Lattice dynamics workflow using Pheasy #1063

hrushikesh-s · 2024-11-22T03:14:35Z

Summary

Include a summary of major changes in bullet points:

Feature 1
Fix 1

Additional dependencies introduced (if any)

List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that add trivial
functionality, e.g., to use one single easily implementable function, is frowned upon.
Justify why that dependency is needed. Especially frowned upon are circular dependencies.

TODO (if any)

If this is a work-in-progress, write something about what else needs to be done.

Feature 1 supports A, but not B.

Checklist

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

Before a pull request can be merged, the following items must be checked:

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 run
pre-commit install and a check will be run prior to allowing commits.

Modified some parts based on Janine's comments.

…atomate2 into atomate2_jz_pheasy

…lacement method.

…group for crystals.

JaGeo · 2024-11-22T20:01:59Z

tests/vasp/flows/test_phonons.py

@@ -202,6 +202,8 @@ def test_phonon_wf_vasp_only_displacements_no_structural_transformation(
    assert_allclose(
        responses[job.jobs[-1].uuid][1].output.primitive_matrix,
        ((0, 1, 0), (0, 0, 1), (1, 0, 0)),
+        rtol=1e-8,


@hrushikesh-s @naik-aakash and I are working on fixing these tests. I think I messed something up with the test files. I might have time later tonight. So, maybe skip those tests first.

Aah. Sorry! Different test 😅. But I meant the update to the latest phonopy. Sorry!

oh okay okay. I was wondering why suddenly the test_phonons.py file was failing 😅

* bug fix for linear strain qha maker * refactor to only rely on one method to generate supercells * fix tests * add test * add test 2 * fix type annotation * fix type annotation * fix docs * fix docs * add test for supercell * fix supercell tests * fix supercell tests

…ialsproject#1064) * fix lints and typos * fix generate_phonon_displacements side effect: removes magmoms of passed structure in-place * fix ruff PYI063 Use PEP 570 syntax for positional-only parameters

Bumps [emmet-core](https://github.com/materialsproject/emmet) from 0.84.3rc3 to 0.84.3rc4. - [Release notes](https://github.com/materialsproject/emmet/releases) - [Changelog](https://github.com/materialsproject/emmet/blob/main/docs/CHANGELOG.md) - [Commits](materialsproject/emmet@0.84.3rc3...0.84.3rc4) --- updated-dependencies: - dependency-name: emmet-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [jobflow](https://github.com/materialsproject/jobflow) from 0.1.18 to 0.1.19. - [Release notes](https://github.com/materialsproject/jobflow/releases) - [Changelog](https://github.com/materialsproject/jobflow/blob/main/CHANGELOG.md) - [Commits](materialsproject/jobflow@v0.1.18...v0.1.19) --- updated-dependencies: - dependency-name: jobflow dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…dration (materialsproject#1072) * update EOS docs * udpate docs with implementation details * add convenience constructor method for forcefield ElasticMaker * allow MLFF enum to treat str(MLFF.) as valid member * precommit * add small MLFF test

* bump phonopy version * Update pyproject.toml * replace bs plotter with pymatgen implementation > reduce code repetition * replace bs plotter with pymatgen implementation > reduce code repetition * switch off grunesien computation at gamma (unstable) * fix assertions to correct expected derived properties * fix failing test (use correct reference data) * remove non used test_data, rename Si_phonons_4 > Si_phonons_3 * point to renamed ref test_data --------- Co-authored-by: J. George <[email protected]>

Bumps mp-api from 0.42.2 to 0.43.0. --- updated-dependencies: - dependency-name: mp-api dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.3 to 8.3.4. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.3.3...8.3.4) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [ipython](https://github.com/ipython/ipython) from 8.29.0 to 8.30.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.29.0...8.30.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [sevenn](https://github.com/MDIL-SNU/SevenNet) from 0.10.1 to 0.10.2. - [Release notes](https://github.com/MDIL-SNU/SevenNet/releases) - [Changelog](https://github.com/MDIL-SNU/SevenNet/blob/main/CHANGELOG.md) - [Commits](MDIL-SNU/SevenNet@v0.10.1...v0.10.2) --- updated-dependencies: - dependency-name: sevenn dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [emmet-core](https://github.com/materialsproject/emmet) from 0.84.3rc4 to 0.84.3rc6. - [Release notes](https://github.com/materialsproject/emmet/releases) - [Changelog](https://github.com/materialsproject/emmet/blob/main/docs/CHANGELOG.md) - [Commits](materialsproject/emmet@0.84.3rc4...v0.84.3rc6) --- updated-dependencies: - dependency-name: emmet-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

hrushikesh-s · 2024-12-10T20:51:26Z

@JaGeo , The test fails because GH can't find FORCECONSTANTS file in the temp folder. However, when I run the same test locally, I am able to successfully run it. Can you pls help?

