fix(dpmodel): reject incompatible LMDB merge type maps

[njzjz-bot]

Fixes #5634

Summary

• preflight every source LMDB type map before replacing or creating the destination
• preserve byte-for-byte merging for sources with identical explicit maps
• preserve legacy behavior when every source omits type-map metadata
• reject reordered maps and explicit/missing mixtures because raw atom-type indices cannot be proven compatible
• include every source path and map in validation errors

This chooses fail-fast validation instead of decoding and rewriting frames. A remapping implementation would also need to keep atom_types, atom_names, atom_numbs, and system_info mutually consistent; rejecting incompatible metadata is the smaller safe change.

Why existing tests missed this

The merge coverage used either two mapless legacy databases or sources with the same ["O", "H"] map. Its type-map test inspected only the merged metadata and never read frames from both source segments. Because every fixture generated the same numeric 0/1 type ordering, raw frame copying preserved all tested shapes, counts, and IDs even though a reversed source map would change their species meaning.

The regular LMDB remapping tests cover one database mapped to a model type map, not multiple source maps being collapsed into one merged metadata map. Reader/dataset consistency checks would also interpret the same corrupted merged metadata and therefore agree with each other.

Validation

• source/tests/pt/test_lmdb_dataloader.py: 53 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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Review details

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: 048e03d1-7ca5-46a8-a5d0-651c604fc343

📥 Commits

Reviewing files that changed from the base of the PR and between 6c3b985 and 3e38522.

📒 Files selected for processing (2)

• deepmd/dpmodel/utils/lmdb_data.py
• source/tests/pt/test_lmdb_dataloader.py

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[codecov]

Codecov Report

❌ Patch coverage is 95.83333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 76.59%. Comparing base (6c3b985) to head (3e38522).

Files with missing lines	Patch %	Lines
deepmd/dpmodel/utils/lmdb_data.py	95.83%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5838      +/-   ##
==========================================
- Coverage   78.58%   76.59%   -1.99%     
==========================================
  Files        1050     1050              
  Lines      120637   120651      +14     
  Branches     4356     4354       -2     
==========================================
- Hits        94801    92417    -2384     
- Misses      24278    26667    +2389     
- Partials     1558     1567       +9     

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[njzjz]

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

• @wanghan-iapcm — 1 commits on changed files; 4 reviews on exact changed files (deepmd/dpmodel/utils/lmdb_data.py, source/tests/pt/test_lmdb_dataloader.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