def test_espresso_input_edit():
"""
Load a structure in from qe_input_1, change the position and cell,
then edit and re-parse
:return:
"""
os.system('cp test_files/qe_input_1.in .')
positions, species, cell, masses = parse_dft_input('./qe_input_1.in')
_, coded_species = get_unique_species(species)
structure = Structure(cell,
coded_species,
positions,
masses,
species_labels=species)
structure.vec1 += np.random.randn(3)
structure.positions[0] += np.random.randn(3)
new_file = edit_dft_input_positions('./qe_input_1.in', structure=structure)
positions, species, cell, masses = parse_dft_input(new_file)
assert np.equal(positions[0], structure.positions[0]).all()
assert np.equal(structure.vec1, cell[0, :]).all()
os.remove('qe_input_1.in')
def test_espresso_calling(qe_input, qe_output):
dft_loc = os.environ.get('PWSCF_COMMAND')
os.system(' '.join(['cp', qe_input, 'pwscf.in']))
positions, species, cell, masses = parse_dft_input(qe_input)
structure = Structure(cell=cell, species=species,
positions=positions,
mass_dict=masses, species_labels=species)
forces = run_dft('pwscf.in',
structure, dft_loc)
ref_forces = parse_dft_forces(qe_output)
assert len(forces) == len(ref_forces)
for i in range(structure.nat):
assert np.isclose(forces[i], ref_forces[i]).all()
cleanup_espresso_run()
def test_espresso_calling(qe_input, qe_output):
dft_loc = os.environ.get('PWSCF_COMMAND')
shutil.copyfile(qe_input, 'pwscf.in')
positions, species, cell, masses = parse_dft_input(qe_input)
structure = Structure(cell=cell,
species=species,
positions=positions,
mass_dict=masses,
species_labels=species)
forces = run_dft_par('pwscf.in', structure, dft_loc, dft_out='pwscf.out')
ref_forces = parse_dft_forces('pwscf.out')
assert len(forces) == len(ref_forces)
for i in range(structure.nat):
assert np.allclose(forces[i], ref_forces[i])
cleanup_espresso_run('pwscf')
def test_cell_parsing(qe_input, exp_cell):
positions, species, cell, masses = parse_dft_input(qe_input)
assert np.all(exp_cell == cell)
def test_species_parsing(qe_input, exp_spec):
positions, species, cell, masses = parse_dft_input(qe_input)
assert len(species) == len(exp_spec)
for i, spec in enumerate(species):
assert spec == exp_spec[i]
