def removedAtoms(extra_atoms, crystal_atoms, identifiers, surface_unit_cell, periodicity):
atoms = Atoms([], cell=extra_atoms.get_cell(), pbc=extra_atoms.get_pbc())
for identifier in identifiers:
number, cell = identifier
if number >= 0:
atom = extra_atoms.copy()[number]
depth = 0
elif number < 0:
number = -(number + 1)
depth, crystal_number = divmod(number, len(crystal_atoms))
atom=crystal_atoms.copy()[crystal_number]
else:
raise Exception
shift = -surface_unit_cell[2]*depth
cell = (cell[0], cell[1], 0)
shift += np.dot(cell, surface_unit_cell)
atom.position += shift
atoms += atom
setCellAndPBC(atoms, periodicity)
return atoms
def addedAtoms(self, coordinates='orth_defect'):
extra_atoms = self.surface().extraAtoms('orth_surface')
unit_cell = self.surface().unitCell('orth_surface')
periodicity = self.periodicity()
atoms = Atoms([], cell=extra_atoms.get_cell(), pbc=extra_atoms.get_pbc())
atoms += self.__added_atoms.copy()
setCellAndPBC(atoms, periodicity)
atoms = self.change(atoms, to=coordinates, fro='orth_surface')
return atoms
