Abinit dfpt by emarazzi · Pull Request #2 · emarazzi/atomate2

emarazzi · 2025-07-23T12:02:04Z

Hi,
this is the PR for the latest implementation of dfpt wf in atomate2 wrt the materialsproject main branch.
We align everything to the discussion we had last week.

To run the dfpt workflow you will need the abipy version you can find in

https://github.com/emarazzi/abipy/tree/phonons_atomate2

there is a lot of differences in the tests part but I think we can discuss them when we will deal with the tests in a later stage

Future things to discuss:

do we want to keep the output['dirs'] in the generate_perts as a list of dirs or a dict of lists of dirs?
do we want to add some classmethod to perform some standard "modifications" of the phonon workflow predefined for the user, e.g. computing LOTO splitting?

pull trunk main

…t_dfpt pull Enrico dfpt

Quick fix

Currently, it does nothing as noted in materialsproject#959. The better PR would be to make it work, but we shouldn't have an unused setting around since that will confused users more.

Bumps [mace-torch](https://github.com/ACEsuit/mace) from 0.3.13 to 0.3.14. - [Release notes](https://github.com/ACEsuit/mace/releases) - [Commits](ACEsuit/mace@v0.3.13...v0.3.14) --- updated-dependencies: - dependency-name: mace-torch dependency-version: 0.3.14 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [custodian](https://github.com/materialsproject/custodian) from 2025.5.12 to 2025.8.13. - [Release notes](https://github.com/materialsproject/custodian/releases) - [Changelog](https://github.com/materialsproject/custodian/blob/master/docs/changelog.md) - [Commits](materialsproject/custodian@v2025.5.12...v2025.8.13) --- updated-dependencies: - dependency-name: custodian dependency-version: 2025.8.13 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [lobsterpy](https://github.com/JaGeo/LobsterPy) from 0.5.0 to 0.5.7. - [Release notes](https://github.com/JaGeo/LobsterPy/releases) - [Changelog](https://github.com/JaGeo/LobsterPy/blob/main/CHANGELOG.md) - [Commits](JaGeo/LobsterPy@v0.5.0...v0.5.7) --- updated-dependencies: - dependency-name: lobsterpy dependency-version: 0.5.7 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [furo](https://github.com/pradyunsg/furo) from 2024.8.6 to 2025.7.19. - [Release notes](https://github.com/pradyunsg/furo/releases) - [Changelog](https://github.com/pradyunsg/furo/blob/main/docs/changelog.md) - [Commits](pradyunsg/furo@2024.08.06...2025.07.19) --- updated-dependencies: - dependency-name: furo dependency-version: 2025.7.19 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 4.4.5 to 4.4.6. - [Release notes](https://github.com/jupyterlab/jupyterlab/releases) - [Changelog](https://github.com/jupyterlab/jupyterlab/blob/main/RELEASE.md) - [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.4.5...@jupyterlab/lsp@4.4.6) --- updated-dependencies: - dependency-name: jupyterlab dependency-version: 4.4.6 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…sproject#1219)

Bumps [matgl](https://github.com/materialsvirtuallab/matgl) from 1.2.7 to 1.3.0. - [Release notes](https://github.com/materialsvirtuallab/matgl/releases) - [Changelog](https://github.com/materialsvirtuallab/matgl/blob/main/changes.md) - [Commits](materialyzeai/matgl@v1.2.7...v1.3.0) --- updated-dependencies: - dependency-name: matgl dependency-version: 1.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* bump ase to 3.26 + add MTKNPT as default for NPT * improve VASP documentation around run_vasp_kwargs, custodian settings, and magmom initialization * remove deprecated forcefield makers that were slated for deletion on 1 January, 2025 * Suppress warnings in file client by default * Fallback methods in MPMorph's automatic volume determination

Bumps [python-ulid](https://github.com/mdomke/python-ulid) from 3.0.0 to 3.1.0. - [Release notes](https://github.com/mdomke/python-ulid/releases) - [Changelog](https://github.com/mdomke/python-ulid/blob/main/CHANGELOG.rst) - [Commits](mdomke/python-ulid@3.0.0...3.1.0) --- updated-dependencies: - dependency-name: python-ulid dependency-version: 3.1.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* minor bug fixes + pytest xdist for on-runner parallelism * bump precommit and remove deprecated pragma * ensure aims test is independent of run order

