def _canonical_from_affine_matrix(self, affine: Array) -> Array:
if self.unit_cell is None:
return comparable(affine)
else:
return np.vstack((
comparable(affine[0:self.ndim, 0:self.ndim]),
comparable_periodic(affine[0:self.ndim, self.ndim]
@ np.linalg.inv(self.unit_cell)),
))
def _clean_site_offsets(site_offsets, atoms_coord, basis_vectors):
"""Check and convert `site_offsets` init argument."""
if atoms_coord is not None and site_offsets is not None:
raise ValueError(
"atoms_coord is deprecated and replaced by site_offsets, "
"so both cannot be specified at the same time.")
if atoms_coord is not None:
warnings.warn(
"atoms_coord is deprecated and may be removed in future versions, "
"please use site_offsets instead",
FutureWarning,
)
site_offsets = atoms_coord
if site_offsets is None:
site_offsets = _np.zeros(basis_vectors.shape[0])[None, :]
site_offsets = _np.asarray(site_offsets)
fractional_coords = site_offsets @ _np.linalg.inv(basis_vectors)
fractional_coords_int = comparable_periodic(fractional_coords)
# Check for duplicates (also across unit cells)
uniques, idx = _np.unique(fractional_coords_int,
axis=0,
return_index=True)
if len(site_offsets) != len(uniques):
site_offsets = site_offsets[idx]
fractional_coords = fractional_coords[idx]
fractional_coords_int = fractional_coords_int[idx]
warnings.warn(
"Some atom positions are not unique. Duplicates were dropped, and "
f"now atom positions are {site_offsets}",
UserWarning,
)
# Check if any site is outside primitive cell (may cause KDTree to malfunction)
if _np.any(fractional_coords_int < comparable(0.0)) or _np.any(
fractional_coords_int > comparable(1.0)):
warnings.warn(
"Some sites were specified outside the primitive unit cell. This may"
"cause errors in automatic edge finding.",
UserWarning,
)
return site_offsets, fractional_coords
def _to_integer_position(self, positions: PositionT) -> Array:
frac_positions = _np.matmul(positions, self._inv_dims)
return comparable_periodic(frac_positions, self.pbc)