def makeSlab(surface, pertubation_length, correlation_length):
vectors = surface.cell(coordinates='orth_crystal')
atoms = makeSample(surface.crystal(), vectors)
surface.change(atoms, to='orth_surface', fro='orth_crystal')
vectors = surface.cell(coordinates='orth_surface')
vectors, repeats = makeLargeEnoughQuiteOrthogonalBox(vectors, pertubation_length)
atoms = atoms.repeat(repeats)
# Make repetitions to satisfy correlation length.
n2 = int(numpy.ceil(correlation_length/vectors[2,2]))
atoms = atoms.repeat((1,1,n2))
# Wrap into box with atoms below zero in third direction.
wrap_vectors = numpy.array([vectors[0], vectors[1], -n2*vectors[2]])
atoms.set_cell(wrap_vectors)
atoms = wrap(atoms)
atoms.set_cell(vectors)
atoms.set_pbc([True, True, False])
# Crop number of layers.
take = atoms.get_positions()[:, 2] > - correlation_length + 1e-5
atoms = atoms[take]
extra_atoms = surface.extraAtoms('orth_surface')
repeats = fitBoxIntoBox(extra_atoms.get_cell()[:2], vectors[:2])
repeats = list(repeats)
repeats.append(1)
extra_atoms = extra_atoms.repeat(tuple(repeats))
extra_atoms.set_cell(vectors)
extra_atoms = wrap(extra_atoms)
extra_atoms = removeCopies(extra_atoms)
atoms += extra_atoms
# Passivate lower surface.
positions = atoms.get_positions()
z_min = min(positions[:,2])
lower_positions = positions[(positions[:,2] < z_min + 1e-5)]
h_positions = [position + [0,0,-0.8] for position in lower_positions]
passivation = Atoms('H%d'%len(h_positions), h_positions)
atoms += passivation
# Make vaccum in the out-of-surface direction.
z_pos = atoms.get_positions()[:, 2]
z_min, z_max = min(z_pos), max(z_pos)
z_diff = z_max - z_min
tot_diff = correlation_length + z_diff
atoms.cell[2] = numpy.array([0,0,tot_diff])
atoms = wrap(atoms)
# Put atoms in order.
atoms = orderAtoms(atoms)
# Fix lowest coordinates.
constraint = FixAtoms(mask=(atoms.get_positions()[:, 2] < -pertubation_length + 1e-5))
atoms.set_constraint(constraint)
return atoms
def makeSample(crystal, vectors):
radius = numpy.max(vectorLength(vectors))
repeats = findNeededRepetitions(crystal.unitCell(), radius)
atoms = crystal.toAseAtoms()
atoms = atoms.repeat(repeats)
atoms.set_cell(vectors)
atoms = wrap(atoms)
atoms = removeCopies(atoms)
return atoms
def makeSlabWithVector(surface, vector, radius):
v1 = numpy.zeros(3, dtype=numpy.int)
v1[:2] = vector
v1 = surface.change(v1, to='orth_surface', fro='surface')
unit_cell = surface.unitCell('orth_surface')
pro = [abs(numpy.dot(v, v1))/vectorLength(v) for v in unit_cell]
v2 = unit_cell[numpy.argmin(pro)]
l1 = vectorLength(v1)
pro = vectorLength(numpy.cross(v1/l1, v2))
n2 = int(numpy.ceil(radius/pro))
v2 *= n2
v3 = surface.outOfPlaneVector('orth_surface')
vectors = numpy.array([v1, v2, v3])
vectors = surface.change(vectors, to='crystal', fro='orth_surface')
layer_distance = surface.outOfPlaneVector('orth_surface')[2]
n_layers = int(numpy.ceil(radius/layer_distance))
atoms = makeSlabWithVectors(surface.crystal(), vectors, n_layers)
surface.change(atoms, to='orth_surface', fro='orth_crystal')
atoms.cell[2, :2] = 0
atoms.set_pbc([True, True, False])
atoms = wrap(atoms)
# Make vaccum in the out-of-surface direction.
z_pos = atoms.get_positions()[:, 2]
z_min, z_max = min(z_pos), max(z_pos)
z_diff = z_max - z_min
tot_diff = radius + z_diff
atoms.cell[2] = numpy.array([0,0,tot_diff])
atoms = wrap(atoms)
# Put atoms in order.
atoms = orderAtoms(atoms)
return atoms
def makeSlabWithVectors(atoms, vectors, n_layers):
unit_cell = atoms.get_cell()
vectors[2] *= -1
vectors = numpy.dot(unit_cell.transpose(), vectors.transpose()).transpose()
repeats = fitBoxIntoBox(unit_cell, vectors)
atoms = atoms.repeat(repeats)
atoms.set_cell(vectors)
atoms = wrap(atoms)
atoms = removeCopies(atoms)
atoms = atoms.repeat((1,1,n_layers))
return atoms
def makePeriodicSample(crystal, radius=5):
unit_cell=crystal.unitCell()
l_b=len(unit_cell)
atoms = crystal.toAseAtoms()
repeats = findNeededRepetitions(unit_cell, numpy.array([radius]*3))
sample = atoms.repeat(repeats)
vectors = makeQuiteOrthogonalVectors(unit_cell, repeats)
sample.set_cell(vectors)
sample = removeCopies(sample)
sample = wrap(sample)
return sample