def analyse_phonopy_equivalent_atoms(atoms,
symprec=1e-5,
angle_tolerance=-1.0):
"""
Args: (read phonopy.structure.spglib for more details)
symprec:
float: Symmetry search tolerance in the unit of length.
angle_tolerance:
float: Symmetry search tolerance in the unit of angle deg.
If the value is negative, an internally optimized routine
is used to judge symmetry.
"""
s.publication_add(publication())
positions = atoms.get_scaled_positions()
cell = atoms.cell
types = atoms.get_chemical_symbols()
types = list(types)
natom = len(types)
positions = np.reshape(np.array(positions), (natom, 3))
cell = np.reshape(np.array(cell), (3, 3))
unitcell = PhonopyAtoms(symbols=types,
cell=cell,
scaled_positions=positions)
ops = spg.get_symmetry(unitcell,
symprec=symprec,
angle_tolerance=angle_tolerance)
return ops['equivalent_atoms']
def _set_symmetry_operations_with_magmoms(self):
cell = (self._cell.get_cell(), self._cell.get_scaled_positions(),
self._cell.get_atomic_numbers(),
self._cell.get_magnetic_moments())
self._symmetry_operations = spg.get_symmetry(
cell, symprec=self._symprec)
self._map_atoms = self._symmetry_operations['equivalent_atoms']
self._set_map_atoms()
def _set_symmetry_operations_with_magmoms(self):
cell = (self._cell.get_cell(), self._cell.get_scaled_positions(),
self._cell.get_atomic_numbers(),
self._cell.get_magnetic_moments())
self._symmetry_operations = spg.get_symmetry(cell,
symprec=self._symprec)
self._map_atoms = self._symmetry_operations['equivalent_atoms']
self._set_map_atoms()
def _set_symmetry_operations_with_magmoms(self):
(self._symmetry_operations,
self._map_atoms) = spg.get_symmetry(self._cell,
use_magmoms=True,
symprec=self._symprec)
self._set_map_atoms()
def _set_symmetry_operations(self):
self._symmetry_operations = spg.get_symmetry(self._cell,
use_magmoms=True,
symprec=self._symprec)
self._set_map_atoms()
def _set_symmetry_operations_with_magmoms(self):
self._symmetry_operations = spg.get_symmetry(self._cell.totuple(),
symprec=self._symprec)
self._map_atoms = self._symmetry_operations['equivalent_atoms']
self._set_map_atoms()
def _symmetry_operations(self):
self.symmetry_operations = \
spg.get_symmetry(self.__cell, self.symprec)
self._map_atoms()
def _set_symmetry_operations_with_magmoms(self):
self._symmetry_operations = spg.get_symmetry(self._cell.totuple(),
symprec=self._symprec)
self._map_atoms = self._symmetry_operations['equivalent_atoms']
self._set_map_atoms()
def _symmetry_operations(self):
self.symmetry_operations = \
spg.get_symmetry(self.__cell, self.symprec)
self._map_atoms()