v2024.9.10

💥 Breaking: NumPy/Cython integer type changed from np.long/np.int_ to int64 on Windows to align with NumPy 2.x, changing the default integer type to int64 on Windows 64-bit systems in favor of the platform-dependent np.int_ type.
Recommendation: Please explicitly declare dtype=np.int64 when initializing a NumPy array if it's passed to a Cythonized pymatgen function like find_points_in_spheres. You may also want to test downstream packages with NumPy 1.x on Windows in CI pipelines.

🛠 Enhancements

• Formatting customization for PWInput by @jsukpark in #4001
• DOS Fingerprints enhancements by @naik-aakash in #3946
• Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. by @hongyi-zhao in #3955
• Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. by @hongyi-zhao in #3967
• Add SOC & multiple PROCAR parsing functionalities by @kavanase in #3890
• Add modification to aims input to match atomate2 magnetic order script by @tpurcell90 in #3878

🐛 Bug Fixes

• Ion: fix CO2- and I3- parsing errors; enhance tests by @rkingsbury in #3991
• Fix ruff PD901 and prefer sum over len+if by @janosh in #4012
• Explicitly use int64 in Numpy/cython code to avoid OS inconsistency by @DanielYang59 in #3992
• Update FermiDos.get_doping() to be more robust by @kavanase in #3879
• Fix missing /src in doc links to source code by @DanielYang59 in #4032
• Fix LNONCOLLINEAR match in Outcar parser by @DanielYang59 in #4034
• Fix in-place VaspInput.incar updates having no effect if incar is dict (not Incar instance) by @janosh in #4052
• Fix typo in Cp2kOutput.parse_hirshfeld add_site_property("hirshf[i->'']eld") by @janosh in #4055
• Fix apply_operation(fractional=True) by @kavanase in #4057

💥 Breaking Changes

• Pascal-case PMG_VASP_PSP_DIR_Error by @janosh in #4048

📖 Documentation

• Docstring tweaks for io.vasp.inputs and format tweaks for some other parts by @DanielYang59 in #3996
• Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark by @DanielYang59 in #4021
• Fix incorrect attribute name in Lobster.outputs.Cohpcar docstring by @DanielYang59 in #4039

🧹 House-Keeping

• Use strict=True with zip to ensure length equality by @DanielYang59 in #4011

🚀 Performance

• add LRU cache to structure matcher by @kbuma in #4036

🚧 CI

• Install optional boltztrap, vampire and openbabel in CI by @DanielYang59 in #3985

💡 Refactoring

• Make AimsSpeciesFile a dataclass by @tpurcell90 in #4054

🧪 Tests

• Remove the skip mark for test_delta_func by @njzjz in #4014
• Recover commented out code in tests and mark with pytest.mark.skip instead by @DanielYang59 in #4027
• Add unit test for io.vasp.help by @DanielYang59 in #4020

🧹 Linting

• Fix failing ruff PT001 on master by @DanielYang59 in #4003
• Fix fixable ruff rules by @DanielYang59 in #4015
• Fix S101, replace all assert in code base (except for tests) by @DanielYang59 in #4017
• Fix ruff PLC0206 and PLR6104 by @janosh in #4035

🏥 Package Health

• Drop Python 3.9 support by @DanielYang59 in #4009
• Avoid importing namespace package pymatgen directly by @DanielYang59 in #4053

🏷️ Type Hints

• Set kpoints in from_str method as integer in auto Gamma and Monkhorst modes by @DanielYang59 in #3994
• Improve type annotations for io.lobster.{lobsterenv/outputs} by @DanielYang59 in #3887

🤷‍♂️ Other Changes

• VaspInputSet.write_input: Improve error message by @yantar92 in #3999

New Contributors

• @yantar92 made their first contribution in #3999
• @kbuma made their first contribution in #4036

Full Changelog: v2024.8.9...v2024.9.10

v2024.8.9

• Revert bad split of sets.py, which broke downstream code.