…lsproject#1036) * ruff * fix PYI063 Use PEP 570 syntax for positional-only arguments * single source of truth for optional deps in pyproject.toml * revert to mace-torch==0.3.6, 0.3.7 still unreleased * fix typo defects -> phonons * lint --------- Co-authored-by: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com> Co-authored-by: esoteric-ephemera <aaron.kaplan.physics@gmail.com>

…terialsproject#1290)

Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 6.2.1 to 6.3.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v6.2.1...v6.3.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-version: 6.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.4.1 to 8.4.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.4.1...8.4.2) --- updated-dependencies: - dependency-name: pytest dependency-version: 8.4.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 4.4.6 to 4.4.7. - [Release notes](https://github.com/jupyterlab/jupyterlab/releases) - [Changelog](https://github.com/jupyterlab/jupyterlab/blob/main/RELEASE.md) - [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.4.6...@jupyterlab/lsp@4.4.7) --- updated-dependencies: - dependency-name: jupyterlab dependency-version: 4.4.7 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 6.3.0 to 7.0.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v6.3.0...v7.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.14.1 to 3.15.0. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest-mock@v3.14.1...v3.15.0) --- updated-dependencies: - dependency-name: pytest-mock dependency-version: 3.15.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

gpetretto

Thanks @emarazzi and @VicTrqt for all the work.
I have added several comments, but hopefully these should not require large changes in the logic and in the code.

I have a few general comments:

I think that there are sometimes some commented parts of old version of the code. If something is outdated or not relevant for the current choices it would be better to remove them.

according to github, there are 206 .gz files that will be added with this PR, for a single test. I just wanted to be sure if this is really the bare minimum that it is required, since they are quite a lot. If all the jobs and files are needed, than it is fine like this. Just one thing though. I think there is a problem in this old part of the code:

atomate2/src/atomate2/cli/dev.py

Lines 370 to 373 in aeee107

    
           empty_file = dest_dirdata / ".empty" 
        
           empty_file.write_text( 
        
               "Empty file for git to be able to have an empty directory" 
        
           )

Here the empty file is always created. As a result:

the .empty file is zipped. I don't know if it is better this, but I am not sure it was intended. It can also stay this way, but would be better to decide.
there are a lot of .empty.gz in folders that are not empty.

So I am wondering:

Is it really needed to have those empty folders in the references?
If yes (or at least we prefer to keep it this way for any reason), can you modify the abinit_test_data function, so that it only creates the file if the directory is actually empty? (Either by creating it only if the directory is really empty or by removing it when a file is copied there).

gpetretto · 2025-09-15T14:48:55Z

      - name: Install conda dependencies
        run: |
-          micromamba install -n a2 -c conda-forge enumlib packmol bader --yes
+          micromamba install -n a2 -c conda-forge enumlib packmol bader abinit --yes


Why is abinit needed? To test stuff like k/q points generation?

In general I am not sure if it is a good idea to have this dependence, since the version on conda-forge is 10.0.3. It may be that in the future this will give raise to incompatibilities between the abinit version availabe and the python, that may require a later or older version.

I think we can leave it like this at the moment and monitor how things will evolve, but if this will be cause for tests failing they may ask us to disable them.

If I remember correctly, it is because it is needed for the tests to generate the proper perturbations

I left a comment to indicate why we need abinit

Fine with me, maybe let's mention this when the real PR is opened.

gpetretto · 2025-09-15T14:49:52Z

 [project.optional-dependencies]
-abinit = ["abipy>=0.9.3"]
+#abinit = ["abipy>=0.9.3"]
+abinit = ["abipy @ git+https://github.com/abinit/abipy.git"] # tmp


just a note to remember to switch to a released abipy version before opening the PR

Bumps [mace-torch](https://github.com/ACEsuit/mace) from 0.3.15 to 0.3.16. - [Release notes](https://github.com/ACEsuit/mace/releases) - [Commits](ACEsuit/mace@v0.3.15...v0.3.16) --- updated-dependencies: - dependency-name: mace-torch dependency-version: 0.3.16 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…files + regenerate shg test