JaGeo · 2024-12-11T08:53:27Z

@hrushikesh-s I will try to look into it. Could you add all installation instructions to the documentation as well?

JaGeo · 2024-12-11T10:57:10Z

@hrushikesh-s Locally, it fails for me with exactly the same error. Are you sure you have the same pheasy, ALM and phonopy versions? I only have a force_matrix.pkl file in the last folder but no FORCE_CONSTANT file

JaGeo · 2024-12-11T11:24:59Z

I also got a numpy error. Something in the pheasy commands seems to go wrong.

hrushikesh-s · 2024-12-12T20:28:32Z

@hrushikesh-s I will try to look into it. Could you add all installation instructions to the documentation as well?
Yes.

Doing this now

@hrushikesh-s Locally, it fails for me with exactly the same error. Are you sure you have the same pheasy, ALM and phonopy versions? I only have a force_matrix.pkl file in the last folder but no FORCE_CONSTANT file

Checking this now

leslie-zheng and others added 30 commits September 9, 2024 14:02

Add pheasy branch for phonon calculation using LASSO

0775785

pheasy_phonons

7891554

add_pheasy_to_vasp_folder

d643fc1

Add_pheasy_to_vasp_file

93219ce

Merge branch 'main' into atomate2_jz_pheasy

f4b59c6

Merge branch 'main' into atomate2_jz_pheasy

e514969

Modified some parts based on Janine's comments.

11d546b

Modified some parts based on Janine's comments.

Merge branch 'atomate2_jz_pheasy' of https://github.com/leslie-zheng/…

13acf5a

…atomate2 into atomate2_jz_pheasy

directly import the class methods from phonons

57ab59f

clean up the code

647fe49

remove some files.

94a1acc

minor change

b92e34e

allow the users to define the number of displacements for random-disp…

05650d0

…lacement method.

format_adjustment

0bf1bf8

format_adjustment

e9cd8a6

small update

2bacc86

clean up the code and add more comments

4535497

minor update

eab1fe6

allow the users to control the symmetry precision

36aa5b7

Lower the symmetry precision to allow pheasy to find a correct space …

c69df93

…group for crystals.

Minor update

92ea25a

minor adjustment

5d6f122

minor update for flow/pheasy.py

e17a316

resuse some jobs from phonons

f46c2fd

clean up the job(generate_phonon_displacements)

34a197e

finished cleaning up the pheasy jobs module

be89bce

finished cleaning up the shemas/pheasy

1316b1d

small adjustment to pass the lint

833205a

raise a error if ALM is not installed.

f741a8c

minor update

30de21a

hrushikesh-s added 2 commits November 22, 2024 10:29

alamode installation -- bug fix 6

9880778

added tol to test_phonons.py

6a6c2aa

JaGeo reviewed Nov 22, 2024

View reviewed changes

JaGeo and others added 22 commits December 9, 2024 23:00

Fix generate_phonon_displacements magmom removal side effect (mater…

6fd44f1

…ialsproject#1064) * fix lints and typos * fix generate_phonon_displacements side effect: removes magmoms of passed structure in-place * fix ruff PYI063 Use PEP 570 syntax for positional-only parameters

add openmm description to docs (materialsproject#1069)

2189373

fix minor code formatting issues + typos (materialsproject#1070)

6eca446

update calorine version (materialsproject#1083)

dc9335e

soften the assert output["relax"]["EOS"]["birch_murnaghan"]["b0"]

31474ef

further softening

a525799

providing absolute path for FC file

b2493f9

changed the location of reading FC file

4618005

changed the run_locally's attribute of create_folders to false

b6964f3

changed it back to True

35a2c40

adding some print statements for debugging

0836d1e

adding more logger statements for debugging

af27d7b

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Lattice dynamics workflow using Pheasy #1063

Lattice dynamics workflow using Pheasy #1063

hrushikesh-s commented Nov 22, 2024

JaGeo Nov 22, 2024

JaGeo Nov 22, 2024

hrushikesh-s Nov 22, 2024

hrushikesh-s commented Dec 10, 2024

JaGeo commented Dec 11, 2024

JaGeo commented Dec 11, 2024

JaGeo commented Dec 11, 2024

hrushikesh-s commented Dec 12, 2024

Lattice dynamics workflow using Pheasy #1063

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Lattice dynamics workflow using Pheasy #1063

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hrushikesh-s commented Nov 22, 2024

Summary

Additional dependencies introduced (if any)

TODO (if any)

Checklist

JaGeo Nov 22, 2024

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JaGeo Nov 22, 2024

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hrushikesh-s Nov 22, 2024

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hrushikesh-s commented Dec 10, 2024

JaGeo commented Dec 11, 2024

JaGeo commented Dec 11, 2024

JaGeo commented Dec 11, 2024

hrushikesh-s commented Dec 12, 2024