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Shallow defect analysis #50

Merged
merged 102 commits into from
Mar 30, 2024
Merged

Shallow defect analysis #50

merged 102 commits into from
Mar 30, 2024

Commits on Feb 1, 2024

  1. added phs identification

    @adair-nicolson
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  2. Merge remote-tracking branch 'origin/develop' into develop

    @adair-nicolson
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  3. added to tips and tricks

    @adair-nicolson
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  4. added test

    @adair-nicolson
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  5. uncommented warning

    @adair-nicolson
    adair-nicolson committed Feb 1, 2024
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  6. fix circular import

    @adair-nicolson
    adair-nicolson committed Feb 1, 2024
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  7. fix invalid escape sequence

    @adair-nicolson
    adair-nicolson committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. fix typo

    @adair-nicolson
    adair-nicolson committed Feb 2, 2024
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  2. add reference to pydefect and vise

    @adair-nicolson
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Commits on Feb 15, 2024

  1. Merge branch 'shallow_defects' into develop

    @kavanase
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  2. Merge pull request #47 from adair-nicolson/develop 

    Shallow defect analysis
    @kavanase
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Commits on Mar 1, 2024

  1. Merge branch 'main' into shallow_defects 

    # Conflicts:
#	doped/analysis.py
    @adair-nicolson
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  2. Updated plotting, fixed p-ratio bug, updated vise check

    @adair-nicolson
    adair-nicolson committed Mar 1, 2024
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  3. New load data with additional warnings

    @adair-nicolson
    adair-nicolson committed Mar 1, 2024
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  4. Add load_phs_data to DefectsParser

    @adair-nicolson
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  5. Improved efficiency load data

    @adair-nicolson
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  6. Fix bes test

    @adair-nicolson
    adair-nicolson committed Mar 1, 2024
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  7. Fix missing Gamma glyph when plotting

    @adair-nicolson
    adair-nicolson committed Mar 1, 2024
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  8. Supress warning missing Gamma glyph when plotting

    @adair-nicolson
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Commits on Mar 2, 2024

  1. Update to tips and tricks

    @adair-nicolson
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  2. Added new tests for wrong vise version and test for no projected orbi… 

    …tals. Updated old tests to include load_phs_data=False to avoid clash with new warnings
    @adair-nicolson
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Commits on Mar 3, 2024

  1. Forgot to commit cu2sise3_phs plot for test

    @adair-nicolson
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  2. Update Tips.rst 

    Sharpen some early text, fix some typos in the shallow defects section, and switch a reference
    @aronwalsh
    aronwalsh committed Mar 3, 2024
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Commits on Mar 4, 2024

  1. Fix legend in plots

    @adair-nicolson
    adair-nicolson committed Mar 4, 2024
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  2. Merge remote-tracking branch 'origin/shallow_defects' into shallow_de… 

    …fects
    @adair-nicolson
    adair-nicolson committed Mar 4, 2024
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Commits on Mar 10, 2024

  1. Merge with develop

    @kavanase
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  2. Update and merge shallow_defects

    @kavanase
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Commits on Mar 11, 2024

  1. Update shallow defects tips page and link in warning message

    @kavanase
    kavanase committed Mar 11, 2024
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  2. Update pydefect and vise requirements

    @kavanase
    kavanase committed Mar 11, 2024
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  3. Update PHS parsing/handling & tests

    @kavanase
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  4. Refactor Cu2SiSe3 data to example data, and some minor updates

    @kavanase
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Commits on Mar 12, 2024

  1. Add plot and style_file options, efficiency/formatting updates, a… 

    …nd add test
    @kavanase
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Commits on Mar 13, 2024

  1. Add monkey patch to ensure defect site always included in neighbour l… 

    …ist. Changed ordering of plot legend
    @adair-nicolson
    adair-nicolson committed Mar 13, 2024
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  2. Update test to include interstitial

    @adair-nicolson
    adair-nicolson committed Mar 13, 2024
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  3. Update tips

    @adair-nicolson
    adair-nicolson committed Mar 13, 2024
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  4. Update advanced_tutorials

    @adair-nicolson
    adair-nicolson committed Mar 13, 2024
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  5. Supress vise info

    @adair-nicolson
    adair-nicolson committed Mar 13, 2024
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  6. Merge branch 'develop' into shallow_defects

    @kavanase
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  7. Missing test files

    @adair-nicolson
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  8. Merge remote-tracking branch 'origin/shallow_defects' into shallow_de… 

    …fects
    @kavanase
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Commits on Mar 14, 2024

  1. Update parsing code so that bulk vasprun only loaded once

    @kavanase
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  2. Make vasprun data parsing more efficient and reduce memory load

    @kavanase
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  3. Add monkey-patched Vasprun._parse_projected_eigen() to make parsing… 

    … more efficient with `load_phs_data=True`
    @kavanase
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Commits on Mar 16, 2024

  1. Merge branch 'develop' into shallow_defects 

    # Conflicts:
#	doped/analysis.py
#	tests/test_analysis.py
    @kavanase
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  2. Merge develop updates – CdTe example defects parsing with PHS state… 

    …s now down to ~1m 37s
    @kavanase
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Commits on Mar 21, 2024

  1. Add PROCAR parsing as default behaviour

    @adair-nicolson
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Commits on Mar 22, 2024

  1. Fix phs parsing in cases where Elements replaced with Species due to … 

    …auto oxidation detection
    @adair-nicolson
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  2. Update doc string, fix parsing cases, update tests

    @adair-nicolson
    adair-nicolson committed Mar 22, 2024
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  3. Refactor PHS parsing, update tests to avoid floating-point error

