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Soc PROCAR handling and more #28

Merged
merged 139 commits into from
Aug 10, 2023
Merged

Soc PROCAR handling and more #28

merged 139 commits into from
Aug 10, 2023

Commits on Jun 26, 2023

  1. Update docs main page

    @kavanase
    kavanase committed Jun 26, 2023
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  2. Update README.md

    @kavanase
    kavanase committed Jun 26, 2023
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  3. Add -h CLI help options

    @kavanase
    kavanase committed Jun 26, 2023
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  4. yapf formatting

    @kavanase
    kavanase committed Jun 26, 2023
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  5. Update Guide docs

    @kavanase
    kavanase committed Jun 26, 2023
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  6. Update NaBiS2 figure to have title centred

    @kavanase
    kavanase committed Jun 26, 2023
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  7. Update atom-projected NaBiS2 figures to have titles centred

    @kavanase
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  8. Refactor Guide to Tutorial as this is more recognisable to people… 

    … in the field (otherwise most will skip to the examples)
    @kavanase
    kavanase committed Jun 26, 2023
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  9. Update publications.md

    @kavanase
    kavanase committed Jun 26, 2023
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  10. Update theory.md

    @kavanase
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  11. Add links to Theory page

    @kavanase
    kavanase committed Jun 26, 2023
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  12. Update Installation docs page

    @kavanase
    kavanase committed Jun 26, 2023
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  13. Recentre Si222 images

    @kavanase
    kavanase committed Jun 26, 2023
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  14. Fix typos and make output more informative

    @kavanase
    kavanase committed Jun 26, 2023
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  15. Add symlinked README.mds for the other examples as well as Si222

    @kavanase
    kavanase committed Jun 26, 2023
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  16. Update Si222 docs example

    @kavanase
    kavanase committed Jun 26, 2023
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  17. Update Si CASTEP docs example

    @kavanase
    kavanase committed Jun 26, 2023
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  18. Update MgO docs example

    @kavanase
    kavanase committed Jun 26, 2023
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  19. Fix colors/cmap handling and docstrings

    @kavanase
    kavanase committed Jun 26, 2023
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  20. Update NaBiS2 example

    @kavanase
    kavanase committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. Merge updates

    @kavanase
    kavanase committed Jun 27, 2023
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  2. Add .DS_Store to gitignore

    @kavanase
    kavanase committed Jun 27, 2023
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  3. Refactor vscale to colour-norm and update help message/docstrings… 

    … as discussed in #10. Tested and works as expected
    @kavanase
    kavanase committed Jun 27, 2023
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  4. Parse PROCAR in current directory by default, and update help messa… 

    …ge accordingly. Tested and works as expected
    @kavanase
    kavanase committed Jun 27, 2023
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  5. Add --atoms option (and corresponding functions) to just specify wh… 

    …ich atoms to project (rather than `atoms_idx`), by reading from POSCAR/CONTCAR. Tested and works as expected. Avoids using `pymatgen` as a dependency also. Will update examples to show this functionality
    @kavanase
    kavanase committed Jun 27, 2023
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  6. Remove completed TODO

    @kavanase
    kavanase committed Jun 27, 2023
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  7. Consolidate colour_norm (formerly vscale) and intensity as they… 

    … do the same thing just in different plotting functions (which depends on whether `--combined` is used). Tested and all works as expected
    @kavanase
    kavanase committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. Make ylim consistent between CLI and plotting module

    @kavanase
    kavanase committed Jun 28, 2023
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  2. Add DOS plotting functionality

    @kavanase
    kavanase committed Jun 28, 2023
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  3. Merge main

    @kavanase
    kavanase committed Jun 28, 2023
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  4. Refactor mpl-style-file to plot command options, as it's the only p… 

    …lace where it affects behaviour (and to avoid user confusion about having to place it after `unfold` but before `plot`)
    @kavanase
    kavanase committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. Update CLI

    @zhubonan
    zhubonan committed Jun 29, 2023
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  2. Clean up the time-reversal symmetry handling 

    Simplify the handling of the time-reversal symmetry
    @zhubonan
    zhubonan committed Jun 29, 2023
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Commits on Jul 2, 2023

