Including VASP surface adsorption flow

[itsduowang]

[This PR is still working in progress.]

Summary

including adsorption flow using VASP into atomate2

There are two files added into /vasp/flows and /vasp/jobs directories in order to implement surface adsorption calculation.

• in /vasp/flows, the adsorption.py defines the general workflow of running the adsorption calculations for different surface-slab configurations and molecules.
• in /vasp/jobs, the adsorption.py includes multiple elementary jobs for such workflow.

TODO

• finish the rest of the code in atomate2/vasp/flows/adsorption.py and atomate2/vasp/jobs/adsorption.py
• finish docstrings
• test over more materials

Checklist

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• Code is in the standard Python style.
  The easiest way to handle this is to run the following in the correct sequence on
  your local machine. Start with running ruff and ruff format on your new code. This will
  automatically reformat your code to PEP8 conventions and fix many linting issues.
• Doc strings have been added in the Numpy docstring format.
  Run ruff on your code.
• Type annotations are highly encouraged. Run mypy to
  type check your code.
• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.

Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the repository. Simply runpre-commit install and a check will be run prior to allowing commits.

[codecov]

Codecov Report

Attention: Patch coverage is 93.78882% with 10 lines in your changes missing coverage. Please review.

Project coverage is 76.31%. Comparing base (8d57884) to head (5e0fa58).
Report is 32 commits behind head on main.

Files with missing lines	Patch %	Lines
src/atomate2/vasp/flows/adsorption.py	89.65%	3 Missing and 3 partials ⚠️
src/atomate2/vasp/jobs/adsorption.py	96.77%	2 Missing and 1 partial ⚠️
src/atomate2/vasp/schemas/adsorption.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #691      +/-   ##
==========================================
+ Coverage   75.70%   76.31%   +0.60%     
==========================================
  Files         147      159      +12     
  Lines       10925    11606     +681     
  Branches     1613     1719     +106     
==========================================
+ Hits         8271     8857     +586     
- Misses       2173     2234      +61     
- Partials      481      515      +34     

Files with missing lines	Coverage Δ
src/atomate2/vasp/schemas/adsorption.py	90.00% <90.00%> (ø)
src/atomate2/vasp/jobs/adsorption.py	96.77% <96.77%> (ø)
src/atomate2/vasp/flows/adsorption.py	89.65% <89.65%> (ø)

... and 4 files with indirect coverage changes

[Zhuoying]

Hi @itsduowang thanks for the PR. You can try to use pre-commit and ruff to fix any lint issues.

Install pre-commit hooks to auto-check types and linting before every commit

pip install -U pre-commit

pre-commit install

Use ruff to check and fix format

ruff format --check .

ruff check --fix

[tpurcell90]

There would be interest in adding this workflow for FHI-aims as well. Do you have any recommendations on when we should port this for FHI-aims?

[itsduowang]

Hi @tpurcell90, I am not familiar with the FHI-aims package. But I would love to work with you together to port this for FHI-aims!

[tpurcell90]

Okay we'd be happy to work with you on that (FHI-aims is a nao basis set code). I think it would make sense for this one to get merged in first since it is already quite large. @utf do you agree with that it should wait for this to get merged in?

[itsduowang]

Yes @tpurcell90, I think it would be better to merge the PR and then we can work on the adding FHI-aims support.

@utf, I have done the debugging for that K point issue and ran the pytest and testing workflow from my end (https://github.com/itsduowang/atomate2/actions/runs/10375913622). Please take a look and help me to rerun the testing. Thanks so much!

[utf]

Thanks @itsduowang. Some more comments - this is almost there now. The main points are:

• Better use of prev_dir.
• Creating a schema for the adsorption data.

Let me know if you have any concerns about the comments.

[utf]

Edit: my comment got posted twice for some reason.

[itsduowang]

Hi @utf, thanks for these updates. I will go through each item and resolve those issues.

[itsduowang]

Hi @utf. I have resolved all the issues you mentioned above and included the schema into the adsorption workflow. Please take a look and let me know for any further issues or concerns.

[utf]

Thanks @itsduowang. This looks great to me.