    @adair-nicolson
    adair-nicolson committed Mar 22, 2024
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  4. Refactors get_band_edge_info

    @adair-nicolson
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  5. pymatgen.io.vasp.outputs.Procar can't parse non-collinear, so have to… 

    … use vasprun.xml for those calculations to get PHS data. Rough fix, need to polish
    @adair-nicolson
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  6. Use easyunfold PROCAR parser instead of pymatgen, so can parse non-co… 

    …llinear PROCAR
    @adair-nicolson
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  7. Can't use gzip Procar

    @adair-nicolson
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  8. Test files

    @adair-nicolson
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Commits on Mar 25, 2024

  1. Fix vise check for parsing PROCAR with SOC

    @adair-nicolson
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  2. Merge branch 'develop' into shallow_defects 

    # Conflicts:
#	docs/Tips.rst
#	doped/analysis.py
#	examples/advanced_analysis_tutorial.ipynb
    @kavanase
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  3. Cleanup tutorial & tips page (output cleared from some cells when mer… 

    …ging notebooks)
    @kavanase
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Commits on Mar 26, 2024

  1. Suggested refactoring ("phs" -> "eigenvalues" etc) and some formatting

    @kavanase
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  2. Futher formatting

    @kavanase
    kavanase committed Mar 26, 2024
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  3. Update file permissions

    @kavanase
    kavanase committed Mar 26, 2024
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  4. Add get_procar to handle PROCAR loading

    @kavanase
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  5. Add _parse_procar, expand docstrings, avoid unnecessary pydefect … 

    …`INFO` warning, allow `get_eigenvalue_analysis` to be used directly (not necessarily `doped` `DefectEntry` object)...
    @kavanase
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  6. Add _load_and_parse_eigenvalue_data to DefectEntry to efficiently… 

    … handle eigenvalue parsing, expand `get_eigenvalue_analysis` docstrings, and update so that eigenvalue data still in correct format after saving/reloading
    @kavanase
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  7. Update eigenvalue data parsing in analysis.py accordingly

    @kavanase
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  8. Pre-commit and formatting updates

    @kavanase
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Commits on Mar 27, 2024

  1. Update vise requirement following release

    @kavanase
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  2. Remove vise version checking test, updated new tests

    @adair-nicolson
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  3. non-collinear test eigenvalue parsing

    @adair-nicolson
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  4. Update test name to reflect file name change

    @adair-nicolson
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  5. Set DefectEntry name during initialisation to avoid unnecessary gue… 

    …ssing before later resetting
    @kavanase
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  6. Add lru_cache for getting potcar stats for neutral nelect guessing,… 

    … to massively speed up charge state guessing
    @kavanase
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  7. Add get_magnetization_from_vasprun and get_nelect_from_vasprun fu… 

    …nctions to `doped.utils.parsing`
    @kavanase
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  8. Add band_edge_properties_from_vasprun and `make_perfect_band_edge_s… 

    …tate_from_vasp` functions to avoid need for `Outcar` with eigenvalue analysis functions
    @kavanase
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Commits on Mar 28, 2024

  1. Redefine _add_eigenvalues to make plotting with many kpoints and ba… 

    …nds much more efficient (~10 seconds -> 0.5 seconds)
    @kavanase
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  2. Expand eigenvalue tests

    @kavanase
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  3. Update tests and add data

    @kavanase
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  4. Update tests and add data pt. 2

    @kavanase
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  5. Update easyunfold requirement following release

    @kavanase
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  6. Update y-limits and legend behaviour, and add ylims and `legend_kwa… 

    …rgs` option for easy user customisation
    @kavanase
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  7. Update and expand tests

    @kavanase
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  8. Fix minor issue in displacements.py (wasn't accounting for disp dic… 

    …t reordering)
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  9. Add from_dict method for DefectEntry to avoid unnecessary `pydefe… 

    …ct` `INFO` messages
    @kavanase
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  10. gzip PROCARs and update tests now new easyunfold released

    @kavanase
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  11. Update default orb and energy similarity criteria from testing, w… 

    …ith dynamic handling and warning if needs be
    @kavanase
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  12. Minor docstrings updates, and use absolute paths in bulk_path/`defe… 

    …ct_path` so later loading of data works even if notebook moved
    @kavanase
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  13. Add orb/energy criterion customisation tests

    @kavanase
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  14. Update tips page

    @kavanase
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  15. Update advanced tutorial

    @kavanase
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  16. Update plotting customisation tutorial

    @kavanase
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  17. Update changelog and version number prior to release

    @kavanase
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  18. Minor paper updates

    @kavanase
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Commits on Mar 29, 2024

  1. Minor updates

    @kavanase
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  2. Analysis tests cleanup

    @kavanase
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Commits on Mar 30, 2024

  1. Make vasprun projected eigenvalue parsing marginally more efficient, … 

    …and avoid logging info messages
    @kavanase
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  2. Update default parsing behaviour; parse from vaspruns preferentially … 

    …as speed mostly the same as PROCAR parsing now, and more accurate/easier
    @kavanase
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  3. Update tests (mostly there...)

    @kavanase
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  4. Updated test for some file combinations.

    @adair-nicolson
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  5. Revert "Updated test for some file combinations." 

    This reverts commit eaa8478.
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  6. Make vasprun parsing a bit more efficient, avoiding unnecessary parsi… 

    …ng of DOS
    @kavanase
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  7. Update eigenvalue tests, use same vasprun.xml/PROCAR JSONs but ac… 

    …count for small numerical differences
    @kavanase
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  8. Reduce testing redundancy

    @kavanase
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  9. Minor TODO and CHANGELOG updates

    @kavanase
    kavanase committed Mar 30, 2024
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