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Addition of JDFTx code #955

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Commits on Jul 12, 2024

  1. initial jdft sets commit

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Commits on Jul 16, 2024

  1. adding sets, jobs, pymatge/io and emmet skeleton files

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Commits on Jul 26, 2024

  1. JDFTx infile parser v1

    @jacobclary
    jacobclary committed Jul 26, 2024
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  2. add JDFTXOutfile parser v1

    @jacobclary
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Commits on Aug 1, 2024

  1. Merge pull request #1 from cote3804/jdftx_parsers 

    JDFTx infile parser v1
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  2. Merge pull request #2 from cote3804/jdft_sets 

    Jdft sets
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Commits on Aug 3, 2024

  1. add example jdftx input files

    @jacobclary
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  2. Merge pull request #3 from cote3804/jdftx_parsers 

    add example jdftx input files
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  3. Merge pull request #4 from cote3804/jdft_sets 

    Merging sets with update example inputs from Jacob
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Commits on Aug 6, 2024

  1. JdftxInputGenerator works from added BaseJdftxSet.yaml

    @cote3804
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  2. Merge pull request #5 from cote3804/jdftx_parsers 

    JdftxInputGenerator works from added BaseJdftxSet.yaml
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Commits on Aug 9, 2024

  1. Initial commit for emmet work

    @cote3804
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  2. Merge pull request #6 from cote3804/emmet 

    Emmet
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Commits on Aug 12, 2024

  1. very simple base script

    @soge8904
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Commits on Aug 13, 2024

  1. Merge pull request #7 from cote3804/jdft_sets 

    very simple base script
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Commits on Sep 3, 2024

  1. empty init

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  2. empty init - these testchecks will have to be migrated over to pymatg… 

    …en once the io functions are migrated there
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  3. example files to use for io testchecking

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  4. Jobs.py uses Custodian's Job class and should be stored there when re… 

    …ady. It takes a .in file and runs the jdftx calculation using a command (Docker command is used atm) and outputs an out file and any requested output. Example and testing are in sample-move-later folder.
    @soge8904
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  5. first testcheck (putting a pin in this to deal with a greater problem)

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  6. Changing reference to "data" module for outside references

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  7. first working test

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Commits on Sep 4, 2024

  1. Merge branch 'main' into jdft_sets

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  2. Merge pull request #8 from cote3804/jdft_sets 

    Initial Jobs scripts via custodian
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  3. moving known values to a comparison dict

    @benrich37
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  4. updates

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  5. Addede schemas and new JDFTXOutfile methods

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  6. Merge pull request #9 from cote3804/emmet 

    Addede schemas and new JDFTXOutfile methods
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  7. updating before merge

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  8. Merge remote-tracking branch 'origin' into io_testchecks

    @benrich37
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  9. Merge branch 'materialsproject:main' into main

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  10. functionalization of outfile reader

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  11. Merge remote-tracking branch 'origin' into io_testchecks

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  12. syntax changes mostly

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  13. Merge branch 'materialsproject:main' into jdft_sets

    @soge8904
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  14. This was working, and now its not. I'm not sure how it was finding th… 

    …is line that doesn't exist before
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  15. Prefix is able to be None if not set in JDFTx

    @benrich37
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  16. Class method for getting the pp type - it assumes either "GBRV" or "S… 

    …G15" appears in the file path of the pseudo file. If both appear, it chooses whichever appears later in the path. If neither, raises value error
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  17. Baby steps into getting class functions to set instance variables

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  18. import fix

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Commits on Sep 5, 2024

  1. Moved code collecting data from lines read from pseudopotential into … 

    …self._set_pseudo_vars, which will eventually be able to fill the same fields for GBRV pseudopotentials
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  2. copy pasting here for now, will eeventually move important functions … 

    …over for trajectory builder
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  3. PSYCH doing it rn (shoutout refactoring)