remove empty test files, fix cli for test gen, gzip pseudos

* Update dependencies. Remove mattersim. * Update pyproject. * Fix CI: update forcefield dep-group matrix to numpy-limited The e3nn-limited extra was removed from pyproject.toml but the testing matrix still referenced it. uv silently skips missing extras, so torch was never installed, breaking test-forcefields collection. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Fix forcefield and electrode tests for matgl 4.x and emmet-core 0.87 matgl >= 4.0 removed the DGL backend: matgl.config.BACKEND and the matgl.ext._ase_{dgl,pyg} modules no longer exist, and all potentials load through the unified matgl.ext.ase.PESCalculator. Update the matgl calculator branch accordingly, drop the obsolete _set_matgl_backend helper, and point CHGNet at the PyG weights (BowenD-UCB/CHGNet-PyG-*). emmet-core 0.87.1 (pulled in by the pymatgen 2026.5.4 bump) dropped the battery_id argument from InsertionElectrodeDoc.from_entries; battery_id is now a computed property derived from each entry's material_id, which is already set before the call. Remove the stale argument. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Remove dead DGL tests and skip guards matgl >= 4.0 removed the DGL backend, so the DGL-specific forcefield tests no longer exercise a real code path: - Drop test_m3gnet_static_maker / test_m3gnet_relax_maker, which monkeypatched the removed matgl.config.BACKEND to 'DGL'. - Drop test_m3gnet_pot, skipped for DGL/PyTorch 2.4 incompatibility and pinned to the legacy M3GNet-MP-2021.2.8 weights matgl 3.x dropped. - Remove the 'import dgl' fallback and the now-always-true 'dgl is None' clauses from the CHGNet skip guards, which had been silently skipping the CHGNet relax tests. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Unpin dependencies and declare conflicting extras via tool.uv Relax == pins to >= across the strict, strict-forcefields-*, jdftx, fireworks, torchsim extras and the tests/docs dependency groups so uv is free to resolve compatible versions; the uv.lock still captures exact versions for reproducibility. Documented constraints are kept: the strict-openff pymatgen pin (openff is pymatgen-sensitive) and the numpy<3 / pymongo / netCDF4 upper bounds. Add [tool.uv] conflicts declaring the four strict-forcefields-* extras and strict-openff as mutually exclusive. These pull in incompatible stacks (nequip needs numpy<2 via matscipy; deepmd/tensorflow and nequip-allegro need numpy>=2; mace/torch-dftd pin different e3nn/torch), so uv lock now builds a separate resolution per group instead of failing to satisfy all at once. Re-enable strict-forcefields-e3nn-limited and add it to the CI test matrix to keep the matrix in sync with the extras. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Add uv.lock and remove it from gitignore. * Update uvloc. * Fix torchsim reporter for torch-sim 0.6 read-only filenames torch-sim-atomistic 0.6 makes TrajectoryReporter.filenames a read-only property and opens the trajectory files in the constructor, so the post-construction 'reporter.filenames = [...]' assignment raised AttributeError. Resolve the paths up front and pass them into the constructor instead. Surfaced by unpinning torch-sim-atomistic to >=0.5. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Require torch-sim-atomistic>=0.6.0 and drop filenames compat shim Pin torch-sim-atomistic to >=0.6.0 now that the reporter code targets its read-only filenames property, and simplify the handling to mutate the (already deep-copied) reporter dict in place. Add the torchsim extra to the [tool.uv] conflicts set: torch-sim 0.6 is incompatible with strict-forcefields-generic (tensorflow pin), and CI already installs torchsim in its own isolated job. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Update uvlock. * Fix jdftx test collection under pytest 9.1 pytest 9.1 rejects a fixture that both declares params= and is overridden by an indirect @parametrize on the same test, raising 'duplicate parametrization of task_name' at collection. The task_name fixture is only consumed by test_taskdoc, which always supplies the value via indirect parametrization, so drop the redundant fixture params and keep it a pure indirect fixture. Surfaced by unpinning pytest to >=9.0.3. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Set fail-fast: false on test-forcefields and test-non-ase matrices A failure in one matrix job was cancelling its still-running siblings, masking the real per-group results (slow forcefields installs never finished). Disable fail-fast so each dep-group and split reports independently. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Cap phonopy<4 to fix Gruneisen force-constants regression phonopy 4.x changed force-constants/primitive-axis handling, breaking the phonon.save -> phonopy.load round-trip in the Gruneisen workflow ('Force constants shape disagrees with crystal structure setting'). Unpinning let phonopy float to 4.2.1; cap below the breaking major version (resolves to 3.5.1) until the workflow is made 4.x-compatible. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Run torch-limited forcefield tests single-process to avoid OOM The torch-limited dep-group loads the heaviest MLIP stack (matgl + nequip + torch with bundled CUDA libs). Under 'pytest -n auto' the parallel xdist workers each hold a copy of the models and exceed the runner's memory, killing the runner mid-test ('received a shutdown signal'). Use -n 1 for torch-limited; other groups keep -n auto. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test influence of neb forcefield test * test influence of neb forcefield test * update test * update test * update test * update test * fix test * fix test * fix test * split torch tests further * deactive more tests * activate this back in * grueneisen * fix import * fix import * add more tests back * switch to mace * fix tests * move tests to mace * fix qha tests * format * fix linting * fix linting * go back to previous forcefield installations * remove energy criterion due to forcefield change * make tests strict again * make tests strict again and fix accidential changes * fix linting test files * upgrade upet --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: jgeorge <janine.george@bam.de>

