def spglib_dataset(s, symprec=1e-5):
s = structure(s)
fracs = s.frac_coords
lattice = s.lattice.matrix
types = [x.number for x in s.species]
ds = spglib.get_symmetry_dataset((lattice, fracs, types), symprec)
if not ds:
error = spglib.get_error_message()
if error == "no error":
error += ". (or so spglib claims...)"
raise SpglibError(spglib.get_error_message())
return ds
def throw(cls):
error = spglib.get_error_message()
if error == "no error": # right...
error = "an unspecified Bad Thing happened while calling spglib"
raise cls(error)
def symmetry(self, symprec=1e-2, angle_tolerance=-1.0):
"""
Returns a dictionary containing space-group information. This information
is computed from the crystal unit cell.
Parameters
----------
symprec : float, optional
Symmetry-search distance tolerance in Cartesian coordinates [Angstroms].
angle_tolerance: float, optional
Symmetry-search tolerance in degrees. If the value is negative (default),
an internally optimized routine is used to judge symmetry.
Returns
-------
info : dict
Dictionary of space-group information. The following keys are available:
* ``'international_symbol'``: International Tables of Crystallography
space-group symbol (short);
* ``'international_full'``: International Tables of
Crystallography space-group full symbol;
* ``'hall_symbol'`` : Hall symbol;
* ``'hm_symbol'`` : Hermann-Mauguin symbol;
*``'centering'``: Centering-type ("P", "F", etc.);
* ``'pointgroup'`` : International Tables of
Crystallography point-group;
* ``'international_number'`` : International Tables of
Crystallography space-group number (between 1 and 230);
* ``'hall_number'`` : Hall number (between 1 and 531).
Raises
------
RuntimeError : if symmetry-determination has not succeeded.
Notes
-----
Note that crystals generated from the Protein Data Bank are often incomplete;
in such cases the space-group information will be incorrect.
"""
dataset = get_symmetry_dataset(cell=self._spglib_cell(),
symprec=symprec,
angle_tolerance=angle_tolerance)
if dataset is None:
raise RuntimeError(
"[SPGLIB] Symmetry-determination has not found a match.")
spg_type = get_spacegroup_type(dataset["hall_number"])
hm_symbol = Hall2HM[dataset["hall"]]
# We do not distinguish between base-centered "A", "B", and "C"
# "A" and "B" are translated to "C"
centering = CenteringType(hm_symbol[0] if hm_symbol[0] not in
{"A", "B"} else "C")
info = {
"international_symbol": dataset["international"],
"hall_symbol": dataset["hall"],
"hm_symbol": hm_symbol,
"centering": centering,
"international_number": dataset["number"],
"hall_number": dataset["hall_number"],
"international_full": spg_type["international_full"],
"pointgroup": spg_type["pointgroup_international"],
}
err_msg = get_error_message()
if err_msg != "no error":
raise RuntimeError(
"[SPGLIB] Symmetry-determination has returned the following error: {err_msg}"
)
return info
def spacegroup_info(self, symprec = 1e-2, angle_tolerance = -1.0):
"""
Returns a dictionary containing space-group information. This information
is computed from the crystal unit cell, and is not taken from records if available.
Parameters
----------
symprec : float, optional
Symmetry-search distance tolerance in Cartesian coordinates [Angstroms].
angle_tolerance: float, optional
Symmetry-search tolerance in degrees. If the value is negative (default),
an internally optimized routine is used to judge symmetry.
Returns
-------
info : dict or None
Dictionary of space-group information. The following keys are available:
* ``'international_symbol'``: International Tables of Crystallography space-group symbol (short);
* ``'international_full'``: International Tables of Crystallography space-group full symbol;
* ``'hall_symbol'`` : Hall symbol;
* ``'pointgroup'`` : International Tables of Crystallography point-group;
* ``'international_number'`` : International Tables of Crystallography space-group number (between 1 and 230);
* ``'hall_number'`` : Hall number (between 1 and 531).
If symmetry-determination has failed, None is returned.
Raises
------
RuntimeError : If symmetry-determination has yielded an error.
Notes
-----
Note that crystals generated from the Protein Data Bank are often incomplete;
in such cases the space-group information will be incorrect.
"""
dataset = get_symmetry_dataset(cell = self._spglib_cell(),
symprec = symprec,
angle_tolerance = angle_tolerance)
if dataset:
spg_type = get_spacegroup_type(dataset['hall_number'])
info = {'international_symbol': dataset['international'],
'hall_symbol' : dataset['hall'],
'international_number': dataset['number'],
'hall_number' : dataset['hall_number'],
'international_full' : spg_type['international_full'],
'pointgroup' : spg_type['pointgroup_international']}
err_msg = get_error_message()
if (err_msg != 'no error'):
raise RuntimeError('Symmetry-determination has returned the following error: {}'.format(err_msg))
return info
return None