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  4. implementing run.py

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  5. Updating out_to_log functions to take that "text" list of str instead… 

    … of the out file path, as well as some typing updates
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  6. Collection of class objects for (relatively) flexible storing of conv… 

    …ergence data
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  7. Updated testing

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Commits on Sep 6, 2024

  1. Organization + typing

    @benrich37
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  2. Moving JEiters test to test_JEiters.py

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  3. taking a leap of faith on forces units

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  4. Staging to pour one out for JAtoms

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  5. Restructuring for convergence info to only be held be JEiters, not an… 

    … individual JEiter
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  6. Restructuring for convergence info to only be held by JEiters, not an… 

    … individual JEiter
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  7. Can't think of anything else to test for this suite of classes

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  8. Adding to eventually replace read_file to remove io time spent on ana… 

    …lyzing an irrelevant out file slice
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  9. Adding JStructures class super to List to be a list of JStructure

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Commits on Sep 7, 2024

  1. Fixing super init

    @benrich37
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  2. typo

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  3. new files to use for testing

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  4. This might be overkill but creating class series for storing input se… 

    …ttings of different minimization stuff
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  5. Set the generic settings types upon init

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  6. Functionalizing existing operations within "from_file" - there's a lo… 

    …t of redundancy here now with the jstrucs but I'm keeping it becuase I'm not 100% sure what the existing code is doing yet
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  7. Commenting this out for now - need to talk to Cooper to discuss

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  8. Made changes to base.py to get it to write input 

    file and run jdftx. It returns a jobflow Response.
Unittest_BaseJdftxMaker.py is a unit test that was
used to test BaseJdftxMaker and passed.
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  9. Docustrings for JStructures suite

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  10. test checks for GC optimizations

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  11. Comment on deprecation

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  12. Updated docustrings (got the format wrong) + changed _set_Nbands's me… 

    …thod (previously assumed nbands was set to only the number of electrons in the calculation)
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  13. docustrings

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  14. Consistent indentation

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  15. No longer using the old out_to_log functions

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  16. docustrings

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  17. Refactoring class objects to their own python file so my IDE stops st… 

    …uttering every 2 seconds
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  18. docustrings

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  19. Accidentally removed get_start_lines needed for read_outfile

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  20. Restructured JDFTXOutfile to be an inherited list of JDFTXOutfileSlic… 

    …e's (which is the same as JDFTXOutfile was but only initializes from an out file slice). All previous functionality is retained by calling and setting attributes to the most recent JDFTXOutfileSlice
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  21. Fixed imports to refer to full path (include atomate2)

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  22. Reorganize so that the helper class functions are at the end, and the… 

    … properties are at the top
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Commits on Sep 8, 2024

  1. Removing unused functions and imports

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  2. Removed comment block

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  3. Removed comment block

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  4. fixed import

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  5. Use jstrucs to get total_electrons

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  6. This shouldn't have been added

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  7. This should've been removed yesterday

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  8. Removing assumption of spin polarization

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  9. misc updates

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  10. Fixing inheritance so that inherited attributes refer to the last sli… 

    …ce instead of the default values
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  11. Choosing the fftgrid to be the first logged fftbox size - later logge… 

    …d box sizes are not indicative of dumped arrays in my experience
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  12. Realizing this value is in units Kelvin, not Hartrees

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  13. fixed expected ordering of lines in an SCF step log

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  14. example files with similar filename pattern

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  15. Satisfied for now

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  16. Renaming JStructure(s) to JOutStructure(s) to avoid confusion with JD… 

    …FTXStructure used in JDFTXInfile
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Commits on Sep 9, 2024

  1. All files seem to work together and do what expected to run a BEAST c… 

    …alculation. Need to get TaskDoc to integrate with jobflow
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  2. Merge branch 'materialsproject:main' into jdft_sets

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  3. merge conflicts resolved with jdft_sets

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  4. Merge branch 'main' into io_testchecks

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  5. Merge pull request #11 from cote3804/io_testchecks 

    Io testchecks
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  6. adding these real quick before pulling main into this branch

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  7. Merge branch 'io_testchecks' of https://github.com/cote3804/atomate2 … 

    …into io_testchecks
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  8. Talked to Jacob - these lines were indeed typos.

