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remake dopedxpy-sc-fermi#46

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alexsquires wants to merge 179 commits intodevelopSMTG-Bham/doped:developfrom dopey_fermiSMTG-Bham/doped:dopey_fermiCopy head branch name to clipboard

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Commits on Jan 10, 2024

• remake dopedxpy-sc-fermi

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Commits on Jan 11, 2024

• implement full functionalility from SK thesis

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• supress py-sc-fermi warnings

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• basic tutorial, full data with CdTe and we can polish it off

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• test py-sc-fermi interface

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Commits on Feb 9, 2024

• start work on new integrated solver

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• example files

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• Merge branch 'develop' of https://github.com/SMTG-Bham/doped into dopey_fermi

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Commits on Feb 14, 2024

• remake interface

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Commits on Feb 15, 2024

• merge upstream changes

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• fix up CdTe example data

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• improve py_sc_fermi tutorial

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• update pyscfermi interface

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• add effective dopant scanning

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• fill out exceptions and effective dopant concentrations

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• tutorials for exceptions and effective dopant concentrations

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• update tests

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Commits on Feb 23, 2024

• add chemical potential grid search

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• significant code redundancy reductions

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Commits on Feb 26, 2024

• finish minimal redudnacy refactor

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• implement iterative grid solver

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Commits on Feb 27, 2024

• tutorials

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• prep for testing

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• base testing

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Commits on Mar 11, 2024

• Merge branch 'develop' into dopey_fermi

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• Fix corrupted JSON file

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• Add py-sc-fermi interface tutorial to docs

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• Update fermi_solver.py; run import checks and warning only when py-sc-fermi functions needed, code/docstrings cleanup, formatting

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• Resolve TODO in thermodynamics

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• Update tutorial notebook

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Commits on Mar 13, 2024

• Cleanup and gzip vaspruns for space

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• Suggested: Refactor fix_defect_species to fix_charge_states as this is more intuitive?

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• Make _get_chempot_term far more efficient (realised was bottleneck in doped concentration calcs, due to inefficient defect.element_changes in pymatgen; avoided now)

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• Add effective_dopant_concentration parameter to doped thermodynamics functions

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• Add effective_dopant_concentration parameter to FermiSolverDoped functions, and fix bug in generate_annealed_defect_system

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• Update tutorial

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Commits on Mar 20, 2024

• defualt multiplicity factor handling

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• change to

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• add docstrings

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Commits on Apr 2, 2024

• linting

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• fix the default chempot behaviour

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Commits on Apr 5, 2024

• Merge branch 'develop' into dopey_fermi

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Commits on Apr 6, 2024

• Merge branch 'develop' into dopey_fermi

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Commits on Apr 10, 2024

• Merge branch 'refs/heads/develop' into dopey_fermi

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Commits on Apr 11, 2024

• Merge branch 'refs/heads/develop' into dopey_fermi

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Commits on May 13, 2024

• Merge branch 'refs/heads/develop' into dopey_fermi

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Commits on May 22, 2024

• supress warnings

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• Fix (most) failing tests, formatting, match other test preferences (np.isclose over assertAlmostEqual etc), pull chempots from DefectThermodynamics if present and not supplied...

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Commits on Jul 9, 2024

• supress py_sc_fermi warnings

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Commits on Jul 11, 2024

• Merge remote-tracking branch 'origin' into dopey_fermi

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• add limits as option to most scans

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• minor tutorial update

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• Merge branch 'refs/heads/develop' into dopey_fermi

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• Merge and formatting

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• Merge branch 'refs/heads/develop' into dopey_fermi

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Commits on Jul 12, 2024

• Use _parse_chempots function from doped.thermodynamics for cleaner chempot handling, and allowing user to set as raw chempot dict with el_refs etc

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• Cleanup; remove unused suppress_warnings etc

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• Tutorial updates and minor code cleanup

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• Update DefectThermodynamics paths in FermiSolver tests

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Commits on Jul 30, 2024

• explicitly add in vertices to grid searches

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• merge

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• Merge branch 'refs/heads/develop' into dopey_fermi

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Commits on Jul 31, 2024

• black

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• update docstrings and example notebook

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Commits on Aug 8, 2024

• fix bug where defect concentrations could not be found from min_max_X

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• tests written and passing locally

