def from_dict(cls, d, lattice=None):
"""
Create PeriodicSite from dict representation.
Args:
d (dict): dict representation of PeriodicSite
lattice: Optional lattice to override lattice specified in d.
Useful for ensuring all sites in a structure share the same
lattice.
Returns:
PeriodicSite
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
lattice = lattice if lattice else Lattice.from_dict(d["lattice"])
return cls(atoms_n_occu, d["abc"], lattice, properties=props)
def from_dict(cls, d, lattice=None):
"""
Create PeriodicSite from dict representation.
Args:
d (dict): dict representation of PeriodicSite
lattice: Optional lattice to override lattice specified in d.
Useful for ensuring all sites in a structure share the same
lattice.
Returns:
PeriodicSite
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
lattice = lattice if lattice else Lattice.from_dict(d["lattice"])
return cls(atoms_n_occu, d["abc"], lattice, properties=props)
def from_dict(cls, d, lattice=None):
"""
Create PeriodicSite from dict representation.
Args:
d (dict): dict representation of PeriodicSite
lattice: Optional lattice to override lattice specified in d.
Useful for ensuring all sites in a structure share the same
lattice.
Returns:
PeriodicSite
"""
species = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
species[sp] = sp_occu["occu"]
props = d.get("properties", None)
if props is not None:
for key in props.keys():
props[key] = json.loads(json.dumps(props[key], cls=MontyEncoder), cls=MontyDecoder)
lattice = lattice if lattice else Lattice.from_dict(d["lattice"])
return cls(species, d["abc"], lattice, properties=props)
def from_dict(d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
sp = Specie.from_dict(sp_occu) if "oxidation_state" in sp_occu \
else Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
return Site(atoms_n_occu, d["xyz"], properties=props)
def from_dict(cls, d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
sp = Specie.from_dict(sp_occu) if "oxidation_state" in sp_occu \
else Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
return cls(atoms_n_occu, d["xyz"], properties=props)
def from_dict(cls, d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
return cls(atoms_n_occu, d["xyz"], properties=props)
def from_dict(cls, d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
return cls(atoms_n_occu, d["xyz"], properties=props)
def from_dict(d, lattice=None):
"""
Create PeriodicSite from dict representation.
Args:
d:
dict representation of PeriodicSite
lattice:
Optional lattice to override lattice specified in d. Useful for
ensuring all sites in a structure share the same lattice.
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
sp = Specie.from_dict(sp_occu) if "oxidation_state" in sp_occu \
else Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
lattice = lattice if lattice else Lattice.from_dict(d["lattice"])
return PeriodicSite(atoms_n_occu, d["abc"], lattice, properties=props)
def from_dict(cls, d: dict):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
sp_occu["element"]):
sp = Specie.from_dict(sp_occu)
elif "oxidation_state" in sp_occu:
sp = DummySpecie.from_dict(sp_occu)
else:
sp = Element(sp_occu["element"])
atoms_n_occu[sp] = sp_occu["occu"]
props = d.get("properties", None)
if props is not None:
for key in props.keys():
props[key] = json.loads(json.dumps(props[key], cls=MontyEncoder), cls=MontyDecoder)
return cls(atoms_n_occu, d["xyz"], properties=props)
def _species_from_bondstr(self, bondstr):
"""
Create a 2-tuple of species objects from a bond string.
Args:
bondstr (str): A string representing a bond between elements or
species, or a combination of the two. For example, "Cl- - Cs+".
Returns:
((Species)): A tuple of pymatgen Species objects in alphabetical
order.
"""
species = []
for ss in bondstr.split(self.token):
try:
species.append(Specie.from_string(ss))
except ValueError:
d = {'element': ss, 'oxidation_state': 0}
species.append(Specie.from_dict(d))
return tuple(species)
def from_dict(cls, d):
return SubStructureSpecie.from_specie(Specie.from_dict(d['specie']), d.get('weight', 0.0))
def from_dict(cls, d):
return SubStructureSite.from_coords_and_specie(d['coords'],
Specie.from_dict(d['specie']), d.get('weight', 0.0))