class Crystal1D(Crystal):
def __init__(
self,
atoms,
parameters=DEFAULT,
):
assert all(atoms.pbc == np.array([False, False, True]))
self.__atoms = Atoms(atoms)
API.System.__init__(
self,
sub_systems=tuple(),
parameters=parameters,
)
def setUpBasisChanger(self):
atoms = self.atoms()
cell = atoms.cell
basis_changer = BasisChanger(
transformations=[Transformation(to='orth_crystal', fro='crystal', trans_matrix=cell.transpose())]
)
return basis_changer
def pbc(self):
return [False, False, True]
def defaultParameters(self, parameters=DEFAULT):
if parameters is DEFAULT:
parameters = CrystalParameters1D()
vectors = parameters['vectors']
if parameters['vectors'] is DEFAULT:
vectors = ((1,),)
kpts = parameters['kpts']
if kpts is DEFAULT:
kpts = parameters.neededKpts(self.__atoms.cell[self.__atoms.pbc])
parameters = parameters.copy(kpts=kpts, vectors=vectors)
return parameters
def inputAtoms(self):
return self.__atoms.copy()
def relaxationFactor(self):
if self.relaxation() is None:
return 1.0
lr = vectorLength(self.relaxation().get_cell()[2])
lu = vectorLength(self.__atoms.get_cell()[2])
return lr/lu
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 makeAtomsRelaxed(self, atoms, relaxation, tolerance=1):
factor = self.relaxationFactor()
atoms.positions *= factor
atoms.cell[2] *= factor
atoms = makeAtomsRelaxed(atoms, self.relaxation(), tolerance=tolerance)
return atoms
def unitCell(self, coordinates='orth_crystal'):
if self.isRelaxed():
unit_cell = self.relaxation().get_cell()
else:
unit_cell = self.__atoms.get_cell()
unit_cell = unit_cell[np.array(self.pbc())]
return self.change(unit_cell, to=coordinates, fro='orth_crystal')
