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DOC: Plasticity documentation update #188

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merged 13 commits into from
Nov 6, 2023

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pgrigorev
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This is a merge request to answer comments in the JOSS review

Avoid cell timeout during documentation build
@pgrigorev pgrigorev marked this pull request as draft October 18, 2023 18:01
Implemented coloring by ovito Identify diamond structure modifier
hiding initial component works better than deleting it for the centering of the view.
@pgrigorev
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I made the updates to address the issues in the JOSS review:

  • Added Installation and testing section in plasticity documentation explaining why most of the tests are skipped.
  • Added examples how to create dislocations in FCC and Diamond Cubic structures.

On top of that I improved the the interactive visualisation to colour the atoms according to crystallographic structures identified by CNA from OVITO. I also managed to modify the info displayed on mouse hover to make it more meaningful. At the moment it is in the file in the docs/applications folder. If this is useful I could put it in matscipy.visualise.py for example.

It seems a bit confusing to try to find documentation for matscipy. If I google matscipy documentation together with updated page on https://libatoms.github.io/matscipy/ I get outdated https://libatoms.github.io/matscipy/matscipy.html and also something on readthedocs: https://matscipy.readthedocs.io/en/latest/. Could we get rid of outdated pages?

@pgrigorev pgrigorev marked this pull request as ready for review November 3, 2023 22:24
@pgrigorev pgrigorev changed the title WIP: Plasticity documentation update DOC: Plasticity documentation update Nov 3, 2023
@jameskermode
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Thank you! The failing CI should be fixed by #198 and is unrelated to changes here so I'll go ahead and merge this now so that #193 can progress.

@jameskermode jameskermode merged commit f96008c into libAtoms:master Nov 6, 2023
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2 participants