Pymatgen

What's Changed

🐛 Bug Fixes

* Fix `BSPlotterProjected.get_projected_plots_dots_patom_pmorb` fix set & list intersect by janosh in https://github.com/materialsproject/pymatgen/pull/3651
* Remove rounding during FEFF writing by matthewcarbone in https://github.com/materialsproject/pymatgen/pull/3345
* Fix `get_niggli_reduced_lattice` if entering A1 case by packer-jp in https://github.com/materialsproject/pymatgen/pull/3657
* Remove BadPoscarWarning when POSCAR elements set by POTCAR by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3662
* Fix RuntimeError triggered in CI of downstream packages by janosh in https://github.com/materialsproject/pymatgen/pull/3664

🛠 Enhancements

* `Kpoint.__eq__` and `PhononBandStructureSymmLine.__eq__` methods + tests by janosh in https://github.com/materialsproject/pymatgen/pull/3650
* LOBSTER IO improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3649

📖 Documentation

* Lobsterout update doc-string to match renamed class variable by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3655
* Fix installation.md formatting by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3661

🧹 House-Keeping

* Use `np.eye(3)` instead of `[[1, 0, 0], [0, 1, 0], [0, 0, 1]]` for identies by janosh in https://github.com/materialsproject/pymatgen/pull/3659

🧪 Tests

* Deprecate `_parse_atomic_densities` in `BaderAnalysis` and fix `Bader` test setup by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3656

🏷️ Type Hints

* Improve INCAR tag check by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3621

🤷‍♂️ Other Changes

* Avoid `bader_caller` from altering compressed file in place by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3660

New Contributors

* matthewcarbone made their first contribution in https://github.com/materialsproject/pymatgen/pull/3345
* packer-jp made their first contribution in https://github.com/materialsproject/pymatgen/pull/3657

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.23...v2024.3.1

🐛 Bug Fixes

* Remove properties from abivars dict as this breaks the interface with… by gmatteo in https://github.com/materialsproject/pymatgen/pull/3642

🛠 Enhancements

* Modified CifParser.check() as one possible solution for issue 3626 by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3628
* Add capability for Vasprun to read KPOINTS_OPT data by bfield1 in https://github.com/materialsproject/pymatgen/pull/3509

🧪 Tests

* Compress test vasprun.xml files by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3648

🤷‍♂️ Other Changes

* Modify `BadInputSetWarning` logic for relaxations of a likely metal by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3634
* Fix Lobsterenv Bug by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3637
* [BugFix] Subclass Construction Locpot<:VolumetricData by jmmshn in https://github.com/materialsproject/pymatgen/pull/3639
* Add interface to icet SQS tools through SQSTransformation by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3593
* Guard `MSONAtoms` definition behind ASE package availability by ml-evs in https://github.com/materialsproject/pymatgen/pull/3645
* Alias `VaspInputSet` to `VaspInputGenerator` by janosh in https://github.com/materialsproject/pymatgen/pull/3566

New Contributors

* bfield1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3509

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.20...v2024.2.23

This release addresses an important security issue that might affect some users of pymatgen who are parsing untrusted user input, for example a server using pymatgen to parse a user-uploaded CIF file. More information is available in the associated [CVE](https://github.com/materialsproject/pymatgen/security/advisories/GHSA-vgv8-5cpj-qj2f). Thank you to [William Khem-Marquez (SteakEnthusiast)](https://github.com/SteakEnthusiast) for the discovery and responsible disclosure of this issue.

