def crystalAtoms(self,
start_layer=0,
end_layer=1,
coordinates='orth_surface',
sub_layers=False,
minimal=True,
):
atoms = self.crystal().atoms()
if sub_layers:
in_equal_layers = self.inequivalentLayers()
repeats = int(np.ceil(end_layer/float(in_equal_layers)))
atoms = atoms.repeat((1, 1, repeats + 1))
atoms.positions -= self.crystal().unitCell()*(repeats)
start_layer += in_equal_layers -1
end_layer += in_equal_layers -1
atoms = orderAtoms(atoms, (2, 1, 0))
sl = slice(start_layer, end_layer)
groups = groupAtoms(atoms)[::-1][sl]
if len(groups) == 0:
atoms = Atoms([], cell=atoms.get_cell(), pbc=atoms.get_pbc())
else:
atoms, indices = groups[0]
for group, indices in groups[1:]:
atoms += group
else:
cell = atoms.unitCell()
atoms = atoms.repeat((1, 1, end_layer-start_layer))
atoms.positions += cell*start_layer
return atoms
