Lammps parser model method#147
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* docs: Add parser testing strategy discussion paper * fixed code highlighting syntax * Added method/force field parameter parsing * removed unneccessary docs page * ForceField.contributions not added to archive * Updated test-data to work with current MDAnalysis (2.10.0). Replaced hardcoded exlusion of GMX2024 with dynamic support check, to reflect major changes in MDAnalysis * Added timestep, thermostat and parostat parameter parsing * Linting fix (#145) * Fixed Linting error * bond_list parsing and test * Added angle and dihedral parsing * patches for processing (#152) * Update src/nomad_simulation_parsers/parsers/lammps/file_parsers.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: ladinesa <67910858+ladinesa@users.noreply.github.com> Co-authored-by: Joseph Rudzinski <JFRudzinski@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* resolve ruff PLC0207 by limiting split operations to one split each * tighten behavior
* Fixed Ruff complaint * Fixed failing test/skipping tests until update of test data * Added creation and parsing of system hierarchy * Fixed system hierarchy not being fully parsed, added tests/data/protein_small, updated tests * Resolved Copilot review comments. * Optimized the system hierarchy parsing, minimizing number of trajectory searches. * Added negation exeption for test data log files to gitignore * Pruned water trajectories to reduce test time
* Temporarily disable mappings to `convergence_tolerance_energy_difference` and `convergence_tolerance_force_maximum` in abinit and gromacs schema packages. This commit restores functionality. Follow-up commit will migrate to the new `WorkflowConvergenceTarget` API.
* Workaround for recursive workflow tasks * Update src/nomad_simulation_parsers/schema_packages/h5md.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Updated test_h5md_parser to accomodate workaround * Added TODO marker to test_h5md_parser for workflow regression workaround --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Add convergence target and SCF steps parsing to 8 parsers Adds support for parsing workflow convergence criteria (`EnergyConvergenceTarget`, `ForceConvergenceTarget`) and SCF iteration data (`SCFSteps`) following schema updates in nomad-simulations#260. **Parsers updated:** abinit, ams, crystal, exciting, fhiaims, gpaw, quantumespresso, vasp **Implementation:** Uses direct class instantiation approach. Future migration to dict-based `m_def` mapping annotations should be tracked separately (see PR #162 for reference). **Testing:** 39 unit tests added, all passing. Validated with production samples in `.tests/pr-150-convergence/`. Depends on nomad-simulations#260 Co-authored-by: Joseph Rudzinski <joseph.rudzinski@physik.hu-berlin.de> Co-authored-by: Nathan Daelman <nathan.daelman@physik.hu-berlin.de>
* implement particle state reassignment fix * revert pyproject.toml changes * add more tests
* Resolved field naming conflict (values -> coupling_parameters) * Renamed coupling_parameters to lambda_values to improve clarity
Add support for capturing k-point mesh configuration from FHI-aims output and control.in files. This is the first step toward full KMesh schema population. Additions: - Add `k_offset` regex capture to out_parser.py for output file - Add `k_grid` and `k_offset` regex captures to ControlParser in common.py - Parse k-grid as integer array and k-offset as float array
Wire up KMesh support through schema annotations to map k-grid and k-offset data to the NOMAD schema. Changes: - Import `numerical_settings` module in fhiaims.py - Add DFT class with numerical_settings mapping annotation - Add NumericalSettings class with KMesh subsection mapping - Add KMesh class with direct field mappings for `grid` and `offset` - Add test for k_mesh (currently shows model_method is empty, needs investigation) Note: model_method population appears to happen during normalization, not during parsing. Further investigation needed to verify k_mesh data flow through the full parsing+normalization pipeline.
Directly populate DFT and KMesh sections after parsing as temporary workaround while investigating why mapping annotations don't trigger section creation. Issue: DFT.m_def annotation with '.@' path does not create DFT section despite being identical to working patterns in VASP, GPAW, etc. Temporary solution: - Create DFT section programmatically after convert() - Extract k_grid/k_offset from parsed data - Instantiate KMesh and add to DFT.numerical_settings This approach works but bypasses the annotation system. Need to find root cause of annotation failure and implement proper fix.
Add k-point mesh (k_grid and k_offset) parsing and mapping to NOMAD schema for FHI-aims. The implementation uses the KSpace → k_mesh → KMesh hierarchy as defined in the NOMAD schema. Changes: - Parse k_grid and k_offset from FHI-aims output using regex quantities - Add KSpace and KMesh schema classes with mapping annotations - Map parsed k-point data to DFT → KSpace → KMesh structure - Add comprehensive test coverage for k-mesh functionality The key insight was that KMesh is not a direct subclass of NumericalSettings - it must be wrapped in KSpace (which is a NumericalSettings) to be added to `DFT.numerical_settings`. This follows the same pattern used by VASP parser.
This reverts commit 28ac2c2.
…ion" This reverts commit 01662ab.
This reverts commit 85778bc.
This reverts commit f860134.
Add `KMesh` support for FHI-aims parser Parse k_grid and k_offset from FHI-aims output and map to `DFT.numerical_settings.KSpace.k_mesh`. Set FHI-aims default offset=[0,0,0] (Gamma-centered) when not present.
* 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 comments, reduced code redundancy in the parser * removed stale dependency --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Corrected annotation for ForceField, ForceCalculation, ParticleParametersContainer * Fixed comments * explicit type annotations for pylance compliance
* Pin nmr schema version * Update nmr version
* Add SCF convergence criteria mapping for FHI-aims Add SelfConsistency annotation using multi-mapper pattern to extract convergence criteria (energy, density, eigenvalues) as separate instances alongside KSpace in DFT.numerical_settings. --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Haoyu Yang <yang@Haoyus-Air.localdomain>
* Add tests * Use utc reference for datetime
* Implement parsing of vasp charge density * Update pyproject.toml * Try using nomad-lab develop * Remove index-url * Revert and exclude vasp entry point * Add charge density annotation to vasp schema
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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
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Testing / Validation
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