[Code scan] Complete CALYPSO safe-distance handling for common elements

[njzjz]

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

parse_traj filters selected CALYPSO frames with a hard-coded safe-distance table:

dpgen2/dpgen2/op/run_caly_model_devi.py

Lines 239 to 267 in 2679611

	safe_dist_dict = {
	"He": 0.0,
	"Li": 1.5,
	"Na": 1.45,
	"K": 2.3,
	"Rb": 2.5,
	"Mg": 1.7,
	"Ca": 2.3,
	"Sr": 2.5,
	"Al": 1.7,
	"Sc": 2.0,
	"Y": 2.1,
	"La": 2.5,
	"Ti": 2.0,
	"Zr": 2.1,
	"Hf": 2.4,
	"Mo": 2.1,
	"W": 2.3,
	"B": 1.1,
	"C": 1.1,
	"Si": 1.6,
	"P": 1.5,
	"As": 2.0,
	"S": 1.5,
	"Se": 2.1,
	"Te": 2.0,
	"Br": 2.3,
	"H": 0.813,
	}

The table is indexed directly for every atom pair:

dpgen2/dpgen2/op/run_caly_model_devi.py

Lines 299 to 314 in 2679611

	# 2nd filter for selected traj. It filters out all FRAMES that are to close.
	i_keep = []
	for t in selected_traj:
	t2 = make_supercell(t, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
	frame_is_reasonable = True
	dist_dict = t2.get_all_distances(mic=True)
	atype = t2.get_chemical_symbols()
	for a in range(len(atype)):
	for b in range(a + 1, len(atype)):
	dd = dist_dict[a][b]
	dr = (
	(safe_dist_dict[atype[a]] + safe_dist_dict[atype[b]])
	* 0.529
	/ 1.2
	)

Many common elements are missing, including O, N, F, Cl, Fe, Ni, and Cu. A trajectory containing any omitted element raises KeyError before model-deviation output is written.

Suggested fix: use a complete element table from a maintained source, fall back with a clear validation error, or reuse the covalent-radius data already present elsewhere in the package. Add a regression test with an element currently missing from the dictionary.