Atomate2 jz pheasy_phonon #976
Conversation
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@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 ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #976 +/- ##
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- Coverage 75.70% 72.36% -3.34%
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Files 147 161 +14
Lines 10925 12030 +1105
Branches 1613 1767 +154
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+ Hits 8271 8706 +435
- Misses 2173 2813 +640
- Partials 481 511 +30
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Thanks Janine @JaGeo , I will make the linting check pass ASAP. |
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@JaGeo Hi Janine, will following all your suggestions and finish modifying it this weekend, thanks for the suggestions. |
Modified some parts based on Janine's comments.
…atomate2 into atomate2_jz_pheasy
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@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. |
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There seem to be more parameters here. Maybe, you can check the whole code again for such points. I might overlook parts here.
Hi Janine, Thanks for the comments.
Sure, will do. I am cleaning up the code these days. When I finished and let you know.
By the way, The pheasy branch is not only focusing on LASSO-based phonon calculations, in the near future, we also integrate the higher-order force constant calculation and phonon renormalization functions into.
…group for crystals.
| with open("force_matrix.pkl","wb") as file: | ||
| pickle.dump(set_of_forces_a,file) | ||
| pickle.dump(dataset_forces_array_disp,file) |
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Can you only use pickle here?
other format also should be fine, any suggestions? because in pheasy, it uses the pickle, so i just simply follow it.
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@JaGeo Hi Janine, after finishing cleaning it up, and I test the whole workflow on our cluster. |
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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. |
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. |
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Hi Janine @JaGeo , I finished adjusting the pheasy workflow based on previous linting checking again. best |
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@leslie-zheng yes, sure. Happy to help out with the tests |
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