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Changelog

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

v2024.2.23

🐛 Bug Fixes

Remove properties from abivars dict as this breaks the interface with… by @gmatteo in #3642

🛠 Enhancements

Modified CifParser.check() as one possible solution for issue #3626 by @kaueltzen in #3628
Add capability for Vasprun to read KPOINTS_OPT data by @bfield1 in #3509

🧪 Tests

Compress test vasprun.xml files by @DanielYang59 in #3648

🤷‍♂️ Other Changes

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

New Contributors

@bfield1 made their first contribