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Defect generation updates #133

Merged
merged 23 commits into from
Aug 13, 2023
Merged

Defect generation updates #133

merged 23 commits into from
Aug 13, 2023

Commits on Jun 19, 2023

  1. Pass VoronoiInterstitialGenerator parameters through to `Topography… 

    …Analyzer` (bugfix)
    @kavanase
    kavanase committed Jun 19, 2023
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  2. Pass min_dist from VoronoiInterstitialGenerator initialisation th… 

    …rough to `InterstitialGenerator` superclass (bugfix)
    @kavanase
    kavanase committed Jun 19, 2023
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  3. Refactor filter_colliding to return coords _and_ index, for correct… 

    … multiplicities (bugfix)
    @kavanase
    kavanase committed Jun 19, 2023
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  4. Refactor multiplicies to multiplicities (small typo)

    @kavanase
    kavanase committed Jun 19, 2023
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  5. Update type hint

    @kavanase
    kavanase committed Jun 19, 2023
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  6. Add equivalent_sites parameter to Defect objects and `target_frac… 

    …_coords` parameter to `get_supercell_structure` to allow choice of generated defect site in supercell
    @kavanase
    kavanase committed Jun 19, 2023
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  7. Add return_site option to get_supercell_structure (useful informa… 

    …tion!)
    @kavanase
    kavanase committed Jun 19, 2023
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Commits on Jun 22, 2023

  1. Update supercell site setting for dummy species as well

    @kavanase
    kavanase committed Jun 22, 2023
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Commits on Jun 25, 2023

  1. Automatically bump max_cell_range to 2 in TopographyAnalyzer if `… 

    …num_atoms < 5`, for accurate/complete Voronoi tessellation (small unit cells anyway so negligible cost!)
    @kavanase
    kavanase committed Jun 25, 2023
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  2. Use oxi_state of substituting specie in the host structure if prese… 

    …nt (when guessing oxi state of substitution defect) – i.e. antisite defects!
    @kavanase
    kavanase committed Jun 25, 2023
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Commits on Jul 14, 2023

  1. Merge remote-tracking branch 'origin/main' 

    # Conflicts:
#	pymatgen/analysis/defects/generators.py
    @kavanase
    kavanase committed Jul 14, 2023
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  2. Add target_frac_coords and return_site to DefectComplex `get_su… 

    …percell_structure` to make compatible with supertype `Defect`
    @kavanase
    kavanase committed Jul 14, 2023
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  3. Linting

    @kavanase
    kavanase committed Jul 14, 2023
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Commits on Jul 30, 2023

  1. Comment cleanup

    @kavanase
    kavanase committed Jul 30, 2023
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Commits on Aug 5, 2023

  1. Also return list of equivalent supercell sites if return_sites set … 

    …to `True`
    @kavanase
    kavanase committed Aug 5, 2023
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Commits on Aug 8, 2023

  1. Merge branch 'main' into defect_generation_updates

    @kavanase
    kavanase authored Aug 8, 2023
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  2. Use self.site if self.equivalent_sites is empty

    @kavanase
    kavanase committed Aug 8, 2023
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  3. Merge remote-tracking branch 'origin/defect_generation_updates' into … 

    …defect_generation_updates
    @kavanase
    kavanase committed Aug 8, 2023
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  4. Make Defect.equivalent_sites match element symbol for Defect.site (ra… 

    …ther than Defect.defect_site) with `Substitution` defects
    @kavanase
    kavanase committed Aug 8, 2023
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  5. Fix typo

    @kavanase
    kavanase committed Aug 8, 2023
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Commits on Aug 12, 2023

  1. Remove oxidation states from defect supercell sites (as well as overa… 

    …ll returned structure)
    @kavanase
    kavanase committed Aug 12, 2023
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  2. Add tests for target_frac_coords with get_supercell_structure for… 

    … `Interstitial` and `Substitution`
    @kavanase
    kavanase committed Aug 12, 2023
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  3. Add test for oxidation state guessing with (antisite) substitution de… 

    …fects
    @kavanase
    kavanase committed Aug 12, 2023
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