Fix atom type consistency#10
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chaibhave merged 3 commits intoIdahoLabResearch:mainfrom Apr 13, 2026
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…LabResearch#9 - Atom.py: use dict.fromkeys instead of set() to preserve insertion order when auto-generating type_map, preventing non-deterministic type IDs. - GBMaker.py: reuse unit_cell.type_map IDs when writing LAMMPS files if atom names are a known subset, preventing ID drift across writes. - GBManipulator.py: accept type_dict as dict[str,int] or dict[int,str] and normalise to both directions internally; auto-derive from unit_cell.type_map when not explicitly supplied; pass type_map to Atom.as_array in remove_atoms/insert_atoms; fix bytes handling in convert_type; fix atoms_to_add keyed by atom_type not ratio; replace identity comparison with equality for central_type check. - tests: add roundtrip test verifying element names survive write→read cycles after translate, remove, insert, slice_and_merge, and soft-mode displacement. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Replace bare dict/list access with None-safe handling throughout _evaluate_generation: wrap gb_energy_func calls in try/except and assign a PENALTY (1e30) to any candidate that errors or produces a missing dump file. - Add _is_valid_file helper to safely test dump file existence. - Guard _make_next_generation against empty files or indices lists. - Filter valid candidates before selection: build valid_old_idxs, valid_energies, and valid_files so selection only operates on survivors; re-seed entirely from the current best when no candidates survive a generation. - Copy initial system arrays (np.array(..., copy=True)) before passing to the energy function to prevent in-place mutation side-effects. - Add **kwargs pass-through to run_MC and preserve type_dict when reconstructing the manipulator after an accepted MC step. - Switch imports: pathlib.Path replaces sys; typing.Optional added. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Both MonteCarloMinimizer and GeneticAlgorithmMinimizer accept an optional initial_structure keyword argument (None, GBMaker, or a file path) that seeds the starting manipulator instead of always constructing one fresh from self.GB. - _make_initial_manipulator() encapsulates this logic on both classes. - Mutator.mutate() now returns (mutation_label, new_system) so callers can record what operation was applied. - MonteCarloMinimizer tracks the full accept/reject history in operation_list as [mutation_label, accepted] pairs; the initial entry is ["START", True]. Closes IdahoLabResearch#7 - GeneticAlgorithmMinimizer seeds one member of the initial population directly from the evaluated initial structure when initial_structure is supplied. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This was referenced Apr 9, 2026
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