Update LAMMPS to latest version

[jan-janssen]

Summary by CodeRabbit

Release Notes

• Chores
  • Updated LAMMPS dependency from version 2024.08.29 to 2025.07.22
  • Made compatibility adjustments for the updated LAMMPS API

[coderabbitai]

Caution

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Pull request was closed or merged during review

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: dacbfaf3-4f4d-41d8-845b-31f8df4f5c12

📥 Commits

Reviewing files that changed from the base of the PR and between aefdbb3 and e175861.

📒 Files selected for processing (2)

• .ci_support/environment-lammps.yml
• src/structuretoolkit/analyse/snap.py

---

📝 Walkthrough

Walkthrough

This PR updates the LAMMPS conda dependency to version 2025.07.22 and adapts the SNAP analysis module to the updated LAMMPS API. The atom creation function now uses atomid instead of id, and per-atom property extraction migrates to a new extraction method signature.

Changes

LAMMPS version upgrade and SNAP API migration

Layer / File(s)	Summary
LAMMPS dependency version update .ci_support/environment-lammps.yml	LAMMPS conda dependency version pinned to 2025.07.22, preserving the openmpi build selector.
SNAP analysis migration to new LAMMPS API src/structuretoolkit/analyse/snap.py	lmp.create_atoms invocation updated to use atomid=None parameter instead of id=None. Per-atom id and type extraction migrated from extract_atom_iarray to lmp.numpy.extract_atom with nelem parameter, preserving atom id validation and type flattening logic.

Possibly related PRs

• pyiron/structuretoolkit#362: Both PRs update .ci_support/environment-lammps.yml to bump the LAMMPS dependency version as part of version maintenance.

🐰 A LAMMPS bump hops along,
With API dances new and strong,
The SNAP analyzer learns to play,
With atomid parameters the modern way! ✨

🎯 2 (Simple) | ⏱️ ~8 minutes

🚥 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 accurately reflects the main objective: updating LAMMPS to a newer version, as evidenced by the environment file change (2024.08.29 → 2025.07.22) and corresponding API adjustments in the code.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch lammps

---

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[jan-janssen]

The package seems to be available:

conda-forge/lammps/2025.07.22/linux-64/lammps-2025.07.22-cpu_py312_h9341614_mpi_openmpi_0.conda

But conda does not find it.

The following package could not be installed
      └─ lammps =2025.7.22 *openmpi* does not exist (perhaps a typo or a missing channel).

[jan-janssen]

======================================================================
ERROR: test_calc_a_matrix_snappy (test_snap.TestSNAPInternal.test_calc_a_matrix_snappy)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_snap.py", line 789, in test_calc_a_matrix_snappy
    mat_a = _calc_snap_derivatives(
        lmp=self.lmp,
    ...<2 lines>...
        cutoff=10.0,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.14/site-packages/structuretoolkit/analyse/snap.py", line 619, in _calc_snap_derivatives
    _set_ase_structure(lmp=lmp, structure=structure)
    ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/miniconda3/envs/test/lib/python3.14/site-packages/structuretoolkit/analyse/snap.py", line 269, in _set_ase_structure
    lmp.create_atoms(
    ~~~~~~~~~~~~~~~~^
        n=len(structure),
        ^^^^^^^^^^^^^^^^^
    ...<5 lines>...
        shrinkexceed=False,
        ^^^^^^^^^^^^^^^^^^^
    )
    ^
TypeError: lammps.create_atoms() got an unexpected keyword argument 'id'

[jan-janssen]

======================================================================
ERROR: test_calc_a_matrix_snappy (test_snap.TestSNAP.test_calc_a_matrix_snappy)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_snap.py", line 678, in test_calc_a_matrix_snappy
    mat_a = stk.analyse.get_snap_descriptor_derivatives(
        structure=self.structure,
    ...<9 lines>...
        cutoff=10.0,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/snap.py", line 159, in get_snap_descriptor_derivatives
    return _calc_snap_derivatives(
        lmp=lmp, structure=structure, bispec_options=bispec_options, cutoff=cutoff
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/snap.py", line 644, in _calc_snap_derivatives
    return _extract_computes_snap(
        lmp=lmp,
    ...<2 lines>...
        num_types=number_species,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/snap.py", line 550, in _extract_computes_snap
    lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'numpy_wrapper' object has no attribute 'extract_atom_iarray'
======================================================================
ERROR: test_calc_a_matrix_snappy (test_snap.TestSNAPInternal.test_calc_a_matrix_snappy)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_snap.py", line 789, in test_calc_a_matrix_snappy
    mat_a = _calc_snap_derivatives(
        lmp=self.lmp,
    ...<2 lines>...
        cutoff=10.0,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/snap.py", line 644, in _calc_snap_derivatives
    return _extract_computes_snap(
        lmp=lmp,
    ...<2 lines>...
        num_types=number_species,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/snap.py", line 550, in _extract_computes_snap
    lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'numpy_wrapper' object has no attribute 'extract_atom_iarray'
----------------------------------------------------------------------

[jan-janssen]

Changes in lammps/lammps#4304

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.90%. Comparing base (aefdbb3) to head (e175861).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #512   +/-   ##
=======================================
  Coverage   97.90%   97.90%           
=======================================
  Files          29       29           
  Lines        2004     2004           
=======================================
  Hits         1962     1962           
  Misses         42       42           

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