fix(tf): preserve non-PBC ASE neighbor semantics

[njzjz-bot]

Closes #5668.

Summary

• preserve the original cells=None decision separately from the identity box required by TensorFlow placeholders
• pass a missing cell to ASE for open systems and make both TF1 neighbor-list builders handle that documented input without creating periodic ghosts
• correct the builders return annotations and document their open-boundary behavior
• add collected regressions for DeepPotential and for DeepTensor eval/eval_full

Why existing tests missed this

• the original external ASE neighbor-list tests were designed around periodic systems and never exercised cells=None
• the parameterized TestDeepPot symbol is replaced by object, so TestDeepPotNeighborList did not inherit the base evaluation tests; collection contained only two locally declared skipped tests
• although the DeepPotential testcase YAML contains a box: null result, it therefore never ran through the ASE-backed evaluator
• DeepTensor neighbor-list tests inherited PBC fixtures and had no native-versus-ASE open-boundary comparison

Validation

• focused DeepPotential no-PBC regression: passed
• focused DeepTensor eval/eval_full no-PBC regression: passed
• full TestDeepDipoleNewPBCNeighborList class: 10 passed, 2 skipped
• TF1 DeepPotential periodic native-versus-ASE parity smoke: passed
• pytest collect-only confirms both new regressions are collected
• ruff format .
• ruff check .
• git diff --check

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

Summary by CodeRabbit

• Bug Fixes

  • Fixed neighbor-list construction for open-boundary (no PBC) systems to preserve correct None/boundary semantics.
  • Prevented internal placeholder/identity cell inputs from affecting periodicity detection during neighbor and ghost-atom generation.
  • Ensured boundary semantics stay consistent across energy, tensor, and dipole evaluation paths.

• Tests

  • Added new open-boundary neighbor-list verification against reference values.
  • Added a dipole test confirming neighbor-list-based outputs match native neighbor-list behavior.

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Review details

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 4ca23923-be01-44f4-a0bb-6ebb137268e1

📥 Commits

Reviewing files that changed from the base of the PR and between f75ab0b and 8d56cb1.

📒 Files selected for processing (1)

• source/tests/tf/test_deepdipole.py

📝 Walkthrough

Walkthrough

The change preserves open-boundary semantics for TensorFlow inference with ASE neighbor lists, separates placeholder cells from boundary cells, updates neighbor-list annotations and documentation, and adds regression tests for DeepEval and DeepDipole.

Changes

Non-PBC neighbor-list inference

Layer / File(s)	Summary
DeepEval boundary handling deepmd/tf/infer/deep_eval.py	DeepEval and DeepEvalOld accept None as an open-boundary cell, use zero cells for neighbor-list construction, preserve periodicity separately, and update return annotations.
DeepTensor boundary handling deepmd/tf/infer/deep_tensor.py	eval and eval_full pass cells to neighbor-list construction only when periodic boundaries are enabled.
Open-boundary regression coverage source/tests/infer/test_models.py, source/tests/tf/test_deepdipole.py	Tests validate non-PBC ASE neighbor-list outputs against reference values and native DeepDipole evaluation.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Suggested labels: Python

Suggested reviewers: njzjz

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely summarizes the main fix: preserving non-PBC ASE neighbor-list semantics in TF inference.
Linked Issues check	✅ Passed	The changes address #5668 by preserving None-cell semantics in DeepEval and DeepTensor and adding non-PBC regression tests.
Out of Scope Changes check	✅ Passed	The PR stays focused on the reported neighbor-list bug, with only related annotation, doc, and regression-test updates.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[codecov]

Codecov Report

❌ Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.90%. Comparing base (6c3b985) to head (f75ab0b).

Files with missing lines	Patch %	Lines
deepmd/tf/infer/deep_eval.py	66.66%	1 Missing ⚠️
deepmd/tf/infer/deep_tensor.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5859      +/-   ##
==========================================
- Coverage   78.58%   76.90%   -1.68%     
==========================================
  Files        1050     1050              
  Lines      120637   120615      -22     
  Branches     4356     4347       -9     
==========================================
- Hits        94801    92758    -2043     
- Misses      24278    26509    +2231     
+ Partials     1558     1348     -210     

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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; 17 reviews on exact changed files (deepmd/tf/infer/deep_eval.py, source/tests/infer/test_models.py).
• @iProzd — 2 commits on changed files (deepmd/tf/infer/deep_eval.py, source/tests/infer/test_models.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