`PhononMaker` add options to `calculate_pdos` and save force constants to file #1008

chouyoudou · 2024-10-06T09:07:55Z

Summary

Include a summary of major changes in bullet points:

Feature: Added functionality to compute and save projected phonon density of states (PDOS). The feature can be controlled by the calculate_pdos parameter in BasePhononMaker.
Fix: Added functionality to control the saving of force constants in the phonopy parameters schema through the store_force_constants parameter in BasePhononMaker. This feature determines whether force constants are saved as part of the phonon data schema, and now it functions correctly as intended.

JaGeo · 2024-10-06T09:27:21Z

Thanks. I will review this. Just to mention, the store_force_constants parameter was referring to the schema and not the file. Should maybe be made clearer in the documentation.

chouyoudou · 2024-10-06T13:50:04Z

Hi @chouyoudou ,

Thanks. I will review this. Just to mention, the store_force_constants parameter was referring to the schema and not the file. Should maybe be made clearer in the documentation.

Thanks for pointing that out. I've updated the documentation to clarify that it refers to controlling whether the force constants are saved in the schema, rather than directly to a file.

JaGeo · 2024-10-07T05:46:38Z

src/atomate2/common/schemas/phonons.py

+        if kwargs.get("calculate_pdos", False):
+            phonon.run_mesh(kpoint.kpts[0], with_eigenvectors=True, is_mesh_symmetry=False)
+            phonon_dos_sigma = kwargs.get("phonon_dos_sigma", None)
+            dos_use_tetrahedron_method = kwargs.get("dos_use_tetrahedron_method", True)
+            phonon.run_projected_dos(
+                sigma=phonon_dos_sigma, use_tetrahedron_method=dos_use_tetrahedron_method
+            )
+            phonon.write_projected_dos()
+


Does it make sense to also add an automatic plot here? Likely a bit more work. I am fine with just adding this for now.

This directly relates to the next question: do you want the option to save it in the schema? If so, you would need to develop a parser.

Does it make sense to also add an automatic plot here? Likely a bit more work. I am fine with just adding this for now.

I think it could be useful to provide summed PDOS, for example by element type or symmetry-equivalent atoms. However, user needs in this area are often quite diverse, making it challenging to implement something that meets all needs as straightforwardly as the TDOS plot.

This directly relates to the next question: do you want the option to save it in the schema? If so, you would need to develop a parser.

The current approach saves the PDOS in an external file, similar to the TDOS format. I believe a simple adjustment to the default filename to match the style of atomate2 (e.g., phonon_pdos.yaml instead of the default projected_dos.dat in phonopy) would suffice.

I am fine with this for now. But is it really a yaml? If not, rather keep the dat

Actually, it is not a yaml; it was just renamed with a .yaml extension in atomate2 for TDOS.

chouyoudou

Apply pre-commit auto-fix for code formatting and linting issues

codecov · 2024-10-07T08:10:28Z

Codecov Report

Attention: Patch coverage is 25.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 65.45%. Comparing base (ec1b598) to head (101e276).
Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
src/atomate2/common/schemas/phonons.py	14.28%	5 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #1008       +/-   ##
===========================================
- Coverage   76.09%   65.45%   -10.65%     
===========================================
  Files         174      175        +1     
  Lines       12690    12744       +54     
  Branches     1892     1899        +7     
===========================================
- Hits         9657     8342     -1315     
- Misses       2494     3853     +1359     
- Partials      539      549       +10

Files with missing lines	Coverage Δ
src/atomate2/common/flows/phonons.py	`87.17% <100.00%> (+0.33%)`	⬆️
src/atomate2/common/schemas/phonons.py	`89.28% <14.28%> (-4.55%)`	⬇️

... and 85 files with indirect coverage changes

Update commit

JaGeo · 2024-10-18T09:01:04Z

@chouyoudou could you make a new option for saving the force constants in a file? Maybe via the kwargs? I don't think storing the force constants in a file should always come with storing them in the database. This is why I haven't merged so far

chouyoudou

add force_constants2file parameter for saving the force constants in a file

JaGeo · 2024-10-21T08:52:41Z

src/atomate2/common/flows/phonons.py

+    force_constants2file: str = None
+    calculate_pdos: bool = False


Could you please make them part of "generate_frequencies_eigenvectors_kwargs" or at least the filename? Additionally, please use "create_force_constants_file" as an additional kwarg in "generate_frequencies_eigenvectors_kwargs" to write the force constant file? Otherwise, this will get very messy. I would also rename "force_constants2file" to "force_constants_filename"

- Add "create_force_constants_file" in "generate_frequencies_eigenvectors_kwargs" - Move "force_constants_filename" and "calculate_pdos" to "generate_frequencies_eigenvectors_kwargs"

janosh · 2024-11-14T21:17:53Z

@JaGeo does this PR have approval?

JaGeo · 2024-11-14T21:21:12Z

@janosh with your updates, it is fine with me. 😀

Thanks!

Yaotang Zhang added 2 commits October 6, 2024 17:19

add calculate_pdos and make force constance can be save

443261a

add calculate_pdos and make force constance can be save

8c9d72c

JaGeo reviewed Oct 7, 2024

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chouyoudou commented Oct 7, 2024

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chouyoudou and others added 2 commits October 7, 2024 16:06

Update phonons.py

fed3be7

Apply pre-commit hooks for code formatting and linting

101e276

chouyoudou and others added 2 commits October 7, 2024 17:24

Merge pull request #1 from materialsproject/main

0467419

Update commit

Fix issues found by pre-commit hooks

17139d9

JaGeo changed the title ~~add calculate_pdos and make force constance can be save~~ add calculate_pdos Oct 7, 2024

JaGeo changed the title ~~add calculate_pdos~~ add calculate_pdos and additionally provide option to save force constants in a file Oct 7, 2024

Merge branch 'main' into main

5ea3757

add force_constants2file parameter

c62b1ac

chouyoudou commented Oct 19, 2024

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JaGeo reviewed Oct 21, 2024

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Yaotang Zhang and others added 4 commits October 22, 2024 00:00

- Renamed "force_constants2file" to "force_constants_filename"

ebc7938

- Add "create_force_constants_file" in "generate_frequencies_eigenvectors_kwargs" - Move "force_constants_filename" and "calculate_pdos" to "generate_frequencies_eigenvectors_kwargs"

Merge branch 'main' into main

061139d

fix doc string placement

cdb55f4

refactor from_forces_born handling create_force_constants_file

fb4fa29

janosh added enhancement Improvements to existing features phonon Phonon workflow related labels Nov 14, 2024

janosh changed the title ~~add calculate_pdos and additionally provide option to save force constants in a file~~ PhononMaker add options to calculate_pdos and save force constants to file Nov 14, 2024

JaGeo approved these changes Nov 14, 2024

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fix typo

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janosh merged commit 7add7ca into materialsproject:main Nov 14, 2024

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`PhononMaker` add options to `calculate_pdos` and save force constants to file #1008

`PhononMaker` add options to `calculate_pdos` and save force constants to file #1008

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		force_constants2file: str = None
		calculate_pdos: bool = False

PhononMaker add options to calculate_pdos and save force constants to file #1008

PhononMaker add options to calculate_pdos and save force constants to file #1008

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`PhononMaker` add options to `calculate_pdos` and save force constants to file #1008

`PhononMaker` add options to `calculate_pdos` and save force constants to file #1008

chouyoudou commented Oct 6, 2024 •

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