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  9. removing unused import

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  10. This line is needed

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  11. for debugging

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  12. storing for now

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  13. Merge branch 'main' into io_testchecks

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  14. Merge pull request #12 from cote3804/io_testchecks 

    Io testchecks
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Commits on Sep 10, 2024

  1. renamed emmet to schemas and finished initial Calculation schema

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  2. Initial TaskDoc completed with from_directory() method implemented

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  3. Merge branch 'emmet'

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  4. Merge branch 'main' of github.com:cote3804/atomate2

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  5. fixed Status doc import

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  6. added jdftx_job wrapper and should_stop_children function as well as … 

    …cleaned up some imports
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  7. removed ASE dependency and fixed import paths in JDFTXOutfileSlice an… 

    …d JOutStructures.py
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  8. wrapped make method of BaseJdftxMaker in jdftx_job()

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  9. fixed imports + added t_s property to JDFTXOutfile

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  10. just committing for less work

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  11. Merge pull request #14 from cote3804/io_testchecks 

    Added t_s property to JDFTXOutfile
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  12. testing to make sure iter_type is defined correctly

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  13. using example_sp.out's beginning lines as a complete in file (all tag… 

    …s and optional arguments written)
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  14. Merge remote-tracking branch 'origin/main' into io_testchecks

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  15. Changing TagContainer's "read" class function to return a list within… 

    … the subdict values where the subtag is allowed to repeat (fixed to get OrthoOrbital subtag to work for density-of-states)
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Commits on Sep 11, 2024

  1. replaced open with zopen and converted os.path to pathlib operations

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  2. made dump-name jdftx. for BaseJdftxSet.yaml

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  3. wrote condense_jdftxinputs() to merge structure and inputs to one jdf… 

    …txinputs class
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  4. cleaning up files to get job to run on Perlmutter

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  5. Merge branch 'main' into emmet

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  6. Merge pull request #15 from cote3804/emmet 

    Changes to get to functional run on Perlmutter
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  7. Fixes from trying to read example_sp.in

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  8. Fixes to old assumptions broken by problem1.out example out file

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  9. Merge pull request #16 from cote3804/io_testchecks 

    Assumption fixes
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  10. Nervous because this file isn't supposed to be edited

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  11. HUGE strides wrt fixing the infile parser (multiformattag was calling… 

    … _write instead of write after getting the right format option which was making everything write as a dictionary, and small stuff here and there
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  12. passing self-consistency test-check now!

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  13. pre-commit changes + jobs/sets changes (deleted jobs.py bc went to cu… 

    …stodian)
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  14. Merge branch 'main' of https://github.com/cote3804/atomate2

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  15. misc

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  16. pre-commit changes

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  17. more pre-commit

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  18. Pushing small restructure of Outfile paser

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  19. Merge branch 'main' into io_testchecks

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  20. Merge pull request #17 from cote3804/io_testchecks 

    JDFTXOutfile restructure
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  21. Removed stray quotation mark

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  22. Restructuring JOutStructures to no longer inherit JOutStructure (shou… 

    …ld inherit Trajectory, but that would require a ton of work so that the metadata of a JOutStructure is not cleared on initialization so it just inherits list for now)
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  23. Restructured inheritance of JEiters for better IDE access of class va… 

    …riables
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  24. not a real dump var

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  25. Fixing refdrences to include

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Commits on Sep 12, 2024

  1. Adding "built-in" functions so outfile acts like a list

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  2. heartbreaking accidental re-use of variable name

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  3. Added known value test to testchecks

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  4. Removing commented out old code, starting change to snake case

