Partial charges and stm #144
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…_STM # Conflicts: # src/py4vasp/_raw/data.py # src/py4vasp/_raw/definition.py
…_.py in calculation.
cleaned up plotting a bit. Added unit tests (not for plotting)
…eights over the surface layer instead of arbitrary units.
intended for plotting heatmaps and contour plots
Note that plotly does not show this label at the moment
Got rid of all attributes and put settings in dataclass. Also added correct py4vasp errors.
Also shift the centers of the points to align with the data
…and fixed the tests that asserted this wrongly.
The axes should be present if that is the case
Do not allow spaces in selection since this is not allowed in other choices either
…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.
…_STM # Conflicts: # core/poetry.lock # poetry.lock
…lowest spot, not surface, which is a bit harder to get right for all cases...
…rguments Co-authored-by: Martin Schlipf <martin.schlipf@gmail.com>
Co-authored-by: Martin Schlipf <martin.schlipf@gmail.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Implements the handling of partial charge densities and the simulation of constant-height and constant-current STM images in the Tersoff-Hamann approximation.
Plotting of the STM is still a prototype and should be moved to a different module for plotting contours and heat-maps.
Branch 735 of the VASP code will need to be merged to write partial charges to hdf5, which will probably happen in 6.5