def __init__(
self,
symbol,
name=DEFAULT,
identifiers=tuple(),
added_atoms=DEFAULT,
periodicity=tuple(tuple()),
charge=0,
initial_state=DEFAULT,
parameters=DEFAULT,
):
self.__name = name
surface = Diamond001(symbol)
if initial_state is DEFAULT:
initial_state = self.defaultInitialState()
Diamond001Defect.__init__(self, name)
SurfaceLineDefect.__init__(self,
surface,
name=name,
identifiers=identifiers,
added_atoms=added_atoms,
charge=charge,
periodicity=periodicity,
initial_state=initial_state,
parameters=parameters,
)
def __init__(self):
surface = Ge001()
identifiers=[(2, (0, 0)), (3, (0, 0)), ]
periodicity = [[0, 1]]
defect = SurfaceLineDefect(surface=surface, identifiers=identifiers, periodicity=periodicity)
pos1 = defect.removedAtoms().get_positions().mean(0) + np.array([3,0,1])
added_atoms = Atoms('Ag', [pos1])
SurfaceLineDefect.__init__(self, surface=Ge001(),
identifiers=identifiers,
added_atoms=added_atoms,
periodicity=periodicity,
)
def __init__(self):
surface = Ge001()
identifiers=[1, 2, 3, ]
periodicity = [[0, 1]]
defect = SurfaceLineDefect(surface=surface, identifiers=identifiers, periodicity=periodicity)
pos1 = defect.removedAtoms().get_positions()[0]
added_atoms = Atoms('Ag', [pos1])
SurfaceLineDefect.__init__(self, surface=Ge001(),
identifiers=identifiers,
added_atoms=added_atoms,
periodicity=periodicity,
)
def __init__(self):
surface = Ge001()
identifiers=[(3, (0, 0)), (2, (1, 0)), (3, (0, 1)), (2, (1, 1))]
periodicity = [[0, 2]]
defect = SurfaceLineDefect(surface=surface, identifiers=identifiers, periodicity=periodicity)
positions = defect.removedAtoms().get_positions()
added_atoms = Atoms('Ag3', [[-1.3,-1.6, 1.1], [-1.3, 1.6, 1.1],[1.3, 0, 1.1]])
SurfaceLineDefect.__init__(self, surface=Ge001(),
identifiers=identifiers,
added_atoms=added_atoms,
periodicity=periodicity,
)
def __init__(self):
surface = Ge001()
identifiers=[(2, (0, 0)), (3, (0, 0)), (-1, (0, 0))]
periodicity = [[0, 1]]
defect = SurfaceLineDefect(surface=surface, identifiers=identifiers, periodicity=periodicity)
pos = defect.removedAtoms().get_positions()[-1]
added_atoms = Atoms('Ag', [pos])
SurfaceLineDefect.__init__(self, surface=Ge001(),
identifiers=identifiers,
added_atoms=added_atoms,
periodicity=periodicity,
)
def __init__(self):
surface = Ge001()
identifiers=[(3, (0, 0)), (2, (1, 0)), (3, (0, 1)), (2, (1, 1))]
periodicity = [[0, 2]]
defect = SurfaceLineDefect(surface=surface, identifiers=identifiers, periodicity=periodicity)
pos = defect.removedAtoms('orth_defect').positions.mean(0)
vector = defect.cell()[0]
pos = np.array([pos + vector*(i/3.0) for i in range(3)])
added_atoms = Atoms('Ag3', pos)
SurfaceLineDefect.__init__(self, surface=Ge001(),
identifiers=identifiers,
added_atoms=added_atoms,
periodicity=periodicity,
)
def name(self):
if self.__name is DEFAULT:
name = self.symbol()
name += SurfaceLineDefect.name(self)
init = self.initialState()
if init != self.defaultInitialState():
name = join(name, init.name())
else:
name = self.__name
return name