  1. Add docstrings

    @kavanase
    kavanase committed Jul 2, 2023
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  2. Ignore unnecessary POTCAR warnings

    @kavanase
    kavanase committed Jul 2, 2023
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  3. Update help messages to be more informative

    @kavanase
    kavanase committed Jul 2, 2023
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  4. Consolidate DOS plot and projected plot colours

    @kavanase
    kavanase committed Jul 2, 2023
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  5. Colour different orbitals for the same atom as different shades of th… 

    …e specified colour
    @kavanase
    kavanase committed Jul 2, 2023
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Commits on Jul 3, 2023

  1. Update PROCAR handling to deal with setting just p or just d fo… 

    …r orbital projections (all directions)
    @kavanase
    kavanase committed Jul 3, 2023
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  2. Update CLI help messages

    @kavanase
    kavanase committed Jul 3, 2023
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  3. Match DOS elements and orbitals with atoms / orbitals options

    @kavanase
    kavanase committed Jul 3, 2023
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  4. Match DOS elements/orbitals with atoms/orbitals for non-projected… 

    … plot
    @kavanase
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  5. Allow non-projected plot to still specify atoms/atoms_idx and/or … 

    …`orbitals` in groups, rather than all as one (e.g. if we want to use weighting with s orbitals from one and p orbitals from a different group of atoms), and sum for the final spectral function plot
    @kavanase
    kavanase committed Jul 3, 2023
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  6. Update unfold docstrings to be more informative

    @kavanase
    kavanase committed Jul 3, 2023
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  7. Add multi-group orbital handling to parse_atoms()

    @kavanase
    kavanase committed Jul 3, 2023
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  8. Formatting

    @kavanase
    kavanase committed Jul 3, 2023
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  9. Handle colours/line-styles for _lm_-decomposed orbital contributions,… 

    … to match the colour projections on the bandstructure
    @kavanase
    kavanase committed Jul 3, 2023
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  10. Linting

    @kavanase
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  11. Ignore other POTCAR warnings

    @kavanase
    kavanase committed Jul 3, 2023
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  12. Update pre-commit requirements

    @kavanase
    kavanase committed Jul 3, 2023
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  13. Update sumo function calling for pylint

    @kavanase
    kavanase committed Jul 3, 2023
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  14. Add NaBiS2 directory test setup

    @kavanase
    kavanase committed Jul 3, 2023
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  15. Add help message option tests

    @kavanase
    kavanase committed Jul 3, 2023
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  16. Add NaBiS2 plotting tests, with all options

    @kavanase
    kavanase committed Jul 3, 2023
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  17. Formatting

    @kavanase
    kavanase committed Jul 3, 2023
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  18. Update tests

    @kavanase
    kavanase committed Jul 3, 2023
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  19. Fix sumo version

    @kavanase
    kavanase committed Jul 3, 2023
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Commits on Jul 4, 2023

  1. Handle older sumo version requirement

    @kavanase
    kavanase committed Jul 4, 2023
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  2. Formatting

    @kavanase
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  3. Add link to NaBiS2 customisation in Si example

    @kavanase
    kavanase committed Jul 4, 2023
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Commits on Jul 5, 2023

  1. Fix missing file link in tutorial

    @kavanase
    kavanase committed Jul 5, 2023
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  2. Update Si222 plots (first plots potential users will see, want them… 

    … looking decent)
    @kavanase
    kavanase committed Jul 5, 2023
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  3. Update MgO example figures, commands, docs (show recommended `--atoms… 

    …` rather than `--atoms-idx`)
    @kavanase
    kavanase committed Jul 5, 2023
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  4. Refactor colors to colours and formatting

    @kavanase
    kavanase committed Jul 5, 2023
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  5. Update NaBiS2 example with new --atoms option, and specific appli… 

    …cation of `--atoms-idx`
    @kavanase
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  6. Update sumo requirement

    @kavanase
    kavanase committed Jul 5, 2023
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  7. Add DOS plot example

    @kavanase
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  8. Relax sumo requirements

    @kavanase
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  9. Formatting

    @kavanase
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  10. Add atom-projected w/DOS example