🐛 Bug Fixes

* Revert back `TransformedStructure.__getattr__` by mjwen in https://github.com/materialsproject/pymatgen/pull/3617
* Fixed Incar object to allow for ML_MODE vasp tag by davidwaroquiers in https://github.com/materialsproject/pymatgen/pull/3625
* Add missing `MPSCANRelaxSet.yaml` parameters and alphabetize by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3615
* Fix `bader_analysis_from_path` using warning as file path and reinstate test by janosh in https://github.com/materialsproject/pymatgen/pull/3632

🛠 Enhancements

* Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates by jinlhr542 in https://github.com/materialsproject/pymatgen/pull/3572
* Handle invalid selective dynamics info in POSCAR by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3539
* Return `self` from all `SiteCollection/Structure/Molecule` in-place modification methods by janosh in https://github.com/materialsproject/pymatgen/pull/3623
* Make the POTCAR setup instructions clearer by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3630

🧹 House-Keeping

* Refactors + types + fix doc string returns to use Google format by janosh in https://github.com/materialsproject/pymatgen/pull/3620

🚀 Performance

* Speeding up `get_nn_info` in local_env.py by ftherrien in https://github.com/materialsproject/pymatgen/pull/3635

💥 Breaking Changes

* Lobsterenv improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3624

🤷‍♂️ Other Changes

* Fix URL joining in OptimadeRester by rdamaral in https://github.com/materialsproject/pymatgen/pull/3613
* Create a `CODEOWNERS` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3616
* Adds support for an `MSONAtoms` class that's an `MSONable` form of an ASE `Atoms` object by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3619
* Lobster io improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3627

New Contributors

* jinlhr542 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3572
* rdamaral made their first contribution in https://github.com/materialsproject/pymatgen/pull/3613
* ftherrien made their first contribution in https://github.com/materialsproject/pymatgen/pull/3635

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.8...v2024.2.20

🐛 Bug Fixes

* Fix `Vasprun.get_potcars` search method; tweak fake POTCARs by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3587

🛠 Enhancements

* Aims input sets by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3482
* Add `SiteCollection.reduced_formula` property by janosh in https://github.com/materialsproject/pymatgen/pull/3610
* Add `Entry.(formula|reduced_formula)` by janosh in https://github.com/materialsproject/pymatgen/pull/3611
* VASP IO `copy()` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3602

📖 Documentation

* Adding FHI-aims inputs developers by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3592

🧹 House-Keeping

* chore: fix a typo by VsevolodX in https://github.com/materialsproject/pymatgen/pull/3609

🧪 Tests

* Add tests for the New Vasp input sets by Zhuoying in https://github.com/materialsproject/pymatgen/pull/3576

🏥 Package Health

* Switch macOS wheel building to new M1 runners by janosh in https://github.com/materialsproject/pymatgen/pull/3596

🤷‍♂️ Other Changes

* Fix text formatting in `bug_report.yaml` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3589
* Minor update to avoid deprecation warning by kavanase in https://github.com/materialsproject/pymatgen/pull/3601

New Contributors

* VsevolodX made their first contribution in https://github.com/materialsproject/pymatgen/pull/3609

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.1.27...v2024.2.8

🐛 Bug Fixes

* Fix label propagation in `Symmetry.from_spacegroup` by stefsmeets in https://github.com/materialsproject/pymatgen/pull/3527
* Bug fix: SpectrumPlotter.add_spectra by minhsueh in https://github.com/materialsproject/pymatgen/pull/3529
* Fix bug in SQSTransformation by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3541
* Fix failing CI due to broken BoltzTraP2 install by janosh in https://github.com/materialsproject/pymatgen/pull/3543
* Enforce `zval` to be an integer to avoid improper syntax in `.cri` file by wladerer in https://github.com/materialsproject/pymatgen/pull/3502
* Fix MaterialsProjectCompatibility run type handling for GGA+U by rkingsbury in https://github.com/materialsproject/pymatgen/pull/3540
* Accept `Path` objects as `filename` in `IStructure.to()` by janosh in https://github.com/materialsproject/pymatgen/pull/3553
* Retain `Structure.properties` in `structure_from_abivars()`/`structure_to_abivars()` round trip by janosh in https://github.com/materialsproject/pymatgen/pull/3552
* Support `magmoms` in `get_phonopy_structure()` by tomdemeyere in https://github.com/materialsproject/pymatgen/pull/3555
* Fix `ValueError: Invalid fmt` with `Structure.to(fmt='yml')` by janosh in https://github.com/materialsproject/pymatgen/pull/3557
* Improve CIF checking, support for isotopes, and correct handling of new VASP 6.4.2 POSCAR format incl. slashes in header by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3542
* Deprecate `Structure.ntypesp` replaced by `Structure.n_elems` by janosh in https://github.com/materialsproject/pymatgen/pull/3562
* Ruff fixes by janosh in https://github.com/materialsproject/pymatgen/pull/3564
* Fix highly-nested parens when formula parsing in `Composition` by janosh in https://github.com/materialsproject/pymatgen/pull/3569
* Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3574
* Support parsing of "final_energy" in Q-Chem 6.1.1 by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3580

