Absorption

[yang-ruoxi]

Summary

• Added AbsorptionFW to run a frequency-dependent dielectric calculation, with two options: independent-particle approximation (IPA) and random-phase approximation (RPA). One can also specify a static run, but it will invoke the MPStaticSet rather than the AbsorptionSet.
• Added absorption task to write input sets for these runs
• Added a section in vasp drones to collect the dielectrics information from RPA calculation, and to calculate the corresponding absorption coefficient for easy access.
• A typical usage of this FW would be :

fw0 = OptimizeFW(structure)
fw1 = AbsorptionFW(mode = "STATIC", parent = fw0) # uses MPStaticSet
fw2 = AbsorptionFW(mode = "IPA", parent = fw1)   # uses AbsorptionSet supplied in pymatgen 
fw3 = AbsorptionFW(mode = "RPA", parent = fw2)  # uses AbsorptionSet supplied in pymatgen 
wf = Workflow([fw0, fw1, fw2, fw3])

[itsshawnwang]

Hello @yang-ruoxi I think now you can run the workflows to test this PR. Please let me know for any problems or concerns.

Thanks for your contribution. Cheers! :)

[janosh]

Would be cool to get this merged!

@itsshawnzhang If @yang-ruoxi enabled edits by maintainers, you should be able to push a small change to this PR yourself and trigger CI that way.

[itsshawnwang]

Would be cool to get this merged!

@itsshawnzhang If @yang-ruoxi enabled edits by maintainers, you should be able to push a small change to this PR yourself and trigger CI that way.

Thanks @janosh and @yang-ruoxi. I will push some changes to this PR and run the new CI at this point.

[janosh]

@itsshawnzhang Is allow edits from maintainers disabled? If so, it might be easier to add a the workflow_dispatch trigger to our test.yml GHA. I think that should allow you to trigger CI through a button and would avoid the need to create a duplicate PR.

[itsshawnwang]

@itsshawnzhang Is allow edits from maintainers disabled? If so, it might be easier to add a the workflow_dispatch trigger to our test.yml GHA. I think that should allow you to trigger CI through a button and would avoid the need to create a duplicate PR.

Will try this! Thanks!

[janosh]

@itsshawnzhang This might be helpful.

- uses: actions/checkout@v2
  with:
    ref: pull/${{ github.event.pull_request.id }}/head

If you want to manually dispatch a Workflow for a Pull Request you could use workflow_dispatch with an input of the Pull Request id that the Workflow then composes the ref from (in the format above).

[itsshawnwang]

This is helpful. Please allow me to look into it and I will create the check workflow for this PR. Thanks so much for the information @janosh :)

[yang-ruoxi]

Thanks @janosh and @yang-ruoxi. I will push some changes to this PR and run the new CI at this point.

Thanks for looking into it! Is there anything I should do from my end to merge it?

[janosh]

@yang-ruoxi If you could push any change to this PR (fix a typo or improve a doc string or something like that) to retrigger CI that would allow @itsshawnzhang to make sure it passes all tests before merging.

[janosh]

@yang-ruoxi The failing tests are due to pymongo v3/v4 incompatibilities. Can you merge or rebase the main branch into your PR?

[itsshawnwang]

Hello @yang-ruoxi . I merged this branch since all the tests are passed in the new environmental settings (see #744). Thank you so much for your contributions. Please let us know for any other problems or concerns. Cheers! : )