    @kavanase
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  11. Add notes/warnings about sumo requirement for DOS plots and not to … 

    …use the `vasprun.xml` from GGA band structure calcs
    @kavanase
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Commits on Jul 7, 2023

  1. Handle case where user sets the same atom in different projection gro… 

    …upings, but with different orbitals
    @kavanase
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  2. Add orbital projected band structure with DOS example

    @kavanase
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  3. Add lm-decomposed orbital projected band structure with DOS example

    @kavanase
    kavanase committed Jul 7, 2023
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  4. Adjust figure sizing

    @kavanase
    kavanase committed Jul 7, 2023
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  5. Update handling of multiple atom-orbital combos with the same atomic … 

    …element for `unfold plot` (not projected)
    @kavanase
    kavanase committed Jul 7, 2023
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  6. Removed unused image

    @kavanase
    kavanase committed Jul 7, 2023
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  7. Refactor usages of Easyunfold to easyunfold (this is the canonica… 

    …l package name I believe?)
    @kavanase
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Commits on Jul 18, 2023

  1. Fix symprec help message

    @kavanase
    kavanase committed Jul 18, 2023
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  2. Hide --yes help option

    @kavanase
    kavanase committed Jul 18, 2023
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  3. Update tutorial to show the scf-kpoints option for hybrid DFT calcu… 

    …lations
    @kavanase
    kavanase committed Jul 18, 2023
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Commits on Jul 25, 2023

  1. Update tutorial to mention --gamma and --ncl options

    @kavanase
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Commits on Jul 29, 2023

  1. Move add_plot_options to just before plot commands (rather than b… 

    …efore `effective_mass` where it isn't used)
    @kavanase
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  2. Refactor mpl_style_option to a decorator to avoid code duplication … 

    …and allow it to be added as an option to `effective_mass`, `plot` and `plot-projections`
    @kavanase
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  3. Merge remote-tracking branch 'origin/pr-cli-update' into dos-plotting 

    # Conflicts:
#	easyunfold/cli.py
    @kavanase
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  4. Revert colour_norm to vscale

    @kavanase
    kavanase committed Jul 29, 2023
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  5. Fix intensity handling from #26

    @kavanase
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  6. Replace all instances of colour-norm/vscale in docs with recommen… 

    …ded `intensity` option
    @kavanase
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  7. Add poscar option to specify POSCAR file as requested, and add te… 

    …st for this
    @kavanase
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  8. Make shell files executable

    @kavanase
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  9. Add help messages and docstrings for --time-reversal, and remove `T… 

    …ODO`
    @kavanase
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  10. Update PROCAR handling to work for all LORBIT >= 11 and add test … 

    …for this
    @kavanase
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  11. Move if dos: block to separate function to avoid code duplication

    @kavanase
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  12. Refactor DOS plotter handling in plotting to separate function to a… 

    …void code duplication
    @kavanase
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  13. Bump version number before next major release with backwards-compatib… 

    …le DOS plotting and other additions
    @kavanase
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  14. pre-commit formatting

    @kavanase
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Commits on Jul 31, 2023

  1. Remove unused ncl and gamma CLI options from plot options (CLI pl… 

    …ot commands require WAVECARs to already have been parsed with `unfold calculate`, so these are just fluff options that do nothing)
    @kavanase
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  2. Overhaul PROCAR handling to handle and amalgamate multiple PROCAR… 

    …s in one `Procar` object. Means that previously-parsed kpoints are skipped (and not double counted), as well as some efficiency boosts and aided handling
    @kavanase
    kavanase committed Jul 31, 2023
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  3. Refactor other modules to updated PROCAR handling

    @kavanase
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  4. Dynamically determine whether PROCARs are SOC or not

    @kavanase
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  5. Make Procar object JSON serializable

    @kavanase
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  6. Add deprecation notice for vscale

    @kavanase
    kavanase committed Jul 31, 2023
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  7. Add notes about passing multiple --procar options for split `PROCAR… 

    …`s in docs
    @kavanase
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  8. Update test_procar() (Gamma point duplicated in k-point path so upd… 

