def test_basis_to_from_json():
basis = Basis.primitive("X")
json_data = basis.to_json()
res = Basis.from_json(json_data)
assert len(basis) == len(res) == 1
assert res[0][0] == basis[0][0]
assert np.array_equal(res[0][1], basis[0][1])
def test_basis_init_not_fractional():
specie = "Fe"
positive_site = np.array([1.5, 0, 0])
negative_site = np.array([-1.5, 0, 0])
# test a positive value
with pytest.raises(ValueError):
_ = Basis([(specie, positive_site)])
# test a negative value
with pytest.raises(ValueError):
_ = Basis([(specie, negative_site)])
def from_json(cls, s: str) -> 'UnitCell':
"""Initializes from a JSON string."""
# load dict from JSON string
data = orjson.loads(s)
# validate type
_type = data.pop("type")
if _type != cls.__name__:
raise TypeError(f"cannot deserialize from type `{_type}`")
# process topology
topology = Topology.from_json(orjson.dumps(data["topology"]))
# process basis
basis = Basis.from_json(orjson.dumps(data["basis"]))
# process lattice parameters
lattice_parameters = LatticeParameters.from_json(
orjson.dumps(data["lattice_parameters"]))
# process spacegroup
spacegroup = Spacegroup.from_json(orjson.dumps(data["spacegroup"]))
# return instance
return cls(basis,
lattice_parameters,
spacegroup,
_graph=topology._graph)
def test_basis_apply_spacegroup_complex_monoclinic():
# complex basis of arbitrary species
basis = Basis([
("X", np.array([0.0, 0.0, 0.0])),
("Y", np.array([0.1, 0.2, 0.3])),
])
# Monoclinic spacegroup from international number
spg = Spacegroup(3)
res = basis.apply_spacegroup(spg)
assert len(res) == 3
target = [
("X", np.array([0.0, 0.0, 0.0])),
("Y", np.array([0.1, 0.2, 0.3])),
("Y", np.array([0.9, 0.2, 0.7])),
]
for (target_specie, target_site), (res_specie,
res_site) in zip(target, res):
assert target_specie == res_specie
assert np.allclose(target_site, res_site)
def test_crystal_to_from_json():
basis = Basis.primitive("Fe")
lattparams = LatticeParameters.cubic(2.85)
spg = Spacegroup("I m -3 m")
unit_cell = UnitCell(basis, lattparams, spg)
crystal = Crystal(unit_cell)
json_data = crystal.to_json()
res = Crystal.from_json(json_data)
assert np.array_equal(
res.lattice_vectors.vectors,
crystal.lattice_vectors.vectors,
)
assert len(res.atoms) == len(crystal.atoms) == 2
def test_unit_cell_hexagonal():
# primitive basis of arbitrary species
basis = Basis.primitive("X")
# cubic lattice parameters
lattparams = LatticeParameters.hexagonal(4.0, 2.5)
# hexagonal spacegroup
spg = Spacegroup("P 6/m c c")
# build the unit cell
unit_cell = UnitCell(basis, lattparams, spg)
assert len(unit_cell.atoms) == 2
target = [
("X", np.array([0.0, 0.0, 0.0])),
("X", np.array([0.0, 0.0, 1.25])),
]
for i, (specie, site) in enumerate(target):
assert unit_cell.atoms[i].specie == specie
assert np.allclose(unit_cell.atoms[i].position, site)
def test_unit_cell_cubic():
# primitive basis of iron
basis = Basis.primitive("Fe")
# cubic lattice parameters
lattparams = LatticeParameters.cubic(2.85)
# BCC spacegroup
spg = Spacegroup("I m -3 m")
# build the unit cell
unit_cell = UnitCell(basis, lattparams, spg)
assert len(unit_cell.atoms) == 2
target = [
("Fe", np.array([0.0, 0.0, 0.0])),
("Fe", np.array([1.425, 1.425, 1.425])),
]
for i, (specie, site) in enumerate(target):
assert unit_cell.atoms[i].specie == specie
assert np.allclose(unit_cell.atoms[i].position, site)
def test_basis_apply_spacegroup_primitive_cubic():
# primitive basis of aluminum
basis = Basis.primitive("Al")
# FCC spacegroup from Hermann Mauguin symbol
spg = Spacegroup("F m -3 m")
res = basis.apply_spacegroup(spg)
assert len(res) == 4
target = [
("Al", np.array([0.0, 0.0, 0.0])),
("Al", np.array([0.0, 0.5, 0.5])),
("Al", np.array([0.5, 0.0, 0.5])),
("Al", np.array([0.5, 0.5, 0.0])),
]
for (target_specie, target_site), (res_specie,
res_site) in zip(target, res):
assert target_specie == res_specie
assert np.allclose(target_site, res_site)
def test_unit_cell_to_from_json():
basis = Basis.primitive("X")
params = LatticeParameters.cubic(10)
spg = Spacegroup("F m -3 m")
unit_cell = UnitCell(basis, params, spg)
json_data = unit_cell.to_json()
res = UnitCell.from_json(json_data)
# test basis
assert res.basis[0][0] == unit_cell.basis[0][0]
assert np.array_equal(res.basis[0][1], unit_cell.basis[0][1])
# test lattice parameters
assert res.lattice_parameters.a == unit_cell.lattice_parameters.a
assert res.lattice_parameters.alpha == unit_cell.lattice_parameters.alpha
# test spacegroup
assert res.spacegroup == unit_cell.spacegroup
# test atoms/bonds
assert len(res.atoms) == len(unit_cell.atoms) == 4
assert len(res.bonds) == len(unit_cell.bonds) == 0
assert np.array_equal(
res.atoms[0].position,
unit_cell.atoms[0].position,
)
assert res.atoms[0].specie == unit_cell.atoms[0].specie