def _set_grid_matrix_by_std_primitive_cell(self, cell, length):
"""Grid generating matrix based on standeardized primitive cell."""
tmat = self._sym_dataset["transformation_matrix"]
centring = self._sym_dataset["international"][0]
pmat = get_primitive_matrix_by_centring(centring)
conv_lat = np.dot(np.linalg.inv(tmat).T, cell.cell)
num_cells = np.prod(length2mesh(length, conv_lat))
self._mesh_numbers = estimate_supercell_matrix(
self._sym_dataset,
max_num_atoms=num_cells * len(self._sym_dataset["std_types"]),
)
inv_pmat = np.linalg.inv(pmat)
inv_pmat_int = np.rint(inv_pmat).astype(int)
assert (np.abs(inv_pmat - inv_pmat_int) < 1e-5).all()
# transpose in reciprocal space
self._grid_matrix = np.array((inv_pmat_int * self._mesh_numbers).T,
dtype="int_",
order="C")
# From input lattice to the primitive lattice in real space
self._transformation_matrix = np.array(np.dot(np.linalg.inv(tmat),
pmat),
dtype="double",
order="C")
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 = pmat
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