[WIP] Updated: Lattice dynamics workflow using hiPhive #1367

thomasloux · 2026-01-02T16:41:55Z

Summary

This is the updated version of #1062: the test tests/vasp/flows/test_hiphive.py runs.

TODO (if any)

Is it ready to merge? No. I mainly updated the code so the test would run. I did not check at all what was actually run.
Suspicious part to be looked at:

atomate2/common/schemas/hipgive.py:727: I need to do this to make the test pass. Maybe it's just a problem with the test.
Check the code. I don't really understand what was the state of the PR.
Hiphive module is from a fork. Is it possible to get this fork to be merged the main repo?

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.

using tags in accordance with atomate LD workflow

1. supports shengBTE, almaBTE & phono3py as of now. 2. before running any of these calculators, make sure to successfully compile them as explained on their respective websites. 3.Also, remember to put the execution command for each of these calculators in atomate2.yaml file

the decision is now made based on whether n_imaginary > 0 from the fitting_data.json @ 0K

1. largest displacement is based on the avg row (periodic table) number of the compound. 2. displacements are skewed towards the large displacement 3. # of displaced structures to generate depends on the n_structures, which depends upon the symmetry of the primitive structure 4. smallest displacement is fixed at 0.01 Å

1. added a job that creates multiples sub jobs for each hiphive fitting and then collects the fitting data & the fcs. fcp, cluster space and other properties corresponding to the best cutoff! 2. setting the min # of displ to 4 & max # of displ to 60

Trying different strategies for perturbing the atoms in the supercell -- 1. Fixed displacement 2. MC Rattle 3. MD informed displacements Adding a penalty to the displacements that are generated out of the distribution.

1. selects cutoffs based on target DOFs for 2nd, 3rd and 4th order.

2. all the functions have doctrings. 3. modified the function that generates perturbed structures 4. updated def get_cutoffs -- generates a grid of cutoffs that satisfy the given # of required DOFs for 2nd, 3rd and 4th order interaction. 5. sequentially performs the linear regression for each cutoff. 6. modified the files that are saved during the execution of workflow

2. removed files that are not required to be saved during the workflow execution.

* Bump monty from 2024.2.2 to 2024.2.26 Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2024.2.2 to 2024.2.26. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.md) - [Commits](materialyzeai/monty@v2024.2.2...v2024.2.26) --- updated-dependencies: - dependency-name: monty dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> * bump pymatgen>=2024.3.1 to fix deprecation removal CI errors --------- Co-authored-by: Janosh Riebesell <[email protected]>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.2 to 8.1.0. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.0.2...8.1.0) --- updated-dependencies: - dependency-name: pytest 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>

pytest-dev/pytest#12069

Co-authored-by: utf <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

Bumps [ipython](https://github.com/ipython/ipython) from 8.22.1 to 8.22.2. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.22.1...8.22.2) --- updated-dependencies: - dependency-name: ipython 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 [chgnet](https://github.com/CederGroupHub/chgnet) from 0.3.4 to 0.3.5. - [Release notes](https://github.com/CederGroupHub/chgnet/releases) - [Commits](CederGroupHub/chgnet@v0.3.4...v0.3.5) --- updated-dependencies: - dependency-name: chgnet 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 [pydantic](https://github.com/pydantic/pydantic) from 2.6.3 to 2.6.4. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.6.3...v2.6.4) --- updated-dependencies: - dependency-name: pydantic 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 [custodian](https://github.com/materialsproject/custodian) from 2024.2.15 to 2024.3.12. - [Release notes](https://github.com/materialsproject/custodian/releases) - [Changelog](https://github.com/materialsproject/custodian/blob/master/docs/changelog.md) - [Commits](materialsproject/custodian@v2024.2.15...v2024.3.12) --- updated-dependencies: - dependency-name: custodian 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 [phonopy](https://phonopy.github.io/phonopy/) from 2.21.2 to 2.22.0. --- updated-dependencies: - dependency-name: phonopy 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 [autodoc-pydantic](https://github.com/mansenfranzen/autodoc_pydantic) from 2.0.1 to 2.1.0. - [Changelog](https://github.com/mansenfranzen/autodoc_pydantic/blob/main/CHANGELOG.md) - [Commits](mansenfranzen/autodoc_pydantic@v2.0.1...v2.1.0) --- updated-dependencies: - dependency-name: autodoc-pydantic 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-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v4.1.0...v5.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps python-ulid from 2.2.0 to 2.3.0. --- updated-dependencies: - dependency-name: python-ulid 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 [cclib](https://github.com/cclib/cclib) from 1.8 to 1.8.1. - [Release notes](https://github.com/cclib/cclib/releases) - [Commits](cclib/cclib@v1.8...v1.8.1) --- updated-dependencies: - dependency-name: cclib 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>

