[njzjz-bot]

Exclude virtual centers and neighbors from minimum-distance and neighbor-count statistics in the generic and Paddle operators. Preserve periodic self-images while excluding only the original self-pair.

Add the short-cell periodic self-image regression and merge current master. The Read the Docs build also timed out during Sphinx execution (build 35461668); local diagnosis reproduced stalled external inventory requests. Set a 30-second connection/read-inactivity timeout so Sphinx can warn and continue when a host stops responding. This is not a deadline for a complete inventory download or the entire build.

Validation:

• Focused generic/Paddle neighbor-stat regressions: four tests and 18 subtests passed, including periodic self-images and virtual atoms.
• The shared Sphinx configuration with the timeout completed a full 1,760-page HTML build, with documentation warnings.
• Ruff, formatting, whitespace checks, and commit hooks passed.

Closes #5630

Coding agent: Codex
Codex version: codex-cli 0.164.0
Model: gpt-6-astra
Reasoning effort: xhigh

Summary by CodeRabbit

• Bug Fixes
  • Neighbor statistics now exclude virtual atoms and self-pairs, preventing them from affecting minimum distances or neighbor counts.
  • Periodic images of an atom continue to count as neighbors, while the original self-pair is excluded.
  • These corrections apply to both mixed-type and per-type neighbor statistics, with or without a periodic cell.

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Walkthrough

NeighborStatOP now excludes self-pairs and virtual atoms from distance and neighbor-count reductions in dpmodel and Paddle. Tests cover both counting modes, periodic and non-periodic cells, and Array API output properties. The Sphinx configuration sets a 30-second intersphinx timeout.

Changes: Virtual atom neighbor statistics

Layer / File(s)	Summary
Valid-pair masking and reductions deepmd/dpmodel/utils/neighbor_stat.py, deepmd/pd/utils/neighbor_stat.py	Both implementations exclude self-pairs, virtual centers, and virtual neighbors. Invalid distances are set to infinity, and neighbor counts use valid pairs.
Neighbor statistics regression coverage source/tests/common/dpmodel/test_neighbor_stat.py, source/tests/common/dpmodel/array_api/test_neighbor_stat.py, source/tests/pd/test_neighbor_stat.py	Tests check virtual-atom exclusion, periodic self-images, counting modes, cell configurations, and Array API output properties.

Sphinx inventory timeout

Layer / File(s)	Summary
Intersphinx request timeout doc/conf.py	The configuration sets intersphinx_timeout to 30 seconds and documents the setting.

Priority: Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Bug fix · Severity of issue fixed: Medium

Possibly related PRs

• deepmodeling/deepmd-kit#6085: Filters graph edges that touch virtual atoms in vesin_graph_builder; this change excludes virtual atoms from neighbor-statistics reductions.

Suggested reviewers: njzjz

Merge Risk: Minimal · up to 37291

The timeout’s scope is now accurately documented, and no actionable merge risk remains after normal checks.

Pre-merge checks: 3 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Out of Scope Changes check		The change to doc/conf.py adds a 30-second intersphinx_timeout for external Sphinx inventory requests. This change does not implement or test the virtual-atom filtering required by issue [#5630]. …	Remove the unrelated doc/conf.py timeout change from this pull request, or move it to a separate pull request.

Passed checks: 3 passed

Check name	Status	Explanation
Title check		The title names the main change: excluding virtual atoms from the neighbor statistics in the dpmodel operator. The changeset matches this. The Paddle operator, the new tests, and the intersphinx timeo…
Linked Issues check		Issue [#5630] requires virtual centers and virtual neighbors to be excluded from minimum-distance and neighbor-count statistics. The generic and Paddle neighbor-stat implementations now apply a valid-…
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.

Full details: Title check

Explanation

The title names the main change: excluding virtual atoms from the neighbor statistics in the dpmodel operator. The changeset matches this. The Paddle operator, the new tests, and the intersphinx timeout in doc/conf.py are secondary parts that the title does not mention, which is expected for a title.

Full details: Linked Issues check

Explanation

Issue [#5630] requires virtual centers and virtual neighbors to be excluded from minimum-distance and neighbor-count statistics. The generic and Paddle neighbor-stat implementations now apply a valid-pair mask before both reductions. The mask excludes virtual centers and neighbors and removes only the original self-pair. Tests cover both mixed-type modes, periodic and non-periodic cases, virtual centers, and virtual neighbors.

