Code

Partial charges and stm#144

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martin-schlipf merged 61 commits intovasp-dev:mastervasp-dev/py4vasp:masterfrom MichaelWolloch:partial_charges_and_STMMichaelWolloch/py4vasp:partial_charges_and_STMCopy head branch name to clipboardMay 17, 2024

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Commits

Commits on Feb 13, 2024

• started to implement partial charges.

  MichaelWolloch

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• Merge remote-tracking branch 'origin/master' into partial_charges_and_STM

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  MichaelWolloch

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• Merge remote-tracking branch 'origin/master' into partial_charges_and_STM

  MichaelWolloch

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Commits on Feb 26, 2024

• 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

• Merge branch 'vasp-dev:master' into partial_charges_and_STM

  MichaelWolloch

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• first version of partial_charge class. Still no tests.

  MichaelWolloch

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• running black and isort

  MichaelWolloch

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Commits on Mar 1, 2024

• Cleaned up the STM_data class.

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  MichaelWolloch

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• Adding the unit tests for real now...

  MichaelWolloch

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Commits on Mar 5, 2024

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

  MichaelWolloch

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Commits on Mar 7, 2024

• changed current units to nA and constant current no outputs correct heights over the surface layer instead of arbitrary units.

  MichaelWolloch

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Commits on Mar 11, 2024

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

  MichaelWolloch

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Commits on Mar 12, 2024

• Add basic Contour class

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  martin-schlipf

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• Add Contour to Graph infrastructure

  martin-schlipf

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• Implement basic rectangular heatmap

  martin-schlipf

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• Implement supercell for Heatmap

  martin-schlipf

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• Add label from Contour to plotly figure

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  martin-schlipf

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• Hide axes if only Contour are present

  martin-schlipf

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• Implement interpolation

  martin-schlipf

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• Put schema and dataclass in alphabetical order.

  MichaelWolloch

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• Removed old plotting and implemented graph.Graph.

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  MichaelWolloch

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• Implement drawing the unit cell

  martin-schlipf

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• Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

  MichaelWolloch

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Commits on Mar 13, 2024

• Fix transpose of data w.r.t. plotly

  martin-schlipf

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• Make plot look prettier by using same scale for axes

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  martin-schlipf

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• Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

  MichaelWolloch

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• Fix plotting supercell with interpolation

  martin-schlipf

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• Choose different default colorscale

  martin-schlipf

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• Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

  MichaelWolloch

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• 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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• fixed test as well

  MichaelWolloch

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• removed testing functions

  MichaelWolloch

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Commits on Mar 14, 2024

• Add documentation to Contour class

  martin-schlipf

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• Introduce a base class to define the API Graph uses

  martin-schlipf

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• Add test combining Contour and Series

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  martin-schlipf

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• Merge remote-tracking branch 'origin/stm' into partial_charges_and_STM

  MichaelWolloch

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• set the height of contour plots to 500 to make STM pics larger

  MichaelWolloch

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• Fix formatting

  martin-schlipf

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• Rename mode to selection for consistency with other classes

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  martin-schlipf

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• Remove undocumented/untested squeeze option from read

  martin-schlipf

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• Make STM settings immutable

  martin-schlipf

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• Use select Tree for selection in partial charge

  martin-schlipf

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• Rename to_array -> to_numpy and use selection instead of spin

  martin-schlipf

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• Refactor to make code more compact

  martin-schlipf

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Commits on Mar 15, 2024

• Refactor partial charge

  martin-schlipf

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• Refactor spline construction

  martin-schlipf

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• Refactor test

  martin-schlipf

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• Fix data access decorators

  martin-schlipf

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• Capitalize STM

  martin-schlipf

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• Update dependencies for scipy

  martin-schlipf

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• Make scipy optional

  martin-schlipf

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Commits on Mar 20, 2024

• corrected format label for constant current scans.

  MichaelWolloch

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Commits on Apr 12, 2024

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

  MichaelWolloch

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Commits on May 15, 2024

• Changed the implementation so that also non-orthogonal z-axis are allowed.

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  MichaelWolloch

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Commits on May 16, 2024

• Merge remote-tracking branch 'origin/master' into partial_charges_and_STM

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  MichaelWolloch

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• fixes of merge conflicts

  MichaelWolloch

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  e56f041

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• fixed lattice plane passing to contour and updated tests accordingly

  MichaelWolloch

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• 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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• fixed poetry.lock that I apparently broke at some point

  MichaelWolloch

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Commits on May 17, 2024

• Using keyword only arguments for tip_height, current, and supercell arguments

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  MichaelWolloch

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  martin-schlipf

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• Remove commented out old version of getting STM plane

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  MichaelWolloch

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  martin-schlipf

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