By default the data is loaded by phonopy.load() instead of phonon.load(). Co-authored-by: Alex Ganose <[email protected]>

* Add trajectory reporter to openmm workflow * respond to janosh review * fix test * slightly stricter asserts in test_trajectory_reporter --------- Co-authored-by: Janosh Riebesell <[email protected]>

input & output VASP files

added the testing python file for hiphive

thomasloux · 2026-01-02T16:43:47Z

@janosh @hrushikesh-s This PR can be of interest to you :)

thomasloux · 2026-01-02T16:46:33Z

Note: A modification needs to be done on hiphive:
https://gitlab.com/jsyony37/hiphive/-/blob/master/hiphive/fitting/fit_methods.py?ref_type=heads#L521:
from sklearn.base import BaseEstimator
class _Estimator(BaseEstimator):

esoteric-ephemera · 2026-01-02T16:55:03Z

Hey @thomasloux, could you please instead make a PR against @hrushikesh-s's branch and coordinate with him to finalize #1062?

thomasloux · 2026-01-02T17:15:34Z

Ok I'll delete the branch and PR his fork once his fork is synchronised with the main branch

hrushikesh-s and others added 30 commits March 29, 2024 13:55

customized INCAR tags

c45b616

using tags in accordance with atomate LD workflow

added anharmonicphonons block in pyproject.yaml

82ef1c0

update the logic to use lambda=0 for TI

8889d3e

the decision is now made based on whether n_imaginary > 0 from the fitting_data.json @ 0K

adding fw configs to individual jobs

60e9a7b

new displacement strategy

300da7b

Trying different strategies for perturbing the atoms in the supercell -- 1. Fixed displacement 2. MC Rattle 3. MD informed displacements Adding a penalty to the displacements that are generated out of the distribution.

added CHGNet MD step to generate displacement snapshots

4f7c264

updateing arguments of the MD run

5283d9e

minor bug fixes to MD flow

2fb63c2

updated MD args for running mp-23339

a249cb8

new cutoffs sampling startegy

d5090fb

1. selects cutoffs based on target DOFs for 2nd, 3rd and 4th order.

1. refactored the hiphive flow

8b0019d

2. removed files that are not required to be saved during the workflow execution.

Merge branch 'main' into hiphive_new_sampling_startegy

8144b7b

revert to pytest 8.0.2, 8.1.0 was yanked due to breaking few plugins

4e90106

pytest-dev/pytest#12069

Auto-update pre-commit hooks (materialsproject#756)

228641a

Co-authored-by: utf <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

Corrected typo in doc (materialsproject#775)

848633a

By default the data is loaded by phonopy.load() instead of phonon.load(). Co-authored-by: Alex Ganose <[email protected]>

utf and others added 26 commits November 15, 2024 16:55

Update changelog

e9aa668

Add trajectory reporter to openmm workflow (materialsproject#1053)

b9c59fc

* Add trajectory reporter to openmm workflow * respond to janosh review * fix test * slightly stricter asserts in test_trajectory_reporter --------- Co-authored-by: Janosh Riebesell <[email protected]>

modifications based on new versions of pymatgen & hiphive

a07ca83

pre-commit fixes schemas/hiphive.py

f7fa784

pre-commit fixes jobs/hiphive.py

b5eac65

pre-commit fixes flows/hiphive.py

22872e5

removing unused code

b49c869

removing the gpu_fworker config tag

68eea2b

test_data -- Si_hiphive

cd36b72

input & output VASP files

tests/vasp/flows/test_hiphive.py

31a8d60

added the testing python file for hiphive

removed old test files for hiphive

2396b42

Merge branch 'upstream_main' into hiphive

a97158f

pre-commit vasp/flows/hiphive.py

09228aa

pre-commit forecefields/flows/hiphive.py

60c5e18

pre-commit src/atomate2/settings.py

fb53491

pre-commit common/jobs/phonons.py

bb52e2b

update to pyproject.toml

4f28310

changing the name of "anharmonicphonons" block to "hiphive"

e32f960

added hiphive dependencies to strict

7c95b6e

soften phono3py version

cc12b08

installing phono3py using conda

8f6b299

Merge branch 'hiphive'

63614e2

ruff, add function deleted in phonopy, adapted to new phonopy version

f91d105

adapt to new atomate force field classes

9ea3709

ruff happy

0b8c2f5

update phono3py version

e9fe0dc

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thomasloux commented Jan 2, 2026

Summary

TODO (if any)

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