Bumps [nequip](https://github.com/mir-group/nequip) from 0.17.1 to 0.18.0. - [Release notes](https://github.com/mir-group/nequip/releases) - [Changelog](https://github.com/mir-group/nequip/blob/main/CHANGELOG.md) - [Commits](mir-group/nequip@v0.17.1...v0.18.0) --- updated-dependencies: - dependency-name: nequip dependency-version: 0.18.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [nequip-allegro](https://github.com/mir-group/allegro) from 0.8.2 to 0.8.3. - [Release notes](https://github.com/mir-group/allegro/releases) - [Changelog](https://github.com/mir-group/allegro/blob/main/CHANGELOG.md) - [Commits](mir-group/allegro@v0.8.2...v0.8.3) --- updated-dependencies: - dependency-name: nequip-allegro dependency-version: 0.8.3 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump monty from 2026.2.18 to 2026.5.18 Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2026.2.18 to 2026.5.18. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialyzeai/monty/blob/master/docs/changelog.md) - [Commits](materialyzeai/monty@v2026.2.18...v2026.5.18) --- updated-dependencies: - dependency-name: monty dependency-version: 2026.5.18 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * update test for new mp api id format * precommit * try to debug slow tests * change chgcar zip method to work better with new pymatgen-core --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com> Co-authored-by: Aaron Kaplan <kaplan@temple.edu>

* Bump jupyterlab from 4.5.7 to 4.5.8 --- updated-dependencies: - dependency-name: jupyterlab dependency-version: 4.5.8 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * fix ff test --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com> Co-authored-by: Aaron Kaplan <kaplan@temple.edu>

Bumps [ipython](https://github.com/ipython/ipython) from 9.13.0 to 9.14.1. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@9.13.0...9.14.1) --- updated-dependencies: - dependency-name: ipython dependency-version: 9.14.1 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com>

Bumps [myst-parser](https://github.com/executablebooks/MyST-Parser) from 5.0.0 to 5.1.0. - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](executablebooks/MyST-Parser@v5.0.0...v5.1.0) --- updated-dependencies: - dependency-name: myst-parser dependency-version: 5.1.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com>

Bumps [openmm](https://github.com/openmm/openmm-org) from 8.5.1 to 8.5.2. - [Commits](https://github.com/openmm/openmm-org/commits) --- updated-dependencies: - dependency-name: openmm dependency-version: 8.5.2 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com>

--- updated-dependencies: - dependency-name: jupyterlab dependency-version: 4.5.9 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: J. George <JaGeo@users.noreply.github.com>

Bumps [sevenn](https://github.com/MDIL-SNU/SevenNet) from 0.12.1 to 0.13.0. - [Release notes](https://github.com/MDIL-SNU/SevenNet/releases) - [Changelog](https://github.com/MDIL-SNU/SevenNet/blob/main/CHANGELOG.md) - [Commits](MDIL-SNU/SevenNet@v.0.12.1...v0.13.0) --- updated-dependencies: - dependency-name: sevenn dependency-version: 0.13.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

