Atomate2 jz pheasy_phonon

leslie-zheng commented 2 weeks ago

Summary

Include a summary of major changes in bullet points:

Using Pheasy code (LASSO) to efficiently extract force constants for phonon calculation
Based on this phonon workflow, a relative small lattice constants (a,b and c axes) can be used to accurately extract second order force constants (usually 12 Angstrum is enough for most of materials)
- Fix 1

Additional dependencies introduced (if any)

Before using it, the a dependent library is necessary: python interface for alamode code: Installation can be found: https://alm.readthedocs.io/en/develop/?badge=develop

TODO (if any)

Quality check for all phonon calculations,
Extracting Higher-order force constants, including up to six order.
Anharmonic phonon renormalization using Modified SSCHA combing the MC method, relaxing atomic site coordinates and bubble self-energy.
Lattice thermal conductivity calculation incorporating diagonal and non-diagonal terms of heat flux operators.

Checklist

Work-in-progress pull requests are encouraged, but please put [WIP] in the pull request title.

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[x] 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.
[x] Doc strings have been added in the Numpy docstring format. Run ruff on your code.
[x] Type annotations are highly encouraged. Run mypy to type check your code.
[x] Tests have been added for any new functionality or bug fixes.
[x] All linting and tests pass.

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JaGeo commented 2 weeks ago

@leslie-zheng Thanks 😃! I haven't looked at the code in detail yet. In any case, we would need tests and also install the pheasy code on the repo. The linting would need to pass as well.

Let me know if you need any advice for any of the points!

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 0% with 585 lines in your changes missing coverage. Please review.

Project coverage is 72.36%. Comparing base (8d57884) to head (93219ce). Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
src/atomate2/common/schemas/pheasy.py	0.00%	305 Missing :warning:
src/atomate2/common/jobs/pheasy.py	0.00%	125 Missing :warning:
src/atomate2/common/flows/pheasy.py	0.00%	113 Missing :warning:
src/atomate2/vasp/flows/pheasy.py	0.00%	34 Missing :warning:
src/atomate2/vasp/jobs/pheasy.py	0.00%	8 Missing :warning:

Additional details and impacted files

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leslie-zheng commented 1 week ago

@leslie-zheng Thanks 😃! I haven't looked at the code in detail yet. In any case, we would need tests and also install the pheasy code on the repo. The linting would need to pass as well.

Let me know if you need any advice for any of the points!

Thanks Janine @JaGeo , I will make the linting check pass ASAP.

leslie-zheng commented 1 week ago

@JaGeo Hi Janine, will following all your suggestions and finish modifying it this weekend, thanks for the suggestions.

JaGeo commented 6 days ago

@leslie-zheng tgabk you! i think the goal should be that we reuse as much code as possible from the phonopy worfklow.

leslie-zheng commented 6 days ago

@leslie-zheng tgabk you! i think the goal should be that we reuse as much code as possible from the phonopy worfklow.

Hi Janine, Sure, I am working on it, already reuse the some repeated functions from phonopy section. After finish it again and will let you know.

leslie-zheng commented 3 days ago

@JaGeo Hi Janine, after finishing cleaning it up, and I test the whole workflow on our cluster. Take silicon as an example, it works well.

leslie-zheng commented 3 days ago

Hi @JaGeo , Maybe we can create a folder called phonon/ and move the /phonopy.py and /pheasy.py into? or a folder called lattice_dynamics/ instead.

JaGeo commented 3 days ago

@JaGeo Hi Janine, after finishing cleaning it up, and I test the whole workflow on our cluster. Take silicon as an example, it works well.

That's great. Could you add test workflows as well? There are many examples in the tests folder. Once this is done, I am happy to do further refactoring.

If you olan to add higher force constants as well, we can also keep the pheasy submodule for now.

leslie-zheng commented 1 day ago

@JaGeo Hi Janine, after finishing cleaning it up, and I test the whole workflow on our cluster. Take silicon as an example, it works well.

That's great. Could you add test workflows as well? There are many examples in the tests folder. Once this is done, I am happy to do further refactoring.

If you olan to add higher force constants as well, we can also keep the pheasy submodule for now.

Hi Janine @JaGeo , sure, will do it. yes, I am planning to add the higher-order force constants into.

leslie-zheng commented 1 day ago

Hi Janine @JaGeo ,

I finished adjusting the pheasy workflow based on previous linting checking again. And test the whole workflow again using silicon, working perfectly. For the pytest, I need help from you, I am not familiar with this process, cause I did not do it before. Could you please help me to write a example?, any documents from the pheasy workflow related to the pytest based on silicon case. I can packed it and shared with you.

best jiongzhi

JaGeo commented 1 day ago

@leslie-zheng yes, sure. Happy to help out with the tests

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