def test_pad_cell(null_lattice_vector_structure):
"""Make sure None values in lattice_vectors are converted to padding float value"""
lattice_vectors, padded_cell = pad_cell(
null_lattice_vector_structure.attributes.lattice_vectors
)
assert not any(value is None for vector in lattice_vectors for value in vector)
assert padded_cell
lattice_vectors, padded_cell = pad_cell(lattice_vectors)
assert not any(value is None for vector in lattice_vectors for value in vector)
assert not padded_cell
def get_aiida_structure_data(
optimade_structure: OptimadeStructure) -> StructureData:
"""Get AiiDA `StructureData` from OPTIMADE structure.
Parameters:
optimade_structure: OPTIMADE structure.
Returns:
AiiDA `StructureData` Node.
"""
if "optimade.adapters" in repr(globals().get("StructureData")):
warn(AIIDA_NOT_FOUND)
return None
attributes = optimade_structure.attributes
# Convert null/None values to float("nan")
lattice_vectors, adjust_cell = pad_cell(attributes.lattice_vectors)
structure = StructureData(cell=lattice_vectors)
# Add Kinds
for kind in attributes.species:
symbols = []
concentration = []
for index, chemical_symbol in enumerate(kind.chemical_symbols):
# NOTE: The non-chemical element identifier "X" is identical to how AiiDA handles this,
# so it will be treated the same as any other true chemical identifier.
if chemical_symbol == "vacancy":
# Skip. This is how AiiDA handles vacancies;
# to not include them, while keeping the concentration in a site less than 1.
continue
else:
symbols.append(chemical_symbol)
concentration.append(kind.concentration[index])
# AiiDA needs a definition for the mass, and for it to be > 0
# mass is OPTIONAL for OPTIMADE structures
mass = kind.mass if kind.mass else 1
structure.append_kind(
Kind(symbols=symbols,
weights=concentration,
mass=mass,
name=kind.name))
# Add Sites
for index in range(attributes.nsites):
# range() to ensure 1-to-1 between kind and site
structure.append_site(
Site(
kind_name=attributes.species_at_sites[index],
position=attributes.cartesian_site_positions[index],
))
if adjust_cell:
structure._adjust_default_cell(
pbc=[bool(dim.value) for dim in attributes.dimension_types])
return structure
def test__pad_iter_of_iters():
"""Test _pad_iter_of_iters"""
iterable = [(0.0, ) * 3, (0.0, ) * 3, (None, ) * 3]
padded_iterable, padded_iterable_bool = pad_cell(iterable)
assert padded_iterable_bool
assert all(math.isnan(_) for _ in padded_iterable[-1])
for i in range(2):
assert padded_iterable[i] == (0.0, ) * 3
for valid_padding_value in (3.0, 3, "3", "3.0"):
padded_iterable, padded_iterable_bool = pad_cell(
iterable, valid_padding_value)
assert padded_iterable_bool
assert padded_iterable[-1] == (float(valid_padding_value), ) * 3
for i in range(2):
assert padded_iterable[i] == (0.0, ) * 3
# Since nan != nan, the above for-loop cannot be used for nan
valid_padding_value = "nan"
padded_iterable, padded_iterable_bool = pad_cell(iterable,
valid_padding_value)
assert padded_iterable_bool
assert all(math.isnan(_) for _ in padded_iterable[-1])
assert all(math.isnan(_) for _ in (float(valid_padding_value), ) * 3)
for i in range(2):
assert padded_iterable[i] == (0.0, ) * 3
invalid_padding_value = "x"
padded_iterable, padded_iterable_bool = pad_cell(iterable,
invalid_padding_value)
assert padded_iterable_bool
assert all(math.isnan(_) for _ in padded_iterable[-1])
for i in range(2):
assert padded_iterable[i] == (0.0, ) * 3
