[Code scan] Make find_neighbors handle mixed PrimitiveCell and SuperCell inputs

[njzjz]

This issue comes from a Codex global scan of deepmodeling/tbplas at commit 4d3652b.

Severity: Medium

The signature allows cell_bra and cell_ket to be either PrimitiveCell or SuperCell, but the implementation dispatches position access mostly from the type of cell_bra. Mixed calls such as primitive-to-supercell or supercell-to-primitive can therefore call attributes/methods that do not exist on cell_ket.

Code reference:

tbplas/tbplas/builder/advanced.py

Lines 402 to 451 in 4d3652b

	def find_neighbors(cell_bra: Union[PrimitiveCell, SuperCell],
	cell_ket: Union[PrimitiveCell, SuperCell] = None,
	a_max: int = 0,
	b_max: int = 0,
	c_max: int = 0,
	max_distance: float = 1.0) -> List[namedtuple]:
	"""
	Find neighbours between the (0, 0, 0) cell of model_bra and nearby cells of
	cell_ket up to given cutoff distance.
	NOTE: only neighbours with distance > 0 will be returned.
	The searching range of nearby cells is:
	[-a_max, a_max] * [-b_max, b_max] * [-c_max, c_max].
	The named tuples have four attributes: rn for cell index, pair for orbital
	indices, rij for Cartesian coordinates of displacement vector in nm and
	distance for the norm of rij.
	:param cell_bra: the 'bra' primitive cell or supercell
	:param cell_ket: the 'ket' primitive cell or supercell
	default to pc_ket if not set
	:param a_max: upper bound of range on a-axis
	:param b_max: upper bound of range on b-axis
	:param c_max: upper bound of range on c-axis
	:param max_distance: cutoff distance in NM
	:return: list of neighbors as named tuples
	:raise PCOrbEmptyError: if cell_bra or cell_ket does not contain orbitals
	"""
	if cell_ket is None:
	cell_ket = cell_bra
	# Check for number of orbitals
	if isinstance(cell_bra, PrimitiveCell):
	cell_bra.verify_orbitals()
	cell_ket.verify_orbitals()
	# Get orbital positions
	if isinstance(cell_bra, PrimitiveCell):
	pos_bra = cell_bra.orb_pos_nm
	pos_ket = cell_ket.orb_pos_nm
	else:
	pos_bra = cell_bra.get_orb_pos()
	pos_ket = cell_ket.get_orb_pos()
	# Get lattice vectors of cell_ket
	if isinstance(cell_ket, PrimitiveCell):
	lat_ket = cell_ket.lat_vec
	else:
	lat_ket = cell_ket.sc_lat_vec

Suggested fix: resolve orbital positions independently for cell_bra and cell_ket, or narrow the accepted API and validate unsupported mixed-type calls explicitly.