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fix(lammps): distinguish neutral charge and dipole columns#1020

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njzjz-bot:fix/issue-995
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fix(lammps): distinguish neutral charge and dipole columns#1020
njzjz-bot wants to merge 2 commits into
deepmodeling:masterfrom
njzjz-bot:fix/issue-995

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Fixes #995.

Improve neutral decimal charge-style detection and prevent dipole fields from being reported as spins.

Tests: cd tests && python -m unittest test_lammps_atom_styles test_lammps_spin

Why existing tests missed it: Existing charge tests used non-integral charges, and no dipole-style fixture checked the optional spin key.

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

Improve automatic six-column detection for neutral decimal charges and restrict legacy spin extraction to atomic-style extension rows so dipole moments are not reported as spins. Add regressions for both cases; existing tests used non-neutral charges and therefore missed the ambiguity.

Coding-Agent: Codex
Codex-Version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning-Effort: xhigh
@dosubot dosubot Bot added size:XS This PR changes 0-9 lines, ignoring generated files. bug Something isn't working lammps labels Jul 16, 2026
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Reviewing files that changed from the base of the PR and between 0416b54 and 6e5764d.

📒 Files selected for processing (2)
  • dpdata/formats/lammps/lmp.py
  • tests/test_lammps_atom_styles.py

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@codspeed-hq

codspeed-hq Bot commented Jul 16, 2026

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Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 2 untouched benchmarks


Comparing njzjz-bot:fix/issue-995 (6e5764d) with master (d2105f6)

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@codecov

codecov Bot commented Jul 16, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.95%. Comparing base (0416b54) to head (6e5764d).
⚠️ Report is 12 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1020      +/-   ##
==========================================
+ Coverage   86.87%   86.95%   +0.07%     
==========================================
  Files          89       90       +1     
  Lines        8266     9182     +916     
==========================================
+ Hits         7181     7984     +803     
- Misses       1085     1198     +113     

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@wanghan-iapcm wanghan-iapcm left a comment

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Both #995 fixes look correct -- the ./e neutral-charge detection inspects the right column, the dipole guard correctly suppresses spurious spins, and the two new tests genuinely fail on pre-fix code. One follow-up on the spin whitelist, see inline.

Comment thread dpdata/formats/lammps/lmp.py Outdated
Restrict legacy spin-column parsing to the atomic layout without referencing an atom style that this branch does not register.

Coding-Agent: Codex
Codex-Version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning-Effort: xhigh
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[Code scan] LAMMPS atom-style parsing misreads neutral charge and dipole data

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