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[WIP] Cp2k and defects #242

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[WIP] Cp2k and defects #242

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nwinner
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@nwinner nwinner commented Aug 6, 2021

This PR adds basic functionality for building defect documents from tasks generated by the CP2K module in atomate.

Contributor Checklist

  • I have broken down my PR scope into the following TODO tasks
    • CP2K module added to emmet/core/cp2k
    • New DefectDoc and DefectThermoDoc added to emmet/core/defect
    • CP2K MaterialsBuilder added to emmet/builders/cp2k
    • CP2K DefectBuilder added to emmet/builders/cp2k
    • CP2K DefectThermoBuilder added to emmet/builders/cp2k
  • I have run the tests locally and they passed.
  • I have added tests, or extended existing tests, to cover any new features or bugs fixed in this PR

nwinner added 30 commits May 30, 2021 18:10
@nwinner
Very first committ of emmet supporting cp2k for defect calculations. …
dc3f263 
…Subject to much change.
@nwinner
Update.
38c10fc
@nwinner
Remove unecessary methods. Update condition.
5955cf5
@nwinner
Update to parameter getter.
bd17382
@nwinner
Clean imports and update doc.
4e96e06
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
665644f 
… cp2k

# Conflicts:
#	emmet-core/emmet/core/settings.py
@nwinner
CP2K settings.
cd814b9
@nwinner
Update imports. stubs gone
dce71e8
@nwinner
Fix imports. Stubs gone.
a3dd4b0
@nwinner
Clean imports
87a6286
@nwinner
Clean imports
9590dc9
@nwinner
Remove validator
9d2947f
@nwinner
Remove sandboxes
f6d3b79
@nwinner
Another log point
bc8f4af
@nwinner
Update to material doc
7bfec2b
@nwinner
Temporary MaterialsBuilder update. Some things are not implemented.
9833317
@nwinner
Some updates, subject to change, for the Defect builder.
c133909
@nwinner
Update for dielectric. Will need further adjustments.
f36f5d0
@nwinner
Cp2kTaskType. Should be unified?
35067ad
@nwinner
Store as int so MPID can work with it.
83a15bf
@nwinner
Use integers
ad48136
@nwinner
Move imports.
ccee065
@nwinner
Improved builders with private methods, more docstrings, and support
e731d28 
for updating existing docs without re-building.
@nwinner
New methods to update document without re-building the whole thing.
a5edc7b
@nwinner
Include BaseTaskDocument
5462795
@nwinner
(1) Reordered the imports.
a28ea14 
(2) Updated the update() method
@nwinner
Update query for defects and reorder imports.
2d36240
@nwinner
Extra log message.
4fd13c7
@nwinner
Update.
ae1698f 
builders/defects.py: use the defect object itself for matching
 after grouping by mpid

core/defect.py: store defect so that new builder works.
@nwinner
Add R2SCAN option
0b4b103
@nwinner
Updates and refinements.
f2b70e0
@nwinner
bug
f51ddd1
@nwinner
Updates
6a3a73b 
Updates to emmet as I work on integrating 2d defects. Fresysoldt sxdefectalign2d code cannot run on MacOS so I'll have to bounce back and force with the cluster to debug some of it.
@mkhorton
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mkhorton commented Mar 7, 2022

Sorry, as a first-time contributor to this repo, I have to manually approve the CI to get it to run. Thanks for the PR! I'm keeping an eye on it.

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mkhorton commented Mar 7, 2022

Let us know when you would like it to be reviewed.

@nwinner
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nwinner commented Mar 7, 2022

Hey Matt. Much like the other repos I modify, I make changes really actively. This one in particular I had to push because MacOS doesn't support a command line program that I'll need to add to the 2D builder. I can continue to push on this WIP, or I can close it until a few weeks from now when I resolve the problems so you don't get notified. Thoughts?

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mkhorton commented Mar 7, 2022

Being notified isn't a problem for me, no worries, do whatever's best for you.

@nwinner
Todos
c0c434e
@nwinner
Merge remote-tracking branch 'upstream/main' into cp2k
598f912
@nwinner
Versions
e6310e9
@nwinner
Import updates
182e820
@nwinner
Changes
9a9baac 
Fixing imports, some formatting problems, add Constrained Optimization
@nwinner
Updates
d53da01
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
f61a481 
… cp2k
@nwinner
Updates
a45100d
@nwinner
Possible additions
c12e5fc
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
30aebee 
… cp2k

# Conflicts:
#	emmet-builders/_version.py
#	emmet-core/_version.py
@nwinner
Update
80f6672
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
893b93a 
… cp2k

# Conflicts:
#	emmet-builders/emmet/builders/settings.py
@nwinner
Updates
bea2f86
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
8c44520 
… cp2k

# Conflicts:
#	emmet-builders/emmet/builders/vasp/materials.py
@nwinner
Merge branch 'main' of https://github.com/materialsproject/emmet into…
ff60417 
… cp2k

# Conflicts:
#	emmet-core/emmet/core/electronic_structure.py
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@nwinner @mkhorton