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STM settings as warg to the to_stm method of the PartialCharge class #158

Merged
merged 68 commits into from
Jun 18, 2024
Merged

STM settings as warg to the to_stm method of the PartialCharge class #158

merged 68 commits into from
Jun 18, 2024

Commits on Feb 13, 2024

  1. started to implement partial charges.

    @MichaelWolloch
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  2. Merge remote-tracking branch 'origin/master' into partial_charges_and… 

    …_STM

# Conflicts:
#	src/py4vasp/_raw/data.py
#	src/py4vasp/_raw/definition.py
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  3. Merge remote-tracking branch 'origin/master' into partial_charges_and… 

    …_STM
    @MichaelWolloch
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Commits on Feb 26, 2024

  1. Small typo fixed in the schema, added 'partial_charge' to the __init_… 

    …_.py in calculation.
    @MichaelWolloch
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Commits on Feb 28, 2024

  1. Merge branch 'vasp-dev:master' into partial_charges_and_STM

    @MichaelWolloch
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  2. first version of partial_charge class. Still no tests.

    @MichaelWolloch
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  3. running black and isort

    @MichaelWolloch
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Commits on Mar 1, 2024

  1. Cleaned up the STM_data class. 

    cleaned up plotting a bit. Added unit tests (not for plotting)
    @MichaelWolloch
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  2. Adding the unit tests for real now...

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Commits on Mar 5, 2024

  1. Slight cleanup, added docstrings, and a couple more tests.

    @MichaelWolloch
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Commits on Mar 7, 2024

  1. changed current units to nA and constant current no outputs correct h… 

    …eights over the surface layer instead of arbitrary units.
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Commits on Mar 11, 2024

  1. Fixed test for constant-current after changing the input units.

    @MichaelWolloch
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Commits on Mar 12, 2024

  1. Add basic Contour class 

    intended for plotting heatmaps and contour plots
    @martin-schlipf
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  2. Add Contour to Graph infrastructure

    @martin-schlipf
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  3. Implement basic rectangular heatmap

    @martin-schlipf
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  4. Implement supercell for Heatmap

    @martin-schlipf
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  5. Add label from Contour to plotly figure 

    Note that plotly does not show this label at the moment
    @martin-schlipf
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  6. Hide axes if only Contour are present

    @martin-schlipf
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  7. Implement interpolation

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  8. Put schema and dataclass in alphabetical order.

    @MichaelWolloch
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  9. Removed old plotting and implemented graph.Graph. 

    Got rid of all attributes and put settings in dataclass.

Also added correct py4vasp errors.
    @MichaelWolloch
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  10. Implement drawing the unit cell

    @martin-schlipf
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  11. Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

    @MichaelWolloch
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Commits on Mar 13, 2024

  1. Fix transpose of data w.r.t. plotly

    @martin-schlipf
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  2. Make plot look prettier by using same scale for axes 

    Also shift the centers of the points to align with the data
    @martin-schlipf
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  3. Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

    @MichaelWolloch
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  4. Fix plotting supercell with interpolation

    @martin-schlipf
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  5. Choose different default colorscale

    @martin-schlipf
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  6. Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

    @MichaelWolloch
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  7. Fixed bug with passing also z component of first two lattice vectors … 

    …and fixed the tests that asserted this wrongly.
    @MichaelWolloch
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  8. fixed test as well

    @MichaelWolloch
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  9. removed testing functions

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Commits on Mar 14, 2024

  1. Add documentation to Contour class

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  2. Introduce a base class to define the API Graph uses

    @martin-schlipf
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  3. Add test combining Contour and Series 

    The axes should be present if that is the case
    @martin-schlipf
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  4. Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

    @MichaelWolloch
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  5. set the height of contour plots to 500 to make STM pics larger

    @MichaelWolloch
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  6. Fix formatting

    @martin-schlipf
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  7. Rename mode to selection for consistency with other classes 

    Do not allow spaces in selection since this is not allowed in other
choices either
    @martin-schlipf
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  8. Remove undocumented/untested squeeze option from read

    @martin-schlipf
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  9. Make STM settings immutable

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  10. Use select Tree for selection in partial charge

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  11. Rename to_array -> to_numpy and use selection instead of spin

    @martin-schlipf
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  12. Refactor to make code more compact

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Commits on Mar 15, 2024

  1. Refactor partial charge

    @martin-schlipf
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  2. Refactor spline construction

    @martin-schlipf
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  3. Refactor test

    @martin-schlipf
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  4. Fix data access decorators

    @martin-schlipf
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  5. Capitalize STM

    @martin-schlipf
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  6. Update dependencies for scipy

    @martin-schlipf
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  7. Make scipy optional

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Commits on Mar 20, 2024

  1. corrected format label for constant current scans.

    @MichaelWolloch
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Commits on Apr 12, 2024

  1. now printing current in nA. Had forget to change that in the tests.

    @MichaelWolloch
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Commits on May 15, 2024

  1. Changed the implementation so that also non-orthogonal z-axis are all… 

    …owed.

Also made sure that strange fractional coordinates (e.g. -2.234) are correctly mapped between 0 and 1.

For constant current mode, the smoothed charge density is now also rolled in a way that values on both sides of the unit cell boarders are possible.

Tests were updated, but I still need to double check if the STM pictures are actually correct in some edge cases.
    @MichaelWolloch
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Commits on May 16, 2024

  1. Merge remote-tracking branch 'origin/master' into partial_charges_and… 

    …_STM

# Conflicts:
#	core/poetry.lock
#	poetry.lock
    @MichaelWolloch
    MichaelWolloch committed May 16, 2024
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  2. fixes of merge conflicts

    @MichaelWolloch
    MichaelWolloch committed May 16, 2024
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  3. fixed lattice plane passing to contour and updated tests accordingly

    @MichaelWolloch
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  4. updated cc height difference to be measured in Angstrom; relative to … 

    …lowest spot, not surface, which is a bit harder to get right for all cases...
    @MichaelWolloch
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  5. fixed poetry.lock that I apparently broke at some point

    @MichaelWolloch
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Commits on May 17, 2024

  1. Using keyword only arguments for tip_height, current, and supercell a… 

    …rguments

Co-authored-by: Martin Schlipf <[email protected]>
    @MichaelWolloch @martin-schlipf
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  2. Remove commented out old version of getting STM plane 

    Co-authored-by: Martin Schlipf <[email protected]>
    @MichaelWolloch @martin-schlipf
    MichaelWolloch and martin-schlipf authored May 17, 2024
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Commits on May 21, 2024

  1. made STM_settings a keyword argument to the to_stm method, so the set… 

    …tings can be changed by the user.
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Commits on May 24, 2024

  1. re-added the stm_settings property

    @MichaelWolloch
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Commits on Jun 18, 2024

  1. small cleanup

    @MichaelWolloch
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  2. fixed mutability of stm settings and tests. apparently broke constant… 

    … current mode. still need to attach settings to graph object.
    @MichaelWolloch
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  3. formatting

    @MichaelWolloch
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  4. formatting

    @MichaelWolloch
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  5. Prevent calling optional scipy in conftest.py

    @martin-schlipf
    martin-schlipf authored Jun 18, 2024
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