🎉 New Features

• Add multiwfn QTAIM parsing capabilities by @espottesmith in #3926

🐛 Bug Fixes

• Fix chemical system method for different oxidation states by @danielzuegner in #3915
• Fix coordination number bug by @jmmshn in #3954
• Fix Ion formula parsing bug; add more special formulas by @rkingsbury in #3942
• Dedup numpydependency in pyproject by @janosh in #3970
• test_graph: add filename only to pdf list by @drew-parsons in #3972
• Bugfix: io.pwscf.PWInput.from_str() by @jsukpark in #3931
• Fix d2k function by @tpurcell90 in #3932
• Assign frame properties to molecule/structure when indexing trajectory by @CompRhys in #3979

🛠 Enhancements

• Element/Species: order full_electron_structure by energy by @rkingsbury in #3944
• Extend CubicSupercell transformation to also be able to look for orthorhombic cells by @JaGeo in #3938
• Allow custom .pmgrc.yaml location via new PMG_CONFIG_FILE env var by @janosh in #3949
• Fix MPRester tests and access phonon properties from the new API without having mp-api installed. by @AntObi in #3950
• Adding Abinit magmoms from netCDF files to Structure.site_properties by @gbrunin in #3936
• Parallel Joblib Process Entries by @CompRhys in #3933
• Add OPTIMADE adapter by @ml-evs in #3876
• Check Inputs to Trajectory. by @CompRhys in #3978

📖 Documentation

• Replace expired BoltzTraP link by @DanielYang59 in #3929
• Correct method get_projection_on_elements docstring under Procar class by @DanielYang59 in #3945

🧹 House-Keeping

• Split VASP input sets into submodules by @janosh in #3865

🚧 CI

• Install some optional dependencies in CI by @DanielYang59 in #3786

💡 Refactoring

• Fix Incar check_params for Union type by @DanielYang59 in #3958

🏥 Package Health

• build against NPY2 by @njzjz in #3894

🏷️ Type Hints

• Improve types for electronic_structure.{bandstructure/cohp} by @DanielYang59 in #3873
• Improve types for electronic_structure.{core/dos} by @DanielYang59 in #3880

🤷‍♂️ Other Changes

• switch to attr access interface for transformation matrix by @tsmathis in #3964
• Fix import sorting by @janosh in #3968
• Don't run issue-metrics on forks by @ab5424 in #3962
• Enable Ruff rule family "N" and "S" by @DanielYang59 in #3892

New Contributors

• @danielzuegner made their first contribution in #3915
• @tsmathis made their first contribution in #3964
• @jsukpark made their first contribution in #3931

Full Changelog: v2024.7.18...v2024.8.8

v2024.7.18

layout: default
title: Change Log

v2024.6.10

layout: default
title: Change Log

v2024.6.4

What's Changed

🐛 Bug Fixes

• Run CI with two different uv resolution strategies: highest and lowest-direct by @janosh in #3852
• Fix filter condition for warn msg of unphysical site occupancy in io.cif by @DanielYang59 in #3853

🛠 Enhancements

• Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] by @janosh in #3858

📖 Documentation

• Clarify argument shift for SlabGenerator.get_slab by @DanielYang59 in #3748

🚧 CI

• Add CI run without 'optional' deps installed by @janosh in #3857

Full Changelog: v2024.5.31...v2024.6.4

v2024.5.31

What's Changed

🐛 Bug Fixes

• Make Beautifulsoup optional by @ab5424 in #3774
• Fix overlayed subplots in BSPlotterProjected.get_projected_plots_dots() by @janosh in #3798
• Fix _get_dipole_info for DDEC6 ChargemolAnalysis and add test case by @JonathanSchmidt1 in #3801
• Cp2kOutput.parse_initial_structure() use regex for line matching to allow arbitrary white space between Atom/Kind/Element/... by @janosh in #3810
• Fix the minor document error in POTCAR Setup. by @hongyi-zhao in #3834
• Use isclose over == for overlap position check in SlabGenerator.get_slabs by @DanielYang59 in #3825
• [Deprecation] Replace Element property is_rare_earth_metal with is_rare_earth to include Y and Sc by @DanielYang59 in #3817

🛠 Enhancements

• Add is_radioactive property to Element class by @AntObi in #3804
• Add a from_ase_atoms() method to Structure by @Andrew-S-Rosen in #3812
• Adapt to the latest version of PWmat output file by @lhycms in #3823
• Update VASP sets to transition atomate2 to use pymatgen input sets exclusively by @esoteric-ephemera in #3835 (slightly breaking, see #3860 for details)

📖 Documentation

• Imperative get_... method and @property doc strings by @janosh in #3802
• Doc string standardization by @janosh in #3805

🧹 House-Keeping

• Add types for core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc) by @DanielYang59 in #3829
• Move test structures out of util directory by @DanielYang59 in #3831

