v2023.6.28

• Use lru_cache to speed up get_el_sp by 400x (@v1kko).
• Related to lru_cache of get_el_sp, Species.properties is now deprecated in favor of setting Species(spin=5). The rationale is
  that spin is the only supported property for Species anyway. Species and DummySpecies is now mostly immutable, i.e., setting specie.spin = 5 have no effect. This is as intended since the first version of pymatgen.

v2023.06.23

We're pleased to ship the latest and greatest Pymatgen v2023.06.23 today! 🎉 👨‍💻 🌮

Besides squashing many bugs, we give you a brand new Molecule.relax() [code] courtesy of @arosen93 in #3044 to match the existing but now matGL-M3GNet-powered Structure.relax() [code].

What's more, we have some shiny new (Structure|Molecule).calculate() [code] methods for single-point ASE calculations if you just want a quick energy estimate for example:

from pymatgen.core import Lattice, Structure

structure = Structure(
    lattice=Lattice.cubic(2.8),
    species=("Fe", "Fe"),
    coords=((0, 0, 0), (0.5, 0.5, 0.5)),
)
print(f"M3GNet energy={structure.calculate().calc.results['energy'][0]:.4} eV")
>>> M3GNet energy=-16.84 eV

What's Changed

• Update DictSet to allow direct initialization by @kavanase in #3031
• DOC: remove "structure" from init by @lbluque in #3030
• MPAqueousCompatiblity: compute hydrate correction using reduced rather than full composition by @rkingsbury in #2886
• Don't do a hard bandgap==0 check in the r2SCAN workflow by @arosen93 in #3036
• Improvements to PDPlotter: unary plots, 2D ternaries, better defaults, and highlight entries by @mattmcdermott in #3032
• Rename VaspInputSet.(potcar_functional->user_potcar_functional) and start testing DictSet by @janosh in #3035
• Simplify dict["key"] if "key" in dict else None to dict.get("key") by @janosh in #3038
• Fix LMAXMIX default in VASP INCAR now set based on element blocks in structure by @janosh in #3041
• Better error message to clarify Structure.species only supported for ordered by @janosh in #3046
• IcohpValue.__str__ don't return None by @janosh in #3052
• PourbaixDiagram wrong composition bug fix by @montoyjh in #3053
• Migrate GHA release job to PyPI trusted publishing by @janosh in #3055
• Add (Structure|Molecule).calculate() + Molecule.relax(), improve Structure.relax() by @arosen93 in #3044
• Don't require ASE as dependency by @arosen93 in #3062
• Update doc in periodic_table.py by @755452800 in #3063
• Skip Molecule.relax() tests by @arosen93 in #3060
• Use self-documenting f-strings instead of hard-coding var names by @janosh in #3064
• Fix ValueError: Unexpected atomic number Z=0 by @janosh in #3066
• PymatgenTest add auto-used tmp_path fixture (replaces ScratchDir) by @janosh in #3067
• Remove assertEqual vestiges in tests by @janosh in #3069
• More pytest.approx() refactoring by @janosh in #3072
• Update test_kpath_lm.py, remove redundant test and simplify tests by @JaGeo in #3073
• AseAtomsAdaptor: Ensure Molecule.charge and Molecule.spin_multiplicity aren't lost upon interconversion by @arosen93 in #3056
• Single-line None assignment by @janosh in #3074
• Breaking: change Composition bad key error type from TypeError to KeyError by @janosh in #3075
• Fix ase tests not running due to pymatgen/io/ase.py shadowing ase package by @janosh in #3077
• Cosmetic fixes to AseAtomsAdaptor dictionary key ordering by @arosen93 in #3076
• Improvements to the documentation of the Lobsterenv module by @JaGeo in #3079
• More precise error message tests and more informative errors in some cases by @janosh in #3081
• Add test_apply_scissor_(insulator|spin_polarized) by @janosh in #3082
• Immutable class defaults by @janosh in #3085
• Fix hill_formula Composition property by @amkrajewski in #3086
• Fix doc string punctuation by @janosh in #3088
• Fix DosPlotterTest.test_get_plot_limits() assert floats equal not using approx by @janosh in #3089
• Check for expected error msg in pytest.raises() by @janosh in #3091
• Fix ValueError when parsing vasprun.xml with only some atom force constants by @janosh in #3092
• Fix test_babel_pc_with_ro_depth_0_vs_depth_10 by @janosh in #3093
• Set hashlib.md5(usedforsecurity=False) when computing POTCAR hashes by @janosh in #3094
• Move get_zmatrix from GaussianInput to Molecule by @JaGeo in #3095