🛠 Enhancements

* Add GitHub Issue Templates by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3528
* Improve `PhononBandStructure.has_imaginary_gamma_freq()` by checking for negative freqs at all q-points close to Gamma by janosh in https://github.com/materialsproject/pymatgen/pull/3530
* Add default issue template labels by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3531
* Add functionality to read ASE *.traj file in Trajectory class method from_file() by exenGT in https://github.com/materialsproject/pymatgen/pull/3422
* Add `PhononDos.r2_score` method by janosh in https://github.com/materialsproject/pymatgen/pull/3535
* Add codespace container for reproducing issues by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3537
* Phonon convenience imports by janosh in https://github.com/materialsproject/pymatgen/pull/3544
* Add diffusive thermal conductivity model proposed by Agne et al. by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3546
* Add flag `write_site_properties = False` in `CifWriter` for writing `Structure.site_properties` as `_atom_site_{prop}` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3550
* Add `pymatgen.io.pwmat` module by lhycms in https://github.com/materialsproject/pymatgen/pull/3512
* Lazy import `pandas` in `Structure.as_dataframe()` to improve startup speed by janosh in https://github.com/materialsproject/pymatgen/pull/3568
* Return `self` in `SiteCollection` spin/oxi state add/remove methods by janosh in https://github.com/materialsproject/pymatgen/pull/3573
* Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR 3574 by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3577

🧹 House-Keeping

* Pass file IO modes as kwarg by janosh in https://github.com/materialsproject/pymatgen/pull/3560
* Remove deprecated `(to|from|as|get)_string` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3561

🧪 Tests

* Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3491
* Add test for `NEBAnalysis.get_plot()` by janosh in https://github.com/materialsproject/pymatgen/pull/3570
* `tests/io/aims` use `numpy.testing.assert_allclose` and `pytest.MonkeyPatch` by janosh in https://github.com/materialsproject/pymatgen/pull/3575

💥 Breaking Changes

* Breaking: remove single-use `PolarizationLattice` which inherited from `Structure` (antipattern) by janosh in https://github.com/materialsproject/pymatgen/pull/3585

🤷‍♂️ Other Changes

* Standardise and update VASP input sets by utf in https://github.com/materialsproject/pymatgen/pull/3484

New Contributors

* DanielYang59 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3528
* minhsueh made their first contribution in https://github.com/materialsproject/pymatgen/pull/3529
* exenGT made their first contribution in https://github.com/materialsproject/pymatgen/pull/3422
* wladerer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3502
* tomdemeyere made their first contribution in https://github.com/materialsproject/pymatgen/pull/3555
* lhycms made their first contribution in https://github.com/materialsproject/pymatgen/pull/3512

