Lammps parser model method

[Bernadette-Mohr]

Purpose

Extends the LAMMPS parser to populate the MolecularDynamicsMethod schema from nomad-simulations, enabling standardized extraction of MD simulation metadata (thermostat/barostat settings, integrator parameters, ensemble type) from LAMMPS log and data files.

Scope

• MolecularDynamicsMethod extraction:
  • Integrator type from run_style command (velocity_verlet, verlet_split, respa, respa_omp)
  • Timestep from timestep command
  • Number of steps from run command
  • Thermodynamic ensemble detection (NVE/NVT/NPH/NPT)
  • Coordinate/velocity/force/thermodynamics save frequencies from dump/thermo commands
  • ThermostatParameters: 4 types (nvt, langevin, temp/berendsen, temp/rescale), reference temperature, coupling constant
• BarostatParameters: 3 types (npt, nph, press/berendsen), reference pressure, coupling constant
• Compressibility extraction: Converts LAMMPS modulus keyword (bulk modulus) to compressibility via 1/modulus formula
• Helper methods:
  • _extract_integrator_type(),
  • _extract_modulus(),
  • existing _extract_thermostat_settings(),
  • _extract_barostat_settings()
• Test coverage: # new test functions

Out of scope (What is explicitly not included (to avoid scope creep)?)

Status

• Draft / In progress (not ready for full review)
• Ready for review
• Blocked (explain below)

Dependencies / Blockers

• None.
• Related PRs:
• Open design questions:
• External dependencies (people, decisions, data, releases):

Testing / Validation

• Unit tests
• Integration tests
• Manual testing (brief description):
• Not applicable (explain why):

Linked Issues / Context

Use GitHub keywords where applicable.

• Fixes #
• Related to #
• Follow-up issues (if known):

Reviewer Notes

Anything reviewers should pay special attention to? Trade-offs, known limitations, or areas of uncertainty.

[coveralls]

Pull Request Test Coverage Report for Build 21947708520

Details

• 337 of 404 (83.42%) changed or added relevant lines in 2 files are covered.
• 15 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.6%) to 68.31%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/nomad_simulation_parsers/parsers/lammps/parser.py	196	223	87.89%
tests/parsers/test_lammps_parser.py	141	181	77.9%

Files with Coverage Reduction	New Missed Lines	%
src/nomad_simulation_parsers/parsers/utils/mdanalysisparser.py	15	36.7%

Totals
Change from base Build 21869152946:	0.6%
Covered Lines:	5930
Relevant Lines:	8681

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💛 - Coveralls