Fix setting initial temperature

[jan-janssen]

Summary by CodeRabbit

• Bug Fixes

  • Velocity initialization now only runs when temperature parameters are specified, preventing unintended velocity setup.
  • Improved parameter handling so input dictionaries passed into calculations are no longer mutated.

• Tests

  • Updated expectations to align with the adjusted velocity behavior in generated simulation inputs.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Conditional initial-velocity creation was added to calc_md (only when initial_temperature is set > 0) and calc_kwargs is now defensively copied to avoid mutating caller-provided dictionaries. A test expectation was adjusted to remove the initial velocity creation line.

Changes

Cohort / File(s)	Summary
Velocity Setup Conditioning src/pyiron_lammps/compatibility/calculate.py	calc_md now calls _set_initial_velocity only if initial_temperature is not None and > 0; when initial_temperature is None or ≤ 0 no initial velocity is appended. Review flows that assume velocity creation.
Defensive Parameter Copying src/pyiron_lammps/compatibility/file.py	calc_kwargs is copied when provided to avoid mutating the caller's dict; ensure downstream modifications still behave as intended.
Test Expectation Update tests/test_compatibility_file.py	Test test_calc_md_nve updated to remove assertion for the velocity all create ... gaussian line from expected LAMMPS input.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 I hopped through bytes and gentle code,

I guarded args on every road,
If temps are zero, no race begins,
I copy papers, dodge the sins,
A tiny tweak — the rabbit grins.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Fix setting initial temperature' directly corresponds to the main change—making initial velocity setup conditional based on initial_temperature value.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing touches

• 📝 Generate docstrings

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.15%. Comparing base (783c651) to head (902dfa3).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #297      +/-   ##
==========================================
+ Coverage   82.12%   82.15%   +0.03%     
==========================================
  Files          11       11              
  Lines        1141     1143       +2     
==========================================
+ Hits          937      939       +2     
  Misses        204      204              

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