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add support for XYZ files #1

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7 tasks done
joshkamm opened this issue Oct 21, 2023 · 0 comments · May be fixed by stokeware-org/FLOUR#13
Open
7 tasks done

add support for XYZ files #1

joshkamm opened this issue Oct 21, 2023 · 0 comments · May be fixed by stokeware-org/FLOUR#13
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@joshkamm

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joshkamm commented Oct 21, 2023 •
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Creating space to tinker around with something when I don't have energy to work on other things.

Todo list:

  • Read multiple XYZ structures from the same file
  • Write multiple XYZ structures to the same file
  • Try out just (winget?) -> wasn't trivial to setup, so could try again later
  • Benchmarks
  • Update python interface (.pyi) file
  • Try running github actions -> it seems like they require secrets from the upstream repo
  • Write a draft PR
@joshkamm joshkamm self-assigned this Oct 21, 2023
joshkamm added a commit that referenced this issue Oct 21, 2023
@joshkamm
wip #1 start test_xyz
7e6a6d3
joshkamm added a commit that referenced this issue Oct 23, 2023
@joshkamm
wip #1 create rust method stub for write_xyz
61cd085
joshkamm added a commit that referenced this issue Oct 24, 2023
@joshkamm
wip #1 read in elements from python list
791475d
joshkamm added a commit that referenced this issue Oct 28, 2023
@joshkamm
wip #1 implementing header in write_xyz
7af3bc9
joshkamm added a commit that referenced this issue Oct 31, 2023
@joshkamm
wip #1 write atomic positions
804fc1c
joshkamm added a commit that referenced this issue Nov 7, 2023
@joshkamm
wip #1 prepping to read XYZ files
c0ddac9
joshkamm added a commit that referenced this issue Nov 8, 2023
@joshkamm
wip #1 experimenting with types in return values
8e6ed28
joshkamm added a commit that referenced this issue Nov 9, 2023
@joshkamm
wip #1 reading in first line of XYZ file
af3c465
joshkamm added a commit that referenced this issue Nov 10, 2023
@joshkamm
wip #1 read comment line
53e4532
joshkamm added a commit that referenced this issue Nov 13, 2023
@joshkamm
wip #1 read positions of XYZ file
caa4c64
joshkamm added a commit that referenced this issue Nov 14, 2023
@joshkamm
wip #1 reading entire XYZ structure
09e6e4b 
able to read elements now
joshkamm added a commit that referenced this issue Dec 2, 2023
@joshkamm
wip #1 added support for reading multiple xyz's
da1c9f5
joshkamm added a commit that referenced this issue Dec 3, 2023
@joshkamm
wip #1 make XyzData class accessible from python
8a689c2
joshkamm added a commit that referenced this issue Dec 4, 2023
@joshkamm
wip #1 write multiple XYZ structures
0cbfb8f 
I'm unsure whether what I did with references and the GIL to get the
rust side to compile is sound and idomatic but it does pass my simple
tests.
joshkamm added a commit that referenced this issue Dec 4, 2023
@joshkamm
wip #1 cleanup
4db2d68
joshkamm added a commit that referenced this issue Dec 11, 2023
@joshkamm
wip #1 adding xyz file benchmarks
1c9e102
joshkamm added a commit that referenced this issue Dec 16, 2023
@joshkamm
wip #1 add type hint .pyi entries for XYZ functions
4cf70cd
@joshkamm joshkamm linked a pull request Dec 18, 2023 that will close this issue
Draft
3 tasks
joshkamm added a commit that referenced this issue Dec 31, 2023
@joshkamm
wip #1 use while let loop
c223a14
joshkamm added a commit that referenced this issue Jan 1, 2024
@joshkamm
wip #1 refactor to fixture in benchmarks
ee3626c
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Add XYZ file support joshkamm/FLOUR
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