def check_symmetry(phonon, optional_structure_info):
# Assumed that primitive cell is the cell that user is interested in.
print(_get_symmetry_yaml(phonon.primitive,
phonon.primitive_symmetry,
phonon.version))
if phonon.unitcell.magnetic_moments is None:
base_fname = get_default_cell_filename(phonon.calculator)
symprec = phonon.primitive_symmetry.get_symmetry_tolerance()
(bravais_lattice,
bravais_pos,
bravais_numbers) = spglib.refine_cell(phonon.primitive, symprec)
bravais = PhonopyAtoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice)
filename = 'B' + base_fname
print("# Symmetrized conventional unit cell is written into %s."
% filename)
trans_mat = guess_primitive_matrix(bravais, symprec=symprec)
primitive = get_primitive(bravais, trans_mat, symprec=symprec)
write_crystal_structure(
filename,
bravais,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
filename = 'P' + base_fname
print("# Symmetrized primitive is written into %s." % filename)
write_crystal_structure(
filename,
primitive,
interface_mode=phonon.calculator,
optional_structure_info=optional_structure_info)
def _get_primitive_matrix(pmat, unitcell, symprec):
if type(pmat) is str and pmat in ('F', 'I', 'A', 'C', 'R', 'auto'):
if pmat == 'auto':
_pmat = guess_primitive_matrix(unitcell, symprec=symprec)
else:
_pmat = get_primitive_matrix_by_centring(pmat)
elif pmat is None:
_pmat = None
elif len(np.ravel(pmat)) == 9:
matrix = np.reshape(pmat, (3, 3))
if matrix.dtype.kind in ('i', 'u', 'f'):
det = np.linalg.det(matrix)
if symprec < det and det < 1 + symprec:
_pmat = matrix
else:
msg = ("Determinant of primitive_matrix has to be larger "
"than 0")
raise RuntimeError(msg)
else:
msg = ("primitive_matrix has to be a 3x3 matrix, None, 'auto', "
"'F', 'I', 'A', 'C', or 'R'")
raise RuntimeError(msg)
return _pmat
def _guess_primitive_matrix(self):
return guess_primitive_matrix(self._unitcell_ideal, symprec=self._symprec)