🧪 Tests

• Improve type annotations for core.(trajectory/units) by @DanielYang59 in #3832

🏷️ Type Hints

• More type annotations by @janosh in #3800
• Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash by @DanielYang59 in #3814
• Guard TYPE_CHECKING only imports by @DanielYang59 in #3827
• Improve type annotations and comments for io.cif by @DanielYang59 in #3820
• Improve type annotations for core.structure by @DanielYang59 in #3837
• Add type annotations for io.vasp.outputs by @DanielYang59 in #3776

🤷‍♂️ Other Changes

• mixing scheme: change default for verbose by @tschaume in #3806
• ruff 0.4.3 auto-fixes by @janosh in #3808
• Re-enable some useful ruff rules by @DanielYang59 in #3813
• pandas.read_csv: replace deprecated delim_whitespace=True with sep="\s+" by @ab5424 in #3846
• Improve unphysical (greater than 1) occupancy handling in CifParser and add missing site label if not check_occu by @DanielYang59 in #3819

Full Changelog: v2024.5.1...v2024.5.31

v2024.5.1

What's Changed

🐛 Bug Fixes

• Fix OPTIMADE rester URL contruction and improve testing by @ml-evs in #3756
• Add fix for SFAC writer by @stefsmeets in #3779
• Fix LobsterSet by @naik-aakash in #3771
• Update vasprun.converged_ionic logic when EDIFFG=0, REDO of PR #3765 by @matthewkuner in #3783
• Fix for incorrect file path in tests/io/test_zeopp.py by @AntObi in #3784
• Fix for writing non-unique site labels in CifWriter by @stefsmeets in #3767
• Homogenize return type of Lattice.get_points_in_sphere to always be np.array(s) by @janosh in #3797

📖 Documentation

• Add note to documentation for usage of CrystalNN by @JaGeo in #3764
• Update to average Grüneisen documentation by @JaGeo in #3773
• Format doc strings by @janosh in #3790
• Imperative doc strings by @janosh in #3792

🧹 House-Keeping

• pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster by @DanielYang59 in #3757
• Separate test files by modules and collect test files csv/cif into folders by @DanielYang59 in #3746

🚧 CI

• Officially support Python 3.12 and test in CI by @janosh in #3685

🏥 Package Health

• Remove gulp from package data, code base and CI tests by @DanielYang59 in #3789

🏷️ Type Hints

• Add type annotations for io.vasp.inputs/optics by @DanielYang59 in #3740
• pyright fixes by @DanielYang59 in #3777
• Convert kpts in Kpoints to Sequence[tuple] and set it as property by @DanielYang59 in #3758

🤷‍♂️ Other Changes

• add get_string->get_str alias for Poscar by @timurbazhirov in #3763
• Fix ruff FURB192 by @janosh in #3785

New Contributors

• @timurbazhirov made their first contribution in #3763
• @AntObi made their first contribution in #3784

Full Changelog: v2024.4.13...2024.5.1

v2024.4.13

Hot fix release for v2024.4.12 to be yanked on PyPI due to #3751.

🐛 Bug Fixes

• Revert mistaken Cohp.has_antibnd_states_below_efermi rename by @JaGeo in #3750
• Fix typing_extension ImportError in downstream packages by @janosh in #3752
• Update some of the OPTIMADE aliases by @ml-evs in #3754

🧹 House-Keeping

• Remove duplicate ruff rule in pyproject.toml by @Andrew-S-Rosen in #3755

Full Changelog: v2024.4.12...v2024.4.13

v2024.4.12

What's Changed

🎉 New Features

• Add pymatgen.io.openff module by @orionarcher in #3729

🐛 Bug Fixes

• Fix blank line bug in io.res.ResWriter by @stefsmeets in #3671
• Reset label for sites changed by Structure.replace_species() by @stefsmeets in #3672
• Fix phonopy.get_pmg_structure site_properties key for magmoms by @JonathanSchmidt1 in #3679
• Improve Bandoverlaps parser by @naik-aakash in #3689
• Convert some staticmethod to classmethod by @DanielYang59 in #3710
• Correct units of Element.atomic_orbitals by @esoteric-ephemera in #3714
• Add a fix for if a parameter is None in AimsControlIn by @tpurcell90 in #3727
• Replace general raise Exception and add missing raise keyword by @DanielYang59 in #3728
• Fix ChemicalPotentialDiagram 2D plot not respecting formal_chempots setting by @uliaschauer in #3734
• Update ENCUT type to float in incar_parameters.json by @yuuukuma in #3741
• Clean up core.surface comments and docstrings by @DanielYang59 in #3691
• Fix io.cp2k.input.DataFile by @DanielYang59 in #3745

