def atoms(self, constrained=True, parameters=DEFAULT):
if parameters is DEFAULT:
parameters = self.parameters()
parameters = self.defaultParameters(parameters)
vectors = np.array(parameters['vectors'])
lengths = vectorLength(vectors, 1)
assert lengths.all()
atoms = self.__atoms.copy()
pos = atoms.get_positions()
size = np.array([pos[:, i].max() - pos[:,i].min() for i in range(3)])
size = size + parameters['length_scales']['correlation_length']
repeats = (1, 1, vectors[0][0])
vectors = atoms.cell[2] * vectors[0][0]
atoms = atoms.repeat(repeats)
atoms.set_cell(size)
atoms.cell[2] = vectors
atoms = removeCopies(atoms)
atoms = orderAtoms(atoms)
atoms = self.makeAtomsRelaxed(atoms, self.relaxation())
return atoms
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 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 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
def atoms(self, constrained=True, parameters=DEFAULT):
parameters = self.defaultParameters(parameters)
vectors = np.array(parameters['vectors'])
lengths = vectorLength(vectors, 1)
assert lengths.all()
atoms = self.__atoms.copy()
vectors = convertFromBasis(vectors, atoms.cell)
repeats = findNeededRepetitions(atoms.cell, 1.5*lengths.max())
atoms = atoms.repeat(repeats)
atoms.cell[atoms.pbc] = vectors
atoms.wrap()
atoms = removeCopies(atoms)
atoms.setTag('Reference', picker=None)
padding = np.logical_not(atoms.pbc)
assert padding.sum() == 0
atoms = self.makeAtomsRelaxed(atoms, self.relaxation())
return atoms
