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Pull request overview
This pull request fixes a typo in the h5md documentation (changing "conjugant_gradient" to "conjugate_gradient") but also includes substantial code changes to the GROMACS parser that enhance atom parameter extraction and enable workflow parsing functionality.
Changes:
- Fixed typo "conjugant_gradient" → "conjugate_gradient" in h5md documentation
- Enhanced GROMACS atom parameter extraction with new
get_atom_parameters()method returning structured atom data (label, element, mass, charge) - Added schema mapping annotations for AtomsState properties (label, chemical_symbol, mass, partial_charge)
- Re-enabled workflow parsing by uncommenting
_parse_workflow_section() - Updated maximum_force regex pattern to extract numeric values more precisely
- Cleaned up documentation formatting (indentation, whitespace, list markers)
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| docs/parsers/h5md/h5md_expl.md | Fixed typo in integrator name and cleaned up formatting (indentation, whitespace, list markers) |
| src/nomad_simulation_parsers/schema_packages/gromacs.py | Added detailed mapping annotations for AtomsState properties instead of generic mapping |
| src/nomad_simulation_parsers/parsers/gromacs/parser.py | Added get_atom_parameters() method for structured atom data extraction, changed configurations to use new method, re-enabled workflow parsing |
| src/nomad_simulation_parsers/parsers/gromacs/log_parser.py | Updated maximum_force regex from generic text extraction to precise numeric value extraction |
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JFRudzinski
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Feb 27, 2026
Bernadette-Mohr
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The integrator is called "conjuga_te_ gradient".