Full Changelog: v2023.05.31...v2023.06.23

v2023.05.31

Attention ⚠️

user_potcar_settings now defaults to {"W": "W_sv"} in all VASP input sets if user_potcar_functional == "PBE_54" (since the 5.4 POTCARs dropped W_pv) (see #3022 for details)

What's Changed

• Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports by @janosh in #2981
• Fix average error by @JaGeo in #2986
• Doc strings by @janosh in #2987
• Suspected Typo Fix in pymatgen.io.vasp.optics by @kavanase in #2989
• Enable ruff doc rules in CI by @janosh in #2990
• Add type hints for pymatgen.io.ase module by @arosen93 in #2991
• Hide all type-hint-only imports behind if TYPE_CHECKING by @janosh in #2992
• Orbital-resolved icohplist by @JaGeo in #2993
• Re-export SiteCollection + DummySpecies from pymatgen.core by @janosh in #2995
• Species parse oxi state from symbol str by @janosh in #2998
• Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None by @janosh in #3002
• Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) by @janosh in #3003
• Lookup MPRester API key in settings if None provided as arg by @ml-evs in #3004
• Update .pytest-split-durations by @janosh in #3005
• Clean up by @janosh in #3010
• Fix ValueError when structure.selective_dynamics has type np.array by @janosh in #3012
• Breaking: Overhaul class PymatgenTest by @janosh in #3014
• Optimize cython find_points_in _spheres by @lbluque in #3015
• MaterialsProjectCompatibility issue deprecation warning by @janosh in #3017
• Tweak variable names by @janosh in #3019
• Unignore ruff PD011 by @janosh in #3020
• Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" by @janosh in #3022

Full Changelog: v2023.5.10...v2023.05.31

v2023.5.10

• Fix mem leak in pbc_shortest_vector cython code. (@stichri)
• Set all cython code to language level 3.

v2023.5.8

❗ 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

v2023.3.23

• Misc bug fixes.
• Enable Structure relaxations with TrajectoryObserver (@janosh)

v2023.3.10

Update docs

v2023.2.28

First release (in a while) with pre-built Linux wheels thanks to @njzjz! 🎉

What's Changed

• use cibuildwheel to build linux wheels by @njzjz in #2800
• Merge setup.cfg into pyproject.toml by @janosh in #2858
• del class AtomicFile, _maketemp(), ask_yesno() by @janosh in #2860
• fix reduced formula in Ion by @yang-ruoxi in #2864
• Prepare release 2023.2.28 by @janosh in #2867

Full Changelog: v2023.2.22...v2023.2.28

What's Changed

• use cibuildwheel to build linux wheels by @njzjz in #2800
• Merge setup.cfg into pyproject.toml by @janosh in #2858
• del class AtomicFile, _maketemp(), ask_yesno() by @janosh in #2860
• fix reduced formula in Ion by @yang-ruoxi in #2864
• Prepare release 2023.2.28 by @janosh in #2867

Full Changelog: v2023.2.22...v2023.2.28

v2023.2.22

What's Changed

• Fix pre-commit.ci isort error by @janosh in #2825
• Changes to Q-Chem IO to allow CDFT and coupling calculations by @espottesmith in #2674
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2834
• Add inplace flag to select whether to adjust entries in place by @peikai in #2841
• Default check_stable to False in PatchedPhaseDiagram.get_decomp_and_e_above_hull() for speed by @janosh in #2842
• Document difference between Composition.get_el_amt_dict() and Composition.as_dict() by @janosh in #2846
• Manually update OPTIMADE database aliases and add option to refresh on init by @ml-evs in #2848
• Add Ruff linter by @janosh in #2847
• Fix auto-fixable pydocstyle errors through ruff by @janosh in #2850
• Fix OPTIMADE client generated filters and URLs by @ml-evs in #2853
• Run pyupgrade and flake8-simplify through ruff by @janosh in #2851
• Fix typo in OPTIMADE client: remove quotes in response fields by @ml-evs in #2856
• Ruff c4+ruf rules by @janosh in #2854
• Add python-version 3.11 to GH action matrix strategy by @janosh in #2714
• 2023.2.22 release by @janosh in #2857

Full Changelog: v2023.1.30...v2023.2.22

v2023.1.30

Update docs