--- updated-dependencies: - dependency-name: jupyterlab dependency-version: 4.6.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [mace-torch](https://github.com/ACEsuit/mace) from 0.3.15 to 0.3.16. - [Release notes](https://github.com/ACEsuit/mace/releases) - [Commits](ACEsuit/mace@v0.3.15...v0.3.16) --- updated-dependencies: - dependency-name: mace-torch dependency-version: 0.3.16 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [wandb](https://github.com/wandb/wandb) from 0.24.0 to 0.27.2. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.24.0...v0.27.2) --- updated-dependencies: - dependency-name: wandb dependency-version: 0.27.2 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 9.0.3 to 9.1.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@9.0.3...9.1.1) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [calorine](https://gitlab.com/materials-modeling/calorine) from 3.3 to 3.4. - [Release notes](https://gitlab.com/materials-modeling/calorine/tags) - [Commits](https://gitlab.com/materials-modeling/calorine/compare/3.3...3.4) --- updated-dependencies: - dependency-name: calorine dependency-version: '3.4' dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [wandb](https://github.com/wandb/wandb) from 0.27.2 to 0.28.0. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.27.2...v0.28.0) --- updated-dependencies: - dependency-name: wandb dependency-version: 0.28.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [ipython](https://github.com/ipython/ipython) from 9.14.1 to 9.15.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@9.14.1...9.15.0) --- updated-dependencies: - dependency-name: ipython dependency-version: 9.15.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Support batching for the elastic workflow * Update model construction due to API changes * Remove unsupported models * Remove legacy models from TorchSimModelType * Add tests for torchsim model wrappers * Revert mattersim changes * skip test if torchsim is not installed * Minimalistic elastic workflow for torchsim * Add tests * WIP: adapt common elastic jobs * Fix Optimizer being casted to its string value when passed to a jobflow.job * squeeze the stress tensor * Support TorchSim symmetry constraints * Convert the stress to kbar * Unit conversion without ASE * Batched phonon workflow * Remove ase and torchsim dependencies from common phonon jobs * Use lighter model * Fix tests * Disable torchsim in test-non-ase jobs * Fix phonon maker type check and improve readability * Include cell forces to the convergence check * Add values check on different phonon derived properties * Improve socket keyword documentation * Add elastic workflow tutorial * Loosen test tolerance --------- Co-authored-by: J. George <JaGeo@users.noreply.github.com>

Enrico Marazzi and others added 27 commits July 23, 2025 12:17

Merge branch 'abinit_dfpt_victor' into abinit_dfpt

8135689

Divide dfpt base and core

a70e38c

dfpt final fixing

220bd05

Merge branch 'main' of github.com:materialsproject/atomate2

9bff883

pull trunk main

Merge branch 'abinit_dfpt' of github.com:emarazzi/atomate2 into abini…

7a99828

…t_dfpt pull Enrico dfpt

fix del_gzip_files with output['dirs'] as dict

db5408a

Merge pull request #3 from VicTrqt/abinit_dfpt

e8d4e04

Quick fix

Remove VASP_VDW_KERNEL_DIR (materialsproject#1267)

34dcf1c

Currently, it does nothing as noted in materialsproject#959. The better PR would be to make it work, but we shouldn't have an unused setting around since that will confused users more.

Fix: Support 3rd and higher order elastic tensor in schema

12ceeb1

[Breaking] ML forcefields - use emmet trajectory by default (material…

20b758c

…sproject#1219)

Bug fixes in force field flows + housekeeping (materialsproject#1286)

a401cd2

* minor bug fixes + pytest xdist for on-runner parallelism * bump precommit and remove deprecated pragma * ensure aims test is independent of run order

Update README.md (materialsproject#1287)

707fd31

migrate unused openff/mm schemas + custom interchange to atomate2 (ma…

6490fda

…terialsproject#1290)

gpetretto reviewed Sep 19, 2025

View reviewed changes

Enrico Marazzi and others added 2 commits September 25, 2025 12:00

Review Phonon wf

f827273

1st round of guido's review + linting

759a140

dependabot Bot and others added 30 commits May 11, 2026 09:42

gzip test pseudos and fix their handling

8203e34

fix test pseudo gz 14si.fhi

dd8d7c6

rm empty test files/dirs and ignore their absence when mocking

4e96e3b

remove path get_differences + fix cli/dev generate abinit test empty …

b638743

…files + regenerate shg test

remove testing CI

0d45cfe

Merge pull request #13 from VicTrqt/abinit_dfpt

598d614

remove empty test files, fix cli for test gen, gzip pseudos

Check abinit phonon tests without empty folders

c13df39

revise warnings for matgl-related models (materialsproject#1479)

48d255c

Fix anaddb outputdoc

17b9b88

Update contributors list (materialsproject#1508)

4a20440

Merge branch 'main' into abinit_dfpt

be780e5

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Abinit dfpt#2

Abinit dfpt#2
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	empty_file = dest_dirdata / ".empty"
	empty_file.write_text(
	"Empty file for git to be able to have an empty directory"
	)

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emarazzi commented Jul 23, 2025 •

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