Found during a Codex global scan of deepmodeling/deepmd-kit at commit 73de44b1f94471b2e3bdb6b11f57b34d7bc791bb.

Problem

Several dpmodel statistics and LMDB reader paths treat negative/virtual atom types as real type indices.

Evidence:

• collect_observed_types() records all unique atom-type values and only filters the upper bound, so -1 passes and becomes type_map[-1]:

  deepmd-kit/deepmd/dpmodel/utils/stat.py

  Lines 52 to 59 in 73de44b

  	observed_indices: set[int] = set()
  	for system in sampled:
  	atype = to_numpy_array(system["atype"]) # shape: [nframes, natoms]
  	observed_indices.update(np.unique(atype).tolist())
  	observed_types = [
  	type_map[i] for i in sorted(observed_indices) if i < len(type_map)
  	]
  	return sort_element_type(observed_types)

• LmdbDataReader._compute_natoms_vec() calls np.bincount(atype, ...), which raises when atype contains negative virtual atoms:

  deepmd-kit/deepmd/dpmodel/utils/lmdb_data.py

  Lines 466 to 477 in 73de44b

  	def _compute_natoms_vec(self, atype: np.ndarray) -> np.ndarray:
  	"""Compute natoms_vec from a frame's atype array.
  	Returns [nloc, nloc, count_type0, count_type1, ...] with length ntypes+2.
  	"""
  	nloc = len(atype)
  	counts = np.bincount(atype, minlength=self._ntypes)[: self._ntypes]
  	vec = np.empty(self._ntypes + 2, dtype=np.int64)
  	vec[0] = nloc
  	vec[1] = nloc
  	vec[2:] = counts
  	return vec

• When an LMDB type map is remapped, the reader indexes self._type_remap[frame["atype"]]; atype == -1 is remapped to the last real model type:

  deepmd-kit/deepmd/dpmodel/utils/lmdb_data.py

  Lines 578 to 582 in 73de44b

  	if "atype" in frame and isinstance(frame["atype"], np.ndarray):
  	frame["atype"] = frame["atype"].reshape(-1).astype(np.int64)
  	# Remap atom types from LMDB's type_map to model's type_map
  	if self._type_remap is not None:
  	frame["atype"] = self._type_remap[frame["atype"]].astype(np.int64)

Simple external checks confirm both symptoms: np.bincount(np.array([0, -1])) raises ValueError, while remap[np.array([0, -1, 1])] maps -1 through the last row.

Impact

Datasets containing virtual atoms can crash LMDB reading, report fake observed elements, or silently convert virtual atoms into a real species after type-map remapping.

Suggested Fix

Filter atom types with 0 <= atype < ntypes for statistics and counts, and preserve negative atom types during LMDB type remapping. Add tests with atype=[0, -1, 1] for observed-type collection, natoms-vector computation, and LMDB remapping.