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 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
