def setUpBasisChanger(self):
crystal = self.crystal()
minimal_unit_cell = self.__minimal_unit_cell
extra_atoms = self.__extra_atoms
shift_origin = self.__shift_origin
surface_cell = self.__surface_cell
cell = np.zeros((3, 3), dtype=float)
cell[:2, :2] = surface_cell
cell[2, 2] = 1
surface_in_minimal = cell
cell = convertFromBasis(cell, self.__minimal_unit_cell)
cell = convertToIntegers(cell)
cell = convertFromBasis(cell, crystal.unitCell())
orth_surface_basis = findOrthogonalBasisSet(cell)
if len(extra_atoms) == 0:
top = 0
else:
top = np.max(extra_atoms.get_positions()[:, 2])
shift = list(shift_origin) + [top]
transformations = [
Transformation(to='minimal_unit_cell', fro='surface', trans_matrix=surface_in_minimal.transpose()),
Transformation(to='orth_crystal', fro='crystal', trans_matrix=crystal.unitCell().transpose()),
Transformation(to='crystal', fro='minimal_unit_cell', trans_matrix=minimal_unit_cell.transpose()),
Transformation(to='from_top', fro='orth_surface', rotation_point=[[0,0,0], shift]),
Transformation(to='orth_crystal',
fro='orth_surface',
trans_matrix=orth_surface_basis.transpose()),
]
basis_changer = BasisChanger(transformations=transformations)
return basis_changer
def groupAtoms(atoms, order=(2,), tolerance=1e-2):
atoms = atoms.copy()
del atoms.constraints
pbc = atoms.get_pbc()
atoms.set_pbc([True]*3)
cell = atoms.get_cell()
positions, remainder = convertToBasis(atoms.get_positions(), cell)
atoms.set_positions(positions)
tolerance1 = convertToBasis(np.array([1,1,1])*tolerance, cell)[0][0]
tolerance2 = convertToBasis(np.array([-1,1,-1])*tolerance, cell)[0][0]
tolerance1 = map(abs, tolerance1)
tolerance2 = map(abs, tolerance2)
tolerance = np.max((tolerance1, tolerance2), 0)
indices = np.arange(len(atoms))
groups = [(atoms, indices)]
for i in order:
new_groups = []
for atoms, indices in groups:
while len(atoms) > 0:
positions = atoms.get_positions()
min_value = np.min(positions[:, i])
group_mask = abs(positions[:, i] - min_value) < tolerance[i]
atom_group = atoms[group_mask]
indices_group = indices[group_mask]
atoms = atoms[np.logical_not(group_mask)]
indices = indices[np.logical_not(group_mask)]
new_groups.append((atom_group, indices_group))
groups = new_groups
for atoms, indices in groups:
positions = convertFromBasis(atoms.get_positions(), cell)
atoms.set_positions(positions)
atoms.set_cell(cell)
return groups
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