    …ated parsing reduces nkpts from 48 to 47)
    @kavanase
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Commits on Aug 1, 2023

  1. Bump version number

    @kavanase
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  2. No ticks on DOS plots

    @kavanase
    kavanase committed Aug 1, 2023
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  3. Use sumo orbital colours in DOS plots (if not atom-projected plot)

    @kavanase
    kavanase committed Aug 1, 2023
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  4. Pre-commit formatting

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    kavanase committed Aug 1, 2023
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  5. Merge branch 'main' into SOC-procar-handling

    @kavanase
    kavanase authored Aug 1, 2023
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  6. Merge remote-tracking branch 'origin/SOC-procar-handling' into SOC-pr… 

    …ocar-handling
    @kavanase
    kavanase committed Aug 1, 2023
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  7. Pre-commit formatting

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    kavanase committed Aug 1, 2023
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Commits on Aug 5, 2023

  1. Code cleanup and efficiency

    @kavanase
    kavanase committed Aug 5, 2023
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  2. Fix weight normalisation

    @kavanase
    kavanase committed Aug 5, 2023
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  3. Add colourspace CLI option for plot-projected

    @kavanase
    kavanase committed Aug 5, 2023
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  4. Code cleanup

    @kavanase
    kavanase committed Aug 5, 2023
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  5. Code cleanup

    @kavanase
    kavanase committed Aug 5, 2023
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  6. Change default colour handling ("g" in matplotlib goes to (0,0.5,0) i… 

    …n RGB space which can give odd interpolation behaviour, so use RGB coordinates as defaults instead)
    @kavanase
    kavanase committed Aug 5, 2023
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  7. Renormalise final interpolated colours appropriately

    @kavanase
    kavanase committed Aug 5, 2023
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  8. Change default colorspace to xyz

    @kavanase
    kavanase committed Aug 5, 2023
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  9. Normalise PROCAR projections so the total orbital projection sums to … 

    …1 (this avoids cases where bands with delocalised contributions become very very faint just because there is less complete orbital basis set assignment to them in VASP, rather than actually having low spectral function intensity (still weighted by the actual spectral function intensity in the plot))
    @kavanase
    kavanase committed Aug 5, 2023
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  10. pre-commit formatting

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    kavanase committed Aug 5, 2023
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Commits on Aug 6, 2023

  1. Darken colour slightly if too white

    @kavanase
    kavanase committed Aug 6, 2023
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  2. Set default colours and colorspace to lablch (to be discussed)

    @kavanase
    kavanase committed Aug 6, 2023
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  3. Add and update tests

    @kavanase
    kavanase committed Aug 6, 2023
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  4. Update test

    @kavanase
    kavanase committed Aug 6, 2023
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Commits on Aug 7, 2023

  1. Default colourspace is LAB everywhere

    @kavanase
    kavanase committed Aug 7, 2023
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  2. Pre commit formatting

    @kavanase
    kavanase committed Aug 7, 2023
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  3. Update MgO projection plots

    @kavanase
    kavanase committed Aug 7, 2023
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  4. Update NaBiS2 projection plots

    @kavanase
    kavanase committed Aug 7, 2023
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  5. Add example outputs mini section

    @kavanase
    kavanase committed Aug 7, 2023
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Commits on Aug 8, 2023

  1. Pre-commit formatting

    @kavanase
    kavanase committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. Bump version number before next release

    @kavanase
    kavanase committed Aug 9, 2023
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  2. GitHub readme doesn't seem to work with symlinks?

    @kavanase
    kavanase committed Aug 9, 2023
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  3. Resize images

    @kavanase
    kavanase committed Aug 9, 2023
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  4. Update README.md

    @kavanase
    kavanase authored Aug 9, 2023
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  5. Subscript formatting

    @kavanase
    kavanase authored Aug 9, 2023
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  6. Subscript formatting

    @kavanase
    kavanase committed Aug 9, 2023
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  7. Merge remote-tracking branch 'origin/SOC-procar-handling' into SOC-pr… 

    …ocar-handling
    @kavanase
    kavanase committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. Remove with from _read method

    @kavanase
    kavanase committed Aug 10, 2023
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