JDFTx IO module #4078
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JDFTx IO module #4078
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…and allowing some variables to remain None
…and allowing some variables to remain None
…and allowing some variables to remain None
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Thanks @benrich37, I will review this |
Input cov
…trospect I think defining __setitem__ explicitly was a misstep and should've been a public set_tag method, but changing it breaks a lot of tests so that is now a whole task. I think enough new code has been written here that my coverage may actually drop
…ng methods since they are never reached by the current code design.
Minor tweaks
@mkhorton Sorry didn't see your comment, will pause on new commits until you're finished. Thank you! Edit: Also, it looks like there are some typos baked into how JDFTx creates out files, which is causing pre-commit to fail on codespell for the example out files I've added. Would it be possible to add 'tests/files/io/jdftx/example_files/*out' to the exclude hook for codespell in .pre-commit-config.yaml? Unless there is a cleaner way to exclude those files |
One-line change - added file to occupy new_files directory in the io files for jdftx
…when reading initial coordinates in joustructures.py (_get_initial_coords), added missing 1/bohr_to_ang when creating a JDFTXInfile from a pmg Structure, added specification of coords-type when creating JDFTXInfile from a pmg Structure, added keyword argument for from_structure to store ion position tags as fractional or cartesian coordinates
…arsed energy types
Jdftx coords
…on_error is None' condition
fixed cartesian coords in from_jdftxinfile method and added Etot to p…
Merge pull request #1 from cote3804/jdftx-coords
Merge updates from main fork
….io tries to raise an "EncondingWarning", changing the dump files dir to be a fixture that creates itself, yields the path, and then removes itself (parts after a "yield" only run once the test using the fixture has finished)
Changing all "zopen" to just "open" due to an error raised when monty…
…als available per ion-type, adding a value check for the bandProjections, improving docustring for JDFTXOutputs
Storing a list of the orbital labels instead of a dictionary of orbit…
… to allow for initialization on calc_dirs with ambiguous out file identity (ie multiple files with the .out suffix)
Oversight that causes ionic positions from previous strucure to be pa…
Reverting old changes to sync with main fork
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Closing this PR until planned changes to integrate inputs and outputs submodules are fully developed |
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Summary
This PR has been divided into the following 3 PR's
valencesproperty to ElementBase and Speciesinputs.pymodule topymatgen.io.jdftxand helper modules for representing and parsing JDFTx inputsoutputs.pymodule topymatgen.io.jdftxand helper modules for representing and parsing JDFTx outputsThis PR can be ignored until those PR's are approved
Todos