrize('indices, expected_mask', [([1], [False, True]), (None, [True, True])]) def test_dict_indices(self, n2_vibdata, indices, expected_mask): vib_data_dict = n2_vibdata.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_jmol_roundtrip(self, testdir, n2_data): ir_intensities = np.random.RandomState(42).rand(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_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_bad_hessian2d(self, n2_data): bad_hessians = (None, 'fish', 1, np.array([1, 2, 3]), n2_data['hessian'], np.array([[[1, 0, 0]], [[0, 0, 1]]])) for bad_hessian in bad_hessians: with pytest.raises(ValueError): VibrationsData.from_2d(n2_data['atoms'], bad_hessian) class TestSlab: "N2 above Ag slab - vibration with frozen molecules" def test_vibration_on_surface(self, testdir): from ase.build import fcc111, add_adsorbate ag_slab = fcc111('Ag', (4, 4, 2), a=2) n2 = Atoms('N2', positions=[[0., 0., 0.], [0., np.sqrt(2), np.sqrt(2)]]) add_adsorbate(ag_slab, n2, height=1, position='fcc') # Add an interaction between the N atoms hessian_bottom_corner = np.zeros((2, 3, 2, 3)) hessian_bottom_corner[-1, :, -2] = [1, 1, 1] hessian_bottom_corner[-2, :, -1] = [1, 1, 1] hessian = np.zeros((34, 3, 34, 3)) hessian[32:, :, 32:, :] = hessian_bottom_corner ag_slab.calc = ForceConstantCalculator(hessian.reshape((34 * 3, 34 * 3)), ref=ag_slab.copy(), f0=np.zeros((34, 3))) # Check that Vibrations with restricted indices returns correct Hessian vibs = Vibrations(ag_slab, indices=[-2, -1]) vibs.run() vibs.read() assert_array_almost_equal(vibs.get_vibrations().get_hessian(), hessian_bottom_corner) # These should blow up if the vectors don't match number of atoms vibs.summary() vibs.write_jmol() for i in range(6): # Frozen atoms should have zero displacement assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.]) # The N atoms should have finite displacement assert np.all(np.any(vibs.get_mode(i)[-2:, :], axis=1))