LAMMPS: Add option to couple xyz for npt

[jan-janssen]

Summary by CodeRabbit

Release Notes

• New Features
  • Added option to couple XYZ molecular motion in pressure-controlled simulations and thermal expansion calculations.

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[coderabbitai]

📝 Walkthrough

Walkthrough

A single-file enhancement adds a couple_xyz boolean parameter to two LAMMPS NPT molecular dynamics functions, enabling conditional runtime selection of the LAMMPS ensemble string with optional "couple xyz" coupling.

Changes

Cohort / File(s)	Summary
NPT Ensemble Coupling Parameter src/atomistics/calculators/lammps/libcalculator.py	Added couple_xyz: bool = False parameter to calc_molecular_dynamics_npt_with_lammpslib() and calc_molecular_dynamics_thermal_expansion_with_lammpslib(). Introduced runtime branching to conditionally append " couple xyz" to LAMMPS_ENSEMBLE_NPT_XYZ string and propagate usage through init and run string construction paths.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 A coupling twist, so xyz and grand,
Two functions dance at my command,
With boolean flags, the ensemble bends,
Where pressure meets motion at both ends! 🎩✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'LAMMPS: Add option to couple xyz for npt' accurately summarizes the main change: adding a couple_xyz parameter to NPT-related LAMMPS functions.

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✨ Finishing touches

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (2)

src/atomistics/calculators/lammps/libcalculator.py (2)

481-481: Consider consistency with NPT function.

The implementation mirrors the pattern from calc_molecular_dynamics_npt_with_lammpslib, which is good for consistency. The same variable naming suggestion applies here: consider using lowercase lammps_ensemble_npt_xyz instead of ALL_CAPS.

The conditional logic (lines 496-499) is duplicated from lines 241-244. While extracting it to a helper function could reduce duplication, with only two occurrences and 4 lines each, this is acceptable as-is.

Also applies to: 496-500

---

236-244: The LAMMPS syntax is correct, but consider lowercase naming for local variables.

The implementation correctly appends " couple xyz" to the ensemble command. LAMMPS documentation confirms this is the proper syntax for coupling NPT ensemble dimensions.

However, the variable LAMMPS_ENSEMBLE_NPT_XYZ uses ALL_CAPS naming typically reserved for module-level constants. Since this is a locally scoped variable, consider renaming it to ensemble_npt_xyz or similar lowercase format to follow Python conventions.

This pattern repeats in the second function as well.

📜 Review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between aee9634 and 9937b3a.

📒 Files selected for processing (1)

• src/atomistics/calculators/lammps/libcalculator.py

🧰 Additional context used

🪛 Ruff (0.14.10)

src/atomistics/calculators/lammps/libcalculator.py

238-238: Do not perform function call OutputMolecularDynamics.keys in argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable

(B008)

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[codecov]

Codecov Report

❌ Patch coverage is 71.42857% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.76%. Comparing base (aee9634) to head (9937b3a).

Files with missing lines	Patch %	Lines
src/atomistics/calculators/lammps/libcalculator.py	71.42%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #609      +/-   ##
==========================================
- Coverage   86.81%   86.76%   -0.05%     
==========================================
  Files          43       43              
  Lines        2419     2425       +6     
==========================================
+ Hits         2100     2104       +4     
- Misses        319      321       +2     

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