def test_cp2k_input_edit():
"""
Load a structure in from cp2k_input_1, change the position and cell,
then edit and re-parse
:return:
"""
positions, species, cell, masses = parse_dft_input(
"./test_files/cp2k_input_1.in")
_, coded_species = get_unique_species(species)
structure = Structure(cell,
coded_species,
positions,
masses,
species_labels=species)
structure.positions[0] += np.random.randn(3)
newfilename = edit_dft_input_positions("./test_files/cp2k_input_1.in",
structure=structure)
positions, species, cell, masses = parse_dft_input(newfilename)
assert np.isclose(positions[0], structure.positions[0]).all()
assert np.isclose(structure.vec1, cell[0, :]).all()
remove(newfilename)
cleanup()
def test_cp2k_calling(cp2k_input, cp2k_output):
dft_loc = environ.get('CP2K_COMMAND')
copyfile(cp2k_input, 'cp2k.in')
positions, species, cell, masses = parse_dft_input(cp2k_input)
structure = Structure(cell=cell, species=species,
positions=positions,
mass_dict=masses, species_labels=species)
forces = run_dft_par('cp2k.in',
structure, dft_loc)
ref_forces = parse_dft_forces(cp2k_output)
assert len(forces) == len(ref_forces)
for i in range(structure.nat):
assert np.isclose(forces[i], ref_forces[i]).all()
cleanup()
def test_cell_parsing(cp2k_input, exp_cell):
positions, species, cell, masses = parse_dft_input(cp2k_input)
assert np.all(exp_cell == cell)
def test_species_parsing(cp2k_input, exp_spec):
positions, species, cell, masses = parse_dft_input(cp2k_input)
assert len(species) == len(exp_spec)
for i, spec in enumerate(species):
assert spec == exp_spec[i]