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doped v2.1 #41

Merged
merged 99 commits into from
Nov 1, 2023
Merged

doped v2.1 #41

merged 99 commits into from
Nov 1, 2023

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kavanase
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@kavanase kavanase commented Nov 1, 2023

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@kavanase
Update paper list
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@kavanase
Ignore unnecessary unset_charge when saving/loading defect entries …
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…to json

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@kavanase
Ensure correct plotting style used in eFNV plots
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@kavanase
Update comments
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@kavanase
Comments and todos
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@kavanase
Update get_defect_name_from_entry to use symmop approach if possible
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@kavanase
Update closest_site_info to work with defect objects
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@kavanase
Add get_defect_name_from_defect function, use this in generation as…
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… quicker and test

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@kavanase
Update herm2sch to work with rearranged point group symbols from `s…
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…pglib`

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@kavanase
Add defect_name_from_structures function and add tests
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@kavanase
Add test for padding kwarg input
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@kavanase
Allow for case of neutral charge state being removed from `DefectsGen…
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…erator` and test

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@kavanase
Update to new FNV corrections code, with our own handling and plottin…
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…g functions

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@kavanase
Nice clean FNV correction plots
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@kavanase
Refactor Makov-Payne/Murphy-Hine/Lany-Zunger corrections to `legacy_c…
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…orrections` module

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@kavanase
Add updated kumagai and freysoldt correction methods and plotting
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@kavanase
Add verbose options for corrections functions
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@kavanase
Update todos
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@kavanase
Add todo
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@kavanase
Add todo
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@kavanase
Add doped_defect_from_pmg_defect function and ensure `closest_site_…
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…info` works with both `doped` and `pymatgen` Defect objects

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@kavanase
Add Xinwei paper to list
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@kavanase
Add todo and update some docstrings
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@kavanase
Run github tests on all platforms
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@kavanase
Remove max parallel constraint from GH Actions testing
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@kavanase
Update oxi state handling for rare elements with no tabulated ICSD va…
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…lues

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@kavanase
Add test for unknown oxi states
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@kavanase
Change show to get_plot in chempots example to avoid pymatgen `…
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…PDPlotter` bug

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@kavanase
Avoid site.properties selective_dynamics warning if user explicit…
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…ly set `T T T` in bulk

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@kavanase
Ensure sorted defect supercell structure returned
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kavanase added 28 commits October 29, 2023 16:11
@kavanase
Add FNV/eFNV plot customisation tests
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@kavanase
Add Kumagai error tolerance test
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@kavanase
Add Freysoldt error tolerance test
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@kavanase
Test returning correction errors
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@kavanase
Update and expand VASP tests
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@kavanase
Add tricky-interstitial test case for eFNV correction
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@kavanase
Use get_defect_name_from_defect if get_defect_name_from_entry fails
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@kavanase
Add test data
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@kavanase
Make VASP IO tests more verbose
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@kavanase
Reduced N-doped diamond defect gen file size, add to-do note
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@kavanase
Update formation_energy_table
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@kavanase
Update get_defect_name_from_entry, now can get point group symmetri…
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…es of _relaxed_ defect structures 🔥

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@kavanase
Update eFNV test to account for new example data
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@kavanase
Ensure plt.clf() so plotting tests don't depend on ordering
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@kavanase
Allow for user_potcar_settings to be None in DefectDictSet tests
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@kavanase
Avoid POTCAR warning when trying to guess defect charge state
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@kavanase
Add symprec option to get_wyckoff
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@kavanase
Fix chemical potentials error
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@kavanase
Avoid charge-state guessing in test_corrections if POTCARs not avai…
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…lable (to work on GH Actions), and INCAR writing/testing for charged defects if POTCARs not available (we through a `ValueError` for this)

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@kavanase
Update CdTe VASP file IO tests
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@kavanase
Update GH Actions plotting tests
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@kavanase
Tweak tests to work on GH Actions
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@kavanase
Bump changelog and version number before release
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@kavanase
Fix typo and rename test folder
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@kavanase
Make tests compatible with python=3.8 and account for rare site-match…
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…ing case with defective supercells used as input

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@kavanase
Update parsing tutorial with new correction plots
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@kavanase
Add sampling region shading to eFNV plots
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@kavanase
Add example formation energy table to tutorial
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@kavanase
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kavanase commented Nov 1, 2023

All tests passing on earlier runs, merging ✌️

@kavanase kavanase merged commit 22cc974 into master Nov 1, 2023
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