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Commits on Aug 11, 2024

• Merge Doped/PyScFermi backends to FermiSolver, docstring fleshing out, formatting etc

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Commits on Aug 13, 2024

• Cleanup and formatting

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• Update tutorial

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Commits on Aug 15, 2024

• Remove Parallel code, add note, use tqdm, formatting and code efficiency

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• Allow bulk_dos to be set in DefectThermodynamics init, or as property (with setter method), and test – quicker init times for FermiSolver

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• Fix some errors, set default (quenched_)temperature to 300K, refactor quenching to quenched to match thermodynamics terminology

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• Update citation info

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• Update to use flexible chempot/el_refs input and handling as in thermodynamics.py, and remove a couple redundant functions

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• Add note to tutorial

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Commits on Aug 16, 2024

• Some tests updates

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• Merge branch 'refs/heads/develop' into dopey_fermi

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• Minor formatting

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• Extend tests to 3.12

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Commits on Aug 20, 2024

• Merge branch 'develop' into dopey_fermi

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Commits on Aug 21, 2024

• Merge branch 'develop' into dopey_fermi

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Commits on Sep 12, 2024

• Merge develop

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Commits on Sep 18, 2024

• fix grid generator, add fixed defects kwarg for py-sc-fermi usage

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Commits on Sep 19, 2024

• docstrings for

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• update tutorial

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• make sure arguement is passed forward correctly

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• add custom fixed_defects to tutorial

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Commits on Sep 20, 2024

• add line scan for min_max_X in binaries

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• fix optional args in min_max_X

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• add fixed_defects to tutorial notebook

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Commits on Sep 26, 2024

• merge fermisolver in thermodynamics and chemicalpotentialgrid into chemical_potentials

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Commits on Oct 2, 2024

• update tutorial

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Commits on Oct 17, 2024

• tests

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Commits on Oct 18, 2024

• tests passing locally

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• test chemical potential grid methods

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Commits on Dec 18, 2024

• Update test data

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Commits on Dec 19, 2024

• Merge branch 'develop' into dopey_fermi

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• Slight docstring cleanup and some todos

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• Avoid unnecessary (as far as I can tell) deepcopy calls to expedite py-sc-fermi code

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• Reduce some code redundancy

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• Ensure output dataframes have consistent formats (resolves TODOs)

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• Ensure sorting in output dataframes is consistent

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Commits on Dec 22, 2024

• Update tests

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Commits on Dec 28, 2024

• Update docstring and add error catch for scan_temperature, and add test

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Commits on Dec 29, 2024

• Use consistent input parameter ordering in most cases for user-facing concentration functions (bulk_dos, temperature, chempots, limit, el_refs, fermi_level), except if chempots is what we're scan…

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• Docstrings updates

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• Fold duplicate code into _get_and_check_thermo_chempots method

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• Refactor temperature settings check code into_check_temperature_settings and use wherever appropriate

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• Add missing free_defects input parameter to equilibrium_solve uses (relevant for total and constrained equilibrium)

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• Fold and simplify duplicate code into _get_min_max_target_values

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• Fix _min_max_X_line (zoomed chempots used arbitrary and potentially unphysical bounds (+/-0.1 eV), now uses midpoints as for grid function, and return target_df placed in while loop but shoul…

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• Add carrier concentration tests to TestGetPyScFermiDosFromFermiDos (most important property)

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• Formatting and minor robustness update (materialsproject/pymatgen#4240)

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• Set Defect (and Charge if per_charge=True) as DataFrame index in doped concentration functions, matching symmetry and transition level outputs

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Commits on Dec 30, 2024

• Add and use _ensure_list convenience function to reduce code verbosity, and use tqdm in scan_chempots too

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• Set free_defects > fixed_defects > fix_charge_states as parameters/docstrings order to match expected popularity

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• Use _solve and scan_chempots functions to reduce code redundancy and aid maintenance

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Commits on Dec 31, 2024

• Update docstrings and tutorial notes to note FermiSolver capabilities and remove TODO

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• Update paper list

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• Remove bulk_voronoi_nodes.json storing/loading code, new doped efficiency functions make this analysis take negligible time 🔥