🛠 Enhancements

• Ensure MSONAtoms is indeed MSONable when Atoms.info is loaded with goodies by @Andrew-S-Rosen in #3670
• Generalize fatband plots from Lobster by @JaGeo in #3688
• Plotting of Multicenter COBIs by @JaGeo in #2926
• Support appending vectors to positions in XSF format by @mturiansky in #3704
• Define needs_u_correction(comp: CompositionLike) -> set[str] utility function by @janosh in #3703
• Add more flexibility to PhononDOSPlotter and PhononBSPlotter by @ab5424 in #3700
• Define ElementType enum in core/periodic_table.py by @janosh in #3726

📖 Documentation

• Reformat docstrings to Google style and add type annotations by @DanielYang59 in #3694

🧹 House-Keeping

• Breaking: all plot methods return plt.Axes by @janosh in #3749
• Clean up test files: VASP outputs by @DanielYang59 in #3653
• Clean up test files: VASP inputs by @DanielYang59 in #3674
• Clean up test files: dedicated VASP directories, xyz, mcif, cssr, exciting, wannier90 by @DanielYang59 in #3681
• Remove exception printing when importing phonopy by @lan496 in #3696
• Standardize test names: e.g. LatticeTestCase -> TestLattice by @janosh in #3693
• Clean up tests by @janosh in #3713
• Fix import order for if TYPE_CHECKING: block by @DanielYang59 in #3711
• Use Self type in Method Signatures by @DanielYang59 in #3705
• Remove deprecated analysis.interface, rename classes to PascalCase and rename with_* to from_* by @DanielYang59 in #3725
• Test EntrySet.ground_states and CIF writing in NEBSet.write_input by @janosh in #3732

🚀 Performance

• Migrate CI dependency installation from pip to uv by @janosh in #3675
• Dynamic __hash__ for BalancedReaction by @DanielYang59 in #3676

🚧 CI

• Prevent GitHub Actions from running docs-related CI on forks by @lan496 in #3697

🧪 Tests

• Clean up tests 2 by @janosh in #3716
• Remove unnecessary unittest.TestCase subclassing by @janosh in #3718

🔒 Security Fixes

• Avoid using exec in code by @DanielYang59 in #3736
• Avoid using eval, replace manual offset in enumerate and rename single letter variables by @DanielYang59 in #3739

🏷️ Type Hints

• Self return type on from_dict methods by @janosh in #3702
• Return self from Structure methods replace, substitute, remove_species, remove_sites by @janosh in #3706
• Self return type on Lattice methods by @janosh in #3707

🤷‍♂️ Other Changes

• os.path.(exists->isfile) by @janosh in #3690

New Contributors

• @JonathanSchmidt1 made their first contribution in #3679
• @uliaschauer made their first contribution in #3734

Full Changelog: v2024.3.1...v2024.4.12

v2024.3.1

What's Changed

🐛 Bug Fixes

• Fix BSPlotterProjected.get_projected_plots_dots_patom_pmorb fix set & list intersect by @janosh in #3651
• Remove rounding during FEFF writing by @matthewcarbone in #3345
• Fix get_niggli_reduced_lattice if entering A1 case by @packer-jp in #3657
• Remove BadPoscarWarning when POSCAR elements set by POTCAR by @esoteric-ephemera in #3662
• Fix RuntimeError triggered in CI of downstream packages by @janosh in #3664

🛠 Enhancements

• Kpoint.__eq__ and PhononBandStructureSymmLine.__eq__ methods + tests by @janosh in #3650
• LOBSTER IO improvements by @naik-aakash in #3649

📖 Documentation

• Lobsterout update doc-string to match renamed class variable by @naik-aakash in #3655
• Fix installation.md formatting by @Andrew-S-Rosen in #3661

🧹 House-Keeping

• Use np.eye(3) instead of [[1, 0, 0], [0, 1, 0], [0, 0, 1]] for identies by @janosh in #3659

🧪 Tests

• Deprecate _parse_atomic_densities in BaderAnalysis and fix Bader test setup by @DanielYang59 in #3656

🏷️ Type Hints

• Improve INCAR tag check by @DanielYang59 in #3621

🤷‍♂️ Other Changes

• Avoid bader_caller from altering compressed file in place by @DanielYang59 in #3660

New Contributors

• @matthewcarbone made their first contribution in #3345
• @packer-jp made their first contribution in #3657

Full Changelog: v2024.2.23...v2024.3.1