def test_special_species(SPECIAL_SPECIES_STRUCTURES):
"""Make sure vacancies and non-chemical symbols ("X") are handled"""
from optimade.adapters.warnings import ConversionWarning
for special_structure in SPECIAL_SPECIES_STRUCTURES:
structure = Structure(special_structure)
if structure.attributes.species[0].mass:
aiida_structure = get_aiida_structure_data(structure)
else:
with pytest.warns(
ConversionWarning,
match=r".*will default to setting mass to 1\.0\.$"):
aiida_structure = get_aiida_structure_data(structure)
assert isinstance(aiida_structure, StructureData)
# Test species.chemical_symbols
if "vacancy" in structure.attributes.species[0].chemical_symbols:
assert aiida_structure.has_vacancies
assert not aiida_structure.is_alloy
elif len(structure.attributes.species[0].chemical_symbols) > 1:
assert not aiida_structure.has_vacancies
assert aiida_structure.is_alloy
else:
assert not aiida_structure.has_vacancies
assert not aiida_structure.is_alloy
# Test species.mass
if structure.attributes.species[0].mass:
if len(structure.attributes.species[0].mass) > 1:
assert aiida_structure.kinds[0].mass == sum([
conc * mass for conc, mass in zip(
structure.attributes.species[0].concentration,
structure.attributes.species[0].mass,
)
])
else:
assert (aiida_structure.kinds[0].mass ==
structure.attributes.species[0].mass[0])
else:
assert aiida_structure.kinds[0].mass == 1.0
def test_special_species(SPECIAL_SPECIES_STRUCTURES):
"""Make sure vacancies and non-chemical symbols ("X") are handled"""
for special_structure in SPECIAL_SPECIES_STRUCTURES:
structure = Structure(special_structure)
aiida_structure = get_aiida_structure_data(structure)
assert isinstance(aiida_structure, StructureData)
if "vacancy" in structure.attributes.species[0].chemical_symbols:
assert aiida_structure.has_vacancies
assert not aiida_structure.is_alloy
elif len(structure.attributes.species[0].chemical_symbols) > 1:
assert not aiida_structure.has_vacancies
assert aiida_structure.is_alloy
else:
assert not aiida_structure.has_vacancies
assert not aiida_structure.is_alloy
def test_null_lattice_vectors(null_lattice_vector_structure):
"""Make sure null lattice vectors are handled"""
assert isinstance(get_aiida_structure_data(null_lattice_vector_structure),
StructureData)
def test_successful_conversion(RAW_STRUCTURES):
"""Make sure its possible to convert"""
for structure in RAW_STRUCTURES:
assert isinstance(get_aiida_structure_data(Structure(structure)),
StructureData)
def test_null_species(null_species_structure):
"""Make sure null species are handled"""
assert isinstance(get_aiida_structure_data(null_species_structure),
StructureData)
def test_null_positions(null_position_structure):
"""Make sure null positions are handled"""
assert isinstance(get_aiida_structure_data(null_position_structure),
StructureData)