Bump pymatgen from 2023.12.18 to 2024.1.27 #693
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Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2023.12.18 to 2024.1.27. - [Release notes](https://github.com/materialsproject/pymatgen/releases) - [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md) - [Commits](materialsproject/pymatgen@v2023.12.18...v2024.1.27) --- updated-dependencies: - dependency-name: pymatgen dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
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Hi @janosh, do you have any idea what could be causing the errors with the new pymatgen version? |
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@utf this error File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/atomate2/vasp/sets/base.py", line 556, in _get_previous
vasprun, outcar = get_vasprun_outcar(prev_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py", line 2734, in get_vasprun_outcar
Vasprun(vsfile, parse_dos=parse_dos, parse_eigen=parse_eigen),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 296, in __init__
self.update_potcar_spec(parse_potcar_file)
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 1054, in update_potcar_spec
if potcar := self.get_potcars(path):
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 1010, in get_potcars
f"{search_path}/{fn}" for fn in os.listdir(search_path) if fn.startswith("POTCAR") and ".spec" not in fnwas fixed in materialsproject/pymatgen#3587 and released in https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.1 |
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hold on, pmg release didn't actually make it to PyPI because i changed to the new (now free) macOS M1 runners which as discussed here don't ship with |
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@utf @JaGeo the 4 remaining failing tests raise in INFO jobflow.managers.local:local.py:118 generate_phonon_displacements failed with exception:
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/jobflow/managers/local.py", line 114, in _run_job
response = job.run(store=store)
^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/jobflow/core/job.py", line 583, in run
response = function(*self.function_args, **self.function_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/atomate2/common/jobs/phonons.py", line 166, in generate_phonon_displacements
phonon = Phonopy(
^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/phonopy/api_phonopy.py", line 171, in __init__
self._primitive_matrix = self._set_primitive_matrix(primitive_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/phonopy/api_phonopy.py", line 3830, in _set_primitive_matrix
return guess_primitive_matrix(self._unitcell, symprec=self._symprec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/phonopy/structure/cells.py", line 1693, in guess_primitive_matrix
raise RuntimeError(msg)
RuntimeError: Can not be used with the unit cell having magnetic moments. |
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I think there was a discussion about this already in the pull request how one can solve it. (see materialsproject/pymatgen#3555 (comment)). |
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A newer version of pymatgen exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged. |
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@dependabot rebase |
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Looks like this PR has been edited by someone other than Dependabot. That means Dependabot can't rebase it - sorry! If you're happy for Dependabot to recreate it from scratch, overwriting any edits, you can request |
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@dependabot recreate |
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Superseded by #719. |
Bumps pymatgen from 2023.12.18 to 2024.1.27.
Release notes
Sourced from pymatgen's releases.
... (truncated)
Changelog
Sourced from pymatgen's changelog.
... (truncated)
Commits
ac8a7e9Update docs5137111Fix monty version.575f404v2024.1.26e9cc87aremove unneeded unittest tearDown methods9a0eb81Breaking: remove single-usePolarizationLatticewhich inherited from `Struc...f345f2ftest nested square bracket in formula strings9604d75Allow square brackets in composition. Fixes #3583.c0c40ddfix variable clash "dist" in zero_d_graph_to_molecule_graph() introduced in 7...cb2f490Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in a...0b8be98Support parsing of "final_energy" in Q-Chem 6.1.1 (#3580)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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