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.12.18...v2024.1.26

🐛 Bug Fixes

* Improve doc strings substitution_probability.py by JaGeo in https://github.com/materialsproject/pymatgen/pull/3477
* Convert all FHI-aims stresses to be 3x3 instead of Voigt notation by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3476
* Revert `pymatgen/symmetry/groups.py` module-scoped `SymmOp` import causing circular import by janosh in https://github.com/materialsproject/pymatgen/pull/3486
* fix reciprocal_density in MPHSEBSSet and tests by fraricci in https://github.com/materialsproject/pymatgen/pull/3499
* fix TypeError when attr force_field not exists by xjf729 in https://github.com/materialsproject/pymatgen/pull/3495
* Fix pdplotter.show with matplotlib backend by lbluque in https://github.com/materialsproject/pymatgen/pull/3493
* Fix legend label order in `PhononBSPlotter.plot_compare()` by janosh in https://github.com/materialsproject/pymatgen/pull/3510

🛠 Enhancements

* Define `PBE64Base.yaml` for new VASP PBE_64 POTCARs by janosh in https://github.com/materialsproject/pymatgen/pull/3470
* `(Structure|Molecule).alphabetical_formula` by janosh in https://github.com/materialsproject/pymatgen/pull/3478
* Improvements to `PhononDosPlotter` and `PhononBSPlotter` by janosh in https://github.com/materialsproject/pymatgen/pull/3479
* `PhononDosPlotter.plot_dos()` add support for existing `plt.Axes` by janosh in https://github.com/materialsproject/pymatgen/pull/3487
* Allow Structure.interpolate to extrapolate by kyledmiller in https://github.com/materialsproject/pymatgen/pull/3467
* Updates for Vasprun with MD simulations by gpetretto in https://github.com/materialsproject/pymatgen/pull/3489
* Add gradient, Hessian, and orbital coeffs scratch file parsers to `pymatgen.io.qchem.outputs` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3483
* Add multipole parsing for Q-Chem IO by espottesmith in https://github.com/materialsproject/pymatgen/pull/3490
* `CifParser` only warn about `primitive` default value change to `False` if not passed to `parse_structures` explicitly by janosh in https://github.com/materialsproject/pymatgen/pull/3505
* `PhononBSPlotter.plot_compare()` add legend labels by janosh in https://github.com/materialsproject/pymatgen/pull/3507
* Define arithmetic ops `__add__` `__sub__` `__mul__` `__neg__` `__eq__` for `PhononDos` with tests by janosh in https://github.com/materialsproject/pymatgen/pull/3511
* Equalize `Phonon(Dos|BS)Plotter` colors, allow custom plot settings per-DOS by janosh in https://github.com/materialsproject/pymatgen/pull/3514
* Add bold flag to `latexify` by janosh in https://github.com/materialsproject/pymatgen/pull/3516
* `Composition` raise `ValueError` if `formula` string is only numbers and spaces by janosh in https://github.com/materialsproject/pymatgen/pull/3517
* Raise `ValueError` for `float('NaN')` in `Composition` by janosh in https://github.com/materialsproject/pymatgen/pull/3519
* Add `PhononDos.mae()` and `PhononBandStructure.has_imaginary_gamma_freq()` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3520
* `PhononDos.get_smeared_densities` return unchanged for `sigma=0` by janosh in https://github.com/materialsproject/pymatgen/pull/3524
* Add `PhononDos.get_last_peak()` by janosh in https://github.com/materialsproject/pymatgen/pull/3525

📖 Documentation

* QCInput: add docstrings for svp and pcm_nonels by rkingsbury in https://github.com/materialsproject/pymatgen/pull/3522

🚀 Performance

* Avoid redirects in `MPRester` requests by tschaume in https://github.com/materialsproject/pymatgen/pull/3496

🧪 Tests

* Fix weak `__str__` tests across pymatgen by janosh in https://github.com/materialsproject/pymatgen/pull/3472
* Test improvements by janosh in https://github.com/materialsproject/pymatgen/pull/3497

🏷️ Type Hints

* `ruff` automatic type annotations by janosh in https://github.com/materialsproject/pymatgen/pull/3498

New Contributors

* kyledmiller made their first contribution in https://github.com/materialsproject/pymatgen/pull/3467

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.11.12...v2023.12.18