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…l-peg into high-pressure
Initial implementation of benchmark for 2D crystal structures from Alexandria database. Uses cell mask to constrain relaxation to in-plane directions only. Metrics: - Area MAE (Ų/atom): In-plane area per atom vs PBE reference - Energy MAE (eV/atom): Energy per atom vs PBE reference - Convergence (%): Percentage of structures that converged Data source: alexandria_2d_001.json.bz2 from Alexandria database Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add generic download_data() and load_structures() functions for both 2D/1D - Add get_length_per_atom() for 1D chain length calculation - Add relax_low_dimensional() with dimensionality parameter for cell masks - Add 1D metrics: Length MAE, Energy MAE, Convergence - Add 1D parity plots for length and energy - Parametrize test function for both 2D and 1D dimensionalities - Update app with 1D plot configurations Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Document the new low-dimensional relaxation benchmark including: - Summary of 2D and 1D structure relaxation - Metrics: Area/Length MAE, Energy MAE, and Convergence for both 2D and 1D - Description of cell masks for constrained relaxation - Data availability from Alexandria database Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add set_vacuum_padding() function that sets lattice constants to 100 Å in non-periodic directions while preserving vector directions: - 2D: sets c vector to 100 Å - 1D: sets b and c vectors to 100 Å Apply vacuum padding before relaxation in test function. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add symmetrize_structure() using spglib.standardize_cell() - Remove FixSymmetry constraint (doesn't work for low-d relaxations) - Apply symmetrization before vacuum padding and relaxation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update DEFAULT_DATA_FILES to use lists (2 files for 2D, 1 for 1D) - Add download_all_data() to download multiple files - Update load_structures() to pool entries from all files before sampling Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace 10 near-identical per-dimensionality fixtures with: - DIM_CONFIGS dict mapping dimensionality to column/label/unit - _compute_mae() and _compute_convergence() helpers - _generate_all_plots() looping over DIM_CONFIGS - Single parity_plots fixture and loop-based metrics fixture Reduces 465 lines to 353 lines with no duplication. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace custom symmetrize_structure implementation with ase.spacegroup.symmetrize.refine_symmetry. Drop spglib import. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…anSchmidt1/ml-peg into low_dimensional_benchmark
- Remove symmetrize_structure(), call refine_symmetry() directly - Add test_get_area_per_atom and test_get_length_per_atom unit tests Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
ElliottKasoar
added
the
new benchmark
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Summary
Adds relaxation of two-dimensional and one-dimensional crystal structures benchmarking energies and areas/lengths.
Linked issue
Resolves #354
Progress
Testing
mace-mpa-0New decorators/callbacks
No