[Code scan] Align CALYPSO optional schema with required input generation

[njzjz]

Found by Codex global repository scan of deepmodeling/dpgen2 at commit 2679611a3704f5c2646c8cb353e34177518db758.

The CALYPSO task-group schema marks atomic_number and distance_of_ions as optional:

dpgen2/dpgen2/exploration/task/make_task_group_from_config.py

Lines 348 to 373 in 2679611

	def caly_task_grp_args():
	return [
	Argument("numb_of_species", int, optional=False, doc="number of species."),
	Argument(
	"name_of_atoms",
	list,
	optional=False,
	doc="name of atoms.",
	),
	Argument(
	"atomic_number",
	list,
	optional=True,
	doc="atomic number of each element.",
	),
	Argument(
	"numb_of_atoms",
	list,
	optional=False,
	doc="number of each atom.",
	),
	Argument(
	"distance_of_ions",
	[list, dict],
	optional=True,
	doc="the distance matrix between different elements.",

CalyTaskGroup.set_params only infers atomic_number for the nested random-choice form; otherwise it can leave self.atomic_number = None and self.distance_of_ions = None:

dpgen2/dpgen2/exploration/task/caly_task_group.py

Lines 144 to 164 in 2679611

	self.atomic_number = [atomic_symbols.index(i) for i in self.name_of_atoms]
	else:
	self.name_of_atoms = name_of_atoms
	self.atomic_number = atomic_number
	if isinstance(distance_of_ions, dict):
	updated_table = copy.deepcopy(covalent_radii)
	for key, value in distance_of_ions.items():
	updated_table[atomic_number_map[key]] = value
	temp_distance_mtx = np.zeros((numb_of_species, numb_of_species))
	for i in range(numb_of_species):
	for j in range(numb_of_species):
	temp_distance_mtx[i][j] = round(
	updated_table[atomic_number_map[self.name_of_atoms[i]]] * 0.7
	+ updated_table[atomic_number_map[self.name_of_atoms[j]]] * 0.7,
	2,
	)
	self.distance_of_ions = temp_distance_mtx
	else:
	self.distance_of_ions = distance_of_ions

make_calypso_input later treats both values as required, calling len(atomic_number) and asserting that distance_of_ions has a square matrix shape:

dpgen2/dpgen2/exploration/task/calypso/caly_input.py

Lines 271 to 281 in 2679611

	distance_of_ions = np.array(distance_of_ions)
	assert (
	numb_of_species
	== len(name_of_atoms)
	== len(atomic_number)
	== len(numb_of_atoms)
	), f"{numb_of_species:}, {name_of_atoms:} {atomic_number:} {numb_of_atoms:}"
	assert distance_of_ions.shape == (
	numb_of_species,
	numb_of_species,
	), f"{distance_of_ions.shape} {numb_of_species:}"

A normalized config that omits these optional fields can crash late during task generation instead of receiving defaults or a clear validation error.

Suggested fix: either make these fields required in the schema, infer them for all supported name_of_atoms forms, or fail validation with an actionable message before make_calypso_input is called.