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Commits on Jan 1, 2025

• Formatting to reposition DefectThermodynamics methods

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• Update periodicity-breaking detection to handle rare cases where interstitial symmetry depends on chemical identity

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• Update DefectThermodynamics to_dict() to ensure pydefect objects correctly serialized and expand tests

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• Test all option combinations for get_symmetries_and_degeneracies, get_equilibrium_concentrations and get_formation_energies

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• Add full tests for get_doping_windows/dopability_limits()

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• Add caching to get_sga to speed up symmetry determination for large supercells

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• Add caching to get_primitive_structure and SpacegroupAnalyzer.get_symmetry() to massively speed up symmetry determination for large supercells

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• Add test for auto symprec adjustment for rare, weird input structures where spglib struggles

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• Formatting and efficiency updates for test_thermodynamics.py

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• Add full check_compatibility tests, all test_thermodynamics TODOs done

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• Refactor get_quenched_fermi_level_and_concentrations to get_fermi_level_and_concentrations

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• Update FermiSolver tutorial

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Commits on Jan 2, 2025

• Update FermiSolver tests

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• Simplify some FermiSolver tests

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• Remove apparently redundant catch

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• Update image link

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• Add tests for all get_equilibrium_fermi_level options

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• Test all uses of skip_check

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• Move _get_constrained_concentrations to separate function

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• Avoid possible small discrepancies in Charge State Population depending on per_site choice

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• Add comprehensive tests for get_fermi_level_and_concentrations

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• Add extra attempt with looser similar_orb_criterion in get_eigenvalue_analysis

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• Ensure no duplicate defect names in warnings

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• Allow relative path for bulk_path in DefectsParser

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• Add _get_in_gap_fermi_level_stability_window convenience method and tests

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• Add is_shallow convenience function and test

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Commits on Jan 3, 2025

• Don't show charge correction error warnings for shallow or unstable defects; with controllable options; and add tests

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• Make _get_element_list and thus _sort_defect_entries and DefectThermodynamics initialisation faster

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• Use scipy clustering to make _get_all_equiv_sites and thus DefectThermodynamics initialisation faster

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• Make group_defects_by_distance and thus DefectThermodynamics initialisation faster

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• Add unstable_entries (and kwargs) to plot(), to control plotting of unstable and/or shallow charge states

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• Add tests for unstable_entries

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• Change chempot_table behaviour, only show by default if multiple chemical potential limits

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• Update legend formatting in plots

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• Update note

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• Update tests

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• Rename skip_check to skip_vbm_check for clarity

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Commits on Jan 6, 2025

• Refactor shallow/unstable entries pruning code to prune_to_stable_entries convenience method and add tests/docs

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• Add notes to tutorials and docs re unstable_entries options

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• Update _get_py_sc_fermi_dos_from_fermi_dos tests; avoid mocking if not needed (easier to maintain & manipulate)

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• Use setUpClass to avoid redundant DefectThermodynamics initialisations and reloads for each test, drops test time from minutes to seconds

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• General FermiSolver tests updates

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• Test actual values in FermiSolver tests, to ensure working correctly

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• Use parametrization to combine tests for different backends, and again test actual values

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• Test actual values in test_scan_temperature_equilibrium

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• Test temperature setting errors for each scan function together, plus fixes from testing

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• Remove tqdm mocking -- unused? And remove some redundant checks for brevity

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• Cleanup (same info as test names)

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• Update TODOs

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Commits on Jan 8, 2025

• fix ZeroDivisionError in fermisolver test

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• Merge remote-tracking branch 'origin/dopey_fermi' into dopey_fermi

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• Add no-chempots error catch tests

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• Add informative error catch for 2D systems with ChemicalPotentialGrid

  kavanase

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• Include Dopant (cm^-3) as column and not as row in FermiSolver dataframe outputs

  kavanase

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• Use dist_tol for grouping defects for concentration calculations (most physically reasonable choice, rather than basing on names) and update docstrings, tutorials etc

  kavanase

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• Refactor _TLD_plot to formation_energy_plot

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• Update FermiSolver tests

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• Add test_equilibrium_solve_700K_no_eff_dopant

  kavanase

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• Add test_pseudo_equilibrium_solve_1400K_no_eff_dopant

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