Full details: Out of Scope Changes check

Explanation

The change to doc/conf.py adds a 30-second intersphinx_timeout for external Sphinx inventory requests. This change does not implement or test the virtual-atom filtering required by issue [#5630]. The neighbor-stat changes and their tests are within scope.

Resolution

Remove the unrelated doc/conf.py timeout change from this pull request, or move it to a separate pull request.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.11%. Comparing base (1ded5d2) to head (372914f).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5834      +/-   ##
==========================================
- Coverage   78.36%   78.11%   -0.25%     
==========================================
  Files        1179     1179              
  Lines      142929   142930       +1     
  Branches     5079     5079              
==========================================
- Hits       112002   111647     -355     
- Misses      28990    29346     +356     
  Partials     1937     1937              

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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 (deepmd/dpmodel/utils/neighbor_stat.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

[njzjz-bot]

Reviewed head 7ddcaae1f677abd65abf7a11b82c55d8f125d726 with three independent full subagent reviews. No actionable findings were identified in this dpmodel-scoped diff. The pair mask correctly excludes virtual centers and neighbors, preserves periodic self-image neighbors, and keeps strict Array API count reductions numeric. One reviewer noted that Paddle has an analogous independent pre-existing implementation; that is outside this PR's declared dpmodel scope and should be tracked separately rather than block this fix. All current checks pass. Because this PR was opened by the active njzjz-bot account, this is a comment-only review rather than a self-approval event.

The quota is about to reset, so I am concentrating the remaining token budget on these reviews.

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh

[wanghan-iapcm]

The fix itself is right, and the regression coverage is real: I ran source/tests/common/dpmodel/test_neighbor_stat.py against the pre-fix neighbor_stat.py and it fails, then against this branch and it passes, so the test genuinely exposes the bug rather than merely accompanying the fix. Requiring both ends of a pair to be real also converges dpmodel onto what the TF backend has done since #3275 (virtual_type_mask_i/virtual_type_mask_j), so this is an alignment rather than a new convention.

One gap, in the inline comment: the Paddle backend keeps its own copy of this operator and does not get the fix.

A second, related point that is why nothing in CI will notice. source/tests/consistent/test_neighbor_stat.py is the only test that compares tf/pt/dp/jax/pd against one another, and its gen_sys() builds np.repeat(0, 27), so no negative type ever reaches NeighborStatOP. Both tests this PR adds call the dpmodel operator directly. That is precisely how the original gap survived unnoticed, and it will keep the Paddle divergence invisible too. Adding the virtual-atom geometry to run_neighbor_stat there, where it runs across all five backends, would close both at once.

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Actionable comments posted: 1

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Verify each finding against current code. Fix only still-valid issues, skip the
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Inline comments:
In `@source/tests/pd/test_neighbor_stat.py`:
- Around line 99-113: Extend the NeighborStatOP parameterized cell cases in the
test around NeighborStatOP to include a periodic cell with at least one axis
shorter than rcut. Add expected assertions for that case verifying the original
self-pair remains excluded while an in-cutoff periodic self-image increases
min_rr2 and max_nnei, without changing the existing non-periodic and large-cell
expectations.

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[njzjz-bot]

Re-reviewed the current head. The earlier backend-consistency gap is now closed: Paddle applies the same real-center/real-neighbor/self-pair mask as the shared dpmodel operator and has direct periodic/non-periodic, mixed/per-type regression coverage. The masking preserves periodic self-image neighbors while excluding virtual atoms from both minimum-distance and neighbor-count reductions. I did not find another blocking issue. The PR is currently not mergeable and will still need a rebase/conflict resolution against master.

This is comment-only because the active GitHub account owns this PR and GitHub does not allow self-approval.

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[njzjz-bot]

Self-review limitation: this PR is authored by the executing account, so GitHub cannot treat this as an independent approval. I reviewed this exact head and found no remaining high-confidence correctness/API blocker in the virtual-atom neighbor-stat exclusion change. From the code-review perspective this head is acceptable, pending an independent reviewer for formal approval.

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Reviewed head: 8b594d7
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Actionable comments posted: 1

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Inline comments:
Review comments at @doc/conf.py:
- Line 148: Update the documentation for intersphinx_timeout to describe it as a
request-inactivity timeout, not a limit on the complete inventory download; do
not claim it guarantees the Read the Docs build budget.

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