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  5. converting modules to snake case

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  6. pep8 nonsense

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  7. Merge branch 'materialsproject:main' into jdftx_parsers

    @jacobclary
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  8. temporary fix for initial-magnetic-moments tag

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  9. Merge branch 'jdftx_parsers' of https://github.com/cote3804/atomate2 … 

    …into jdftx_parsers
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  10. Merge branch 'main' into jdftx_parsers

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  11. Merge pull request #18 from cote3804/jdftx_parsers 

    Merging changes to make magnetic moments tag compliant with subclass methods being the same as parent class. Kept Ben's read()
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  12. pre-commit changes on schemas

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  13. Merge branch 'main' into io_testchecks

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  14. Merge pull request #19 from cote3804/io_testchecks 

    RENAMING MODULES
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  15. more minor schema changes

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  16. minor schema changes

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  17. jobs/base.py import fixes

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  18. merged main to emmet

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  19. removed unused core schemas folder

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  20. Added JDFTX_CMD to settings.py

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  21. Fixed JDFTX_CMD typo

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  22. Fixed JDFTX_CMD description

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  23. PEP8 reformatting + adding full DFT functional options in jdftxinfile… 

    …_ref_options.py
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  24. Moved common deepcopy tag containers to jdftxinfile_ref_options

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  25. added deepcopy to references to func options lists

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  26. Renaming elec_ec_corr_func... to func... for line lengths + PEP8

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  27. PEP8

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  28. Now passes pre-commit

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  29. PEP8 fix for JEiters requires restructuring. No longer inherits JEite… 

    …r nor list and is just its own class. Likely going to be doing the same for higher up classes.
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  30. Renaming to snake case (pytest files are modules apparently)

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  31. snake case test functions too

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  32. PEP8

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  33. Moving global functions to a helper module

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  34. sacrificial commit to pre-commit gods - not much restructuring here a… 

    …ctually
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Commits on Sep 13, 2024

  1. minimal pre-commit sacrifices

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  2. updates for pre-commit - putting a pin in this for now

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  3. removed unused code from task.py in schemas

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  4. minor schema changes

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  5. set default filenames in files.py

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  6. pre-commit adjustments

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Commits on Sep 14, 2024

  1. Partial satisfaction of pre-commit

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  2. Merge pull request #20 from cote3804/io_testchecks 

    Partial pre-commit satisfaction
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  3. fixed FILE_NAMES sircular import by moving from files to sets/base.py

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  4. Merge branch 'main' into emmet 

    merging parser changes
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  5. Incomplete import

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Commits on Sep 16, 2024

  1. working on vasp sets bc cp2k not working

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  2. Working on tests so making changes to vasp and 

    cp2k tests.
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Commits on Sep 17, 2024

  1. Merge branch 'main' of https://github.com/cote3804/atomate2 into tests

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  2. Issues with parser and 'freq' tag. Committing to give acces to Ben.

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  3. minor changes to set filename conventions

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  4. Merge pull request #21 from cote3804/emmet 

    Made changes across sets, jobs and schemas
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  5. Merge branch 'main' of https://github.com/cote3804/atomate2 into tests

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  6. Pushing to update changes. Need to finish check_input in conftest but… 

    … works for now
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Commits on Sep 18, 2024

  1. test_core_new.py works with conftest.py. _conftest_old.py is just to … 

    …try some things and can be deleted. The next thing to do is to get the name from CURRENT_JOB.job.name instead of hardcoding it into conftest.py.
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Commits on Sep 22, 2024

  1. Finished updating JDFTx conftest.py and jobs test_core.py

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Commits on Sep 26, 2024

  1. final core tests

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Commits on Sep 29, 2024

  1. Changed imports to pymatgen io.

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  2. pre-commit changes on test scripts

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  3. .

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  4. Merge pull request #22 from cote3804/tests 

    Tests
    @soge8904
    soge8904 authored Sep 29, 2024
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