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
def crystalAtoms(self,
start_layer=0,
end_layer=1,
coordinates='orth_surface',
vectors=((1,0),(0,1)),
sub_layers=False,
minimal=True,
):
sl = slice(start_layer, end_layer)
if minimal:
unit_cell = self.minimalCell('crystal')
else:
unit_cell = self.cell('crystal')
catoms = self.crystal().atoms()
catoms.purgeTags()
atoms = makeSlabWithVectors(catoms, unit_cell, sl.stop)
atoms = self.change(atoms, to=coordinates, fro='orth_crystal')
unit_cell = self.crystal().change(unit_cell, to='orth_crystal', fro='crystal',
difference=True,)[:2]
unit_cell = self.change(unit_cell, to='orth_surface', fro='orth_crystal')
if len(atoms)==0:
return atoms
if minimal:
vectors = unit_cell
else:
vectors = np.array(vectors)
vectors = np.dot(unit_cell.transpose(), vectors.transpose()).transpose()
repeats = fitBoxIntoBox(unit_cell, vectors)
atoms = atoms.repeat(list(repeats) + [1])
out_vector = atoms.cell[2]
out_vector[:2] = 0
vectors = np.array([vectors[0], vectors[1], out_vector])
atoms.set_cell(vectors)
atoms.set_pbc([True, True, False])
atoms = removeCopies(atoms)
atoms.wrap()
atoms = orderAtoms(atoms, (2, 1, 0))
if sub_layers:
groups = groupAtoms(atoms)[sl]
if len(groups) == 0:
return Atoms([], cell=atoms.get_cell(), pbc=atoms.get_pbc())
atoms, indices = groups[0]
for atoms_group, indices in groups[1:]:
atoms += atoms_group
return atoms
def __init__(self,
crystal,
direction=1,
extra_atoms=Atoms([]),
parameters=DEFAULT,
):
self.__direction = int(np.sign(direction))
self.__extra_atoms = extra_atoms
atoms = crystal.atoms()
groups = groupAtoms(atoms)
self.__inequivalent_layers = len(groups)
Surface.__init__(
self,
sub_systems=[crystal],
parameters=parameters,
)
def inequivalentLayers(self):
atoms = self.crystalAtoms()
groups = groupAtoms(atoms)
return len(groups)