FAIRmat-NFDI / nomad-parser-plugins-simulation / 24240333703

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Commit Message

Gromacs parser results (#156)

* Added parsing of masses and (partial) charges

* Rebasing onto current develop

* Extended atom parameter parsing to include chemical_symbol and atomic_number, if available

* WIP

* Adapted schema to archive derived properties from MolecularDynamicsResults

* Implemented explicitly archiving ParticleParameters, generalized all references to atom to particle

* Fixed Ruff complaint

* Added temporary check for availability of new feature in nomad_simulations

* More guards

* Adjusted parser and schema to changes in nomad-simulations.force_field, updated program.version regex

* Recovered some missing quantities

* Added some more missing Quantities

* fix: block MappingParser Level 3 task recursion for GROMACS workflows

* Extended parser to handle CG systems, started adding free energy parameter parsing

* corrected model_method structure, added workarounds for nested subsection issues

* Added free energy parameter parsing

* fix: clean up unused imports, remove magic numbers

* implemented atom/particle classification

* fix: organize inputs

* added parsing of free energy parameters

* fix: rename lambdas valuse -> coupling_parameters to resolve naming conflict with MappingParser

* Adapted parser to reflect resolved field naming conflict

* Resolved field naming conflict (values -> lambda_values) (#169)

* Resolved field naming conflict (values -> coupling_parameters)

* Renamed coupling_parameters to lambda_values to improve clarity

* renamed coupling_parameters to lambda_values

* closed implementation gap to add free-energy inputs via XVG parser.

* linting stuff

* Conditionally skip test until related PR is merged

* optimized tests, adressed Copilot comments

* fix: rename Outpus -> Outputs in gromacs schema, update TODO PR ref to #375

* Update src/nomad_simulation_parsers/parsers/gromacs/parser.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* reabsing

* adressed review comment... (continued)

Coverage Stats

447 of 466 new or added lines in 7 files covered. (95.92%)

3 existing lines in 1 file now uncovered.

7612 of 10274 relevant lines covered (74.09%)

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