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….parsing``) to ``doped.core``
…propriate name now
…s & spin degeneracy
…mes & potential loaders
…d-driven discovery & warnings)
…utputs` with any calculator)
…alculationOutputs`)
…ation base class)
…e_projected_eigen`
…develop merge) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
# Conflicts: # doped/analysis.py # doped/core.py # doped/utils/parsing.py # doped/vasp.py # examples/GGA_workflow_tutorial.ipynb # examples/Se/F_i_C2_-1_20Å_Stenciled_POSCAR # examples/Se/F_i_C2_1_20Å_Stenciled_POSCAR # examples/Se/H_Se_-1_20Å_Stenciled_POSCAR # examples/Se/H_Se_0_20Å_Stenciled_POSCAR # examples/Se/Se_20Å_Supercell_POSCAR # examples/Se/Se_i_C2_-1_20Å_Stenciled_POSCAR # examples/Se/Se_i_C2_-2_20Å_Stenciled_POSCAR # examples/Se/Se_i_C2_0_20Å_Stenciled_POSCAR # examples/Se/v_Se_-1_20Å_Stenciled_POSCAR # examples/Se/v_Se_-2_20Å_Stenciled_POSCAR # examples/Se/v_Se_0_20Å_Stenciled_POSCAR # examples/chemical_potentials_tutorial.ipynb
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…mpeting-phase branch Both sides branched from c85a5bd. Kept from this branch: the light `read_gpw`/ULM reader, `_open_gpaw_restart` (stored-results check for all four `.gpw` readers), the charge check removal, and the example's primitive-cell host, Niggli-reduced phases and 400 eV / k-density 4 settings. Taken from d3bc935: GPAW `check_entry_compatibility` (k-point/grid meshes excluded), the `find_calc_output` backend hook for analyzer file selection, competing-phase wording in the multiple-files warning, k-point meshes from `get_bz_k_points()`, `converged_electronic`, no duplicated `entry.parameters`, no unused `subfolder` argument, the example docstrings and the real-calculation tests (phase fixture, analyzer, file priority, settings mismatch, k-point mesh and example inputs). Changed relative to d3bc935: - `find_calc_output` errors (`ValueError` for ambiguous filenames, as well as `FileNotFoundError`) fall back to the generic file pick with a warning, rather than failing the whole analysis. - The list-mode docstring uses the wording already on IO_refactor (57faf9b), to merge cleanly there. - Dropped `_read_gpaw_calculation` (superseded by `_open_gpaw_restart`), the charge check test, and `test_gpaw_restart_without_energy` (covered by `test_restart_without_results_raises`). - `pytest.warns` -> `_run_func_and_capture_stdout_warnings`; lazy `ase` k-point import; doped-style docstrings; `find_calc_output` documented in Adding_Calculators.rst. - Remaining review nits: doped-style Args layouts and the singular/plural protocol-name comment.
…arsing Add GPAW competing-phase output parsing for chemical potentials
Port develop's changes into the relocated IO_refactor modules: - doped/vasp.py -> doped/io/vasp/inputs.py: INCAR helpers (_parse_incar_value, _is_hybrid, _use_user_nupdown, _update_incar_settings), DopedDictSet._kpts (KSPACING support), user EDIFF(_PER_ATOM)/NUPDOWN/NKRED/MAGMOM/ KSPACING/POTCAR settings handling and DefectRelaxSet._singlepoint_incar_settings - CompetingPhases VASP input methods -> doped.io.vasp.inputs module functions (KSPACING support, user EDIFF handling, _revert_sparse_tetrahedron_smearing) - doped/utils/parsing.py -> doped/io/vasp/outputs.py: parse_projected_eigen override removed (and dropped from the doped.utils.parsing deprecation shim) - doped/utils/symmetry.py: _SPGLIB_ERRORS handling; _check_spglib_version and is_periodic_image removed - CompetingPhasesAnalyzer skipped-folder warnings and to_json/from_json were already on IO_refactor (keeping the backend-agnostic calc_output naming) - New develop tests ported to tests/test_vasp.py and tests/test_generation.py
Port develop's VASP handling compaction (8d3fd3d) to doped/io/vasp/inputs.py (DefectRelaxSet NKRED logic, _singlepoint_incar_settings override warnings and user_incar_settings docstrings), and update two get_vasprun kwargs docstring examples for develop's removal of parse_mag
…id DFT, no symmetry, PreconLBFGS optimiser
…and edge determination in GPAW (to boost generalisability, handle metallic / high-smearing systems etc)
Port develop's `_update_incar_settings` -> `_handle_EDIFF_and_update_incar_settings` rename to `doped/io/vasp/inputs.py` (keeping the `doped/vasp.py` shim), and map the consolidated `tests/.pytest_split_durations` to the IO test layout (`test_analysis.py` -> `test_parsing.py`).
Port develop's `doped/vasp.py` changes (`_handle_EDIFF_and_update_incar_settings` rename, non-collinear `MAGMOM` fix) to `doped/io/vasp/inputs.py` and its `load_bulk_gap_data` MP band-structure updates to `doped/parsing.py`, and map the consolidated `tests/.pytest_split_durations` to the IO test layout (`test_analysis.py` -> `test_parsing.py`).
Determine GPAW band edges from occupations
…ort paths) in CI, until release
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This PR implements a refactoring of calculation I/O in
doped, moving all calculator-specific (e.g. VASP) code to adoped.iosubpackage, where each calculator then has its own subpackage asdoped.io.<calculator>withinputs,outputsand optionallyutilssub-modules (e.g.doped.io.vasp.outputs). A unified interface is then used for calculation inputs and outputs, streamlining the addition of new calculators (Quantum Espresso, GPAW, FHI-aims, ...) todoped.