fix(dpmodel): preserve virtual atom types in data utilities

[njzjz-bot]

Fixes #5633

Summary

• ignore negative virtual atom sentinels when collecting observed species
• count only configured real types in LMDB natoms vectors while retaining every coordinate slot in nloc
• share one atom-type remapping helper between training and test readers so negative sentinels survive type-map changes
• retain explicit NumPy bounds errors for malformed positive atom types

Why existing tests missed this

The observed-type tests covered valid types and a positive out-of-range index, but never a negative value. That omitted Python negative-index semantics, where type_map[-1] silently aliases the final real species.

The LMDB fixtures generated only type 0 and type 1 atoms. Existing reversed and superset type-map tests therefore exercised remapping without a virtual sentinel, and natoms-vector tests never passed a negative value to np.bincount. The dpmodel/PyTorch consistency coverage also uses the same LMDB reader on both sides, so it could only confirm a shared result rather than expose this shared bug. Existing virtual-atom model tests construct virtual atoms in memory instead of serializing them through these LMDB/stat utility paths.

Validation

• source/tests/common/dpmodel/test_observed_type.py
• source/tests/common/dpmodel/test_lmdb_data.py
• 79 tests passed
• ruff format .
• ruff check .

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh

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Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: fa4734a6-e90c-4e79-8aeb-1a4c59e35b0d

📥 Commits

Reviewing files that changed from the base of the PR and between 6c3b985 and b4d47b8.

📒 Files selected for processing (4)

• deepmd/dpmodel/utils/lmdb_data.py
• deepmd/dpmodel/utils/stat.py
• source/tests/common/dpmodel/test_lmdb_data.py
• source/tests/common/dpmodel/test_observed_type.py

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[njzjz]

Possible reviewers based on changed lines, exact file history, and exact-file review history:

• @wanghan-iapcm — 4 commits on changed files; 4 reviews on exact changed files (deepmd/dpmodel/utils/lmdb_data.py, deepmd/dpmodel/utils/stat.py, source/tests/common/dpmodel/test_lmdb_data.py).
• @iProzd — 6 commits on changed files (deepmd/dpmodel/utils/lmdb_data.py, deepmd/dpmodel/utils/stat.py, source/tests/common/dpmodel/test_lmdb_data.py, source/tests/common/dpmodel/test_observed_type.py).

No review request was made automatically.

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh