def __init__(self,
symbol="X",
position=(0, 0, 0),
tag=None,
momentum=None,
mass=None,
magmom=None,
charge=None,
atoms=None,
index=None,
pse=None,
element=None,
**qwargs):
if element is None:
element = symbol
SparseArrayElement.__init__(self, **qwargs)
# super(SparseArrayElement, self).__init__(**qwargs)
# verify that element is given (as string, ChemicalElement object or nucleus number
if pse is None:
pse = PeriodicTable()
if element is None or element == "X":
if "Z" in qwargs:
el_symbol = pse.atomic_number_to_abbreviation(qwargs["Z"])
self._lists["element"] = pse.element(el_symbol)
else:
if isinstance(element, string_types):
el_symbol = element
self._lists["element"] = pse.element(el_symbol)
elif isinstance(element, str):
el_symbol = element
self._lists["element"] = pse.element(el_symbol)
elif isinstance(element, ChemicalElement):
self._lists["element"] = element
else:
raise ValueError("Unknown element type")
# KeyError handling required for user defined elements
try:
ASEAtom.__init__(self,
symbol=symbol,
position=position,
tag=tag,
momentum=momentum,
mass=mass,
magmom=magmom,
charge=charge,
atoms=atoms,
index=index)
except KeyError:
symbol = pse.Parent[symbol]
ASEAtom.__init__(self,
symbol=symbol,
position=position,
tag=tag,
momentum=momentum,
mass=mass,
magmom=magmom,
charge=charge,
atoms=atoms,
index=index)
# ASE compatibility for tags
for key, val in qwargs.items():
self.data[key] = val
def __init__(self, position, charge):
Atom.__init__(self, position=position, charge=charge)
def __init__(self, position, charge):
Atom.__init__(self, position=position, charge=charge)
