def from_dict(cls, d):
"""
Parameters
----------
d: dict
Returns
-------
site_centers: list
Center coordinates at each groups
groups: list
List of groups
"""
site_centers = read_matrix(d["coords"])
groups = []
for g in d["groups"]:
name = g["name"]
species = g.get("species", [name])
n = len(species)
coords = read_tensor(g.get("coords", [[[0, 0, 0]]]), rank=3)
m = coords.shape[1]
if n != 0 and m != n:
raise InputError(
'number of atoms mismatch in group [{}]: "species"={}, "coords"={}'
.format(name, n, m))
relaxation = read_matrix(g.get("relaxation", np.ones((n, 3))),
dtype=bool)
m = relaxation.shape[0]
if n != 0 and m != n:
raise InputError(
'number of atoms mismatch in group [{}]: "species"={}, "relaxation"={}'
.format(name, n, m))
mag = read_vector(g.get("magnetization", np.zeros(n)))
m = len(mag)
if n != 0 and m != n:
raise InputError(
'number of atoms mismatch in group [{}]: "species"={}, "magnetization"={}'
.format(name, n, m))
groups.append(
group(
name,
species,
coords=coords,
relaxations=relaxation,
magnetizations=mag,
))
return cls(site_centers, groups)
def __init__(self, dconfig):
"""
Get information from dictionary
Parameters
----------
dconfig: dict
Dictionary
"""
if "config" in dconfig:
dconfig = dconfig["config"]
if "unitcell" not in dconfig:
raise InputError(
'"unitcell" is not found in the "config" section.')
self.lat = Lattice(read_matrix(dconfig["unitcell"]))
self.supercell = dconfig.get("supercell", [1, 1, 1])
if "base_structure" not in dconfig:
raise InputError(
'"base_structure" is not found in the "config" section.')
self.base_structure = base_structure(self.lat,
dconfig["base_structure"])
if "defect_structure" not in dconfig:
raise InputError(
'"defect_structure" is not found in the "config" section.')
self.defect_sublattices = [
defect_sublattice.from_dict(ds)
for ds in dconfig["defect_structure"]
]
self.num_defects = [{g["name"]: g["num"]
for g in ds["groups"]}
for ds in dconfig["defect_structure"]]
def base_structure(lat, dict_str):
"""
Parameters
----------
lat: pymatgen.Lattice
dict_str: dict
Dictionary of base structure
Returns
-------
st: pymatgen.Structure
"""
if len(dict_str) == 1 and not dict_str[0]:
return Structure(
lattice=lat,
species=[],
coords=[],
site_properties={
"seldyn": np.zeros((0, 3), dtype=bool),
"magnetization": np.zeros(0),
},
)
elems = []
coords = []
relaxations = []
magnetizations = []
for tc in dict_str:
if "type" not in tc:
raise InputError('"type" is not found in "base_structure"')
sp = tc["type"]
crds = read_matrix(tc["coords"])
n = crds.shape[0]
if "relaxation" in tc:
relax = read_matrix(tc["relaxation"], dtype=bool)
m = relax.shape[0]
if m != n:
raise InputError(
'number of base atoms mismatch: "coords"={}, "relaxation"={}'
.format(n, m))
else:
relax = np.ones((n, 3), dtype=bool) # all True
if "magnetization" in tc:
mag = tc["magnetization"]
if not isinstance(mag, list):
raise InputError('"magnetization" should be a list of floats')
try:
mag = [float(x) for x in mag]
except ValueError:
raise InputError('"magnetization" should be a list of floats')
m = len(mag)
if m != n:
raise InputError(
'number of base atoms mismatch: "coords"={}, "magnetization"={}'
.format(n, m))
else:
mag = np.zeros(n)
elems.append([sp] * n)
coords.append(crds)
relaxations.append(relax)
magnetizations.append(mag)
elems = sum(elems, [])
coords = np.concatenate(coords, axis=0)
relaxations = np.concatenate(relaxations, axis=0)
magnetizations = np.concatenate(magnetizations, axis=0)
return Structure(
lattice=lat,
species=elems,
coords=coords,
site_properties={
"seldyn": relaxations,
"magnetization": magnetizations
},
)