pymatgen 2023.5.8

v2023.5.8

on Python PyPI

❗ The Yb_2 deprecation release ❗

This release changes the Ytterbium (Yb) pseudo-potential (PSP) from Yb_2 to Yb_3 for all PBE_54 VASP input sets.

Background: The A-lab revealed that as a result of using Yb_2 the energy on Yb compounds is off by a lot, resulting in supposedly stable things being unsynthesizable. While an unfortunate mistake, it's also great to see how experiment can help surface simulation errors.

On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results for most systems since Yb is most often in oxidation state Yb3+.

Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds.

For more details see #2968 and #2969.

What's Changed

• Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in #2907
• Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in #2908
• Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in #2909
• Update team.rst by @jmmshn in #2912
• Faff by @janosh in #2915
• Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in #2916
• Modified dosplotter by @kaueltzen in #2844
• auto version by @jmmshn in #2925
• bug fix for potcar parsing by @jmmshn in #2910
• Fix breaking changes from pandas v2 by @janosh in #2935
• add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in #2927
• fix on reading multiple route in Gaussian input file by @Ameyanagi in #2939
• Fix CI errors by @janosh in #2940
• Add ResParser support for reading files with spin values by @ScottNotFound in #2941
• Ignore bad unicode characters in Structure.from_file() by @janosh in #2948
• Minor modification for symmetrically distinct Miller index generation by @fyalcin in #2949
• Fixed Wulff shape for new versions of matplotlib by @CifLord in #2950
• Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in #2953
• Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in #2954
• For MPcules: Molecule Trajectory and graph hashes by @espottesmith in #2945
• self.assertArrayEqual->assert by @janosh in #2955
• fix GaussianOutput bug with multiple route lines by @xjf729 in #2937
• Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in #2951
• Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in #2962
• Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in #2959
• Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in #2960
• Bump numpy from 1.23.2 to 1.24.3 by @dependabot in #2963
• Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in #2961
• Bump pandas from 1.4.4 to 2.0.1 by @dependabot in #2964
• Link /addons from new subsection on /contributing page by @janosh in #2967
• Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in #2969
• fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in #2973
• Revert to Yb_2 on pre-PBE_54 input sets by @janosh in #2972
• Enable flake8-pytest-style via ruff by @janosh in #2975
• Enable all ruff pylint rules (excl. PLR) by @janosh in #2977
• only return unique point group operations by @mueslo in #2942

New Contributors

• @kaueltzen made their first contribution in #2844
• @chiang-yuan made their first contribution in #2951
• @mueslo made their first contribution in #2942

Full Changelog: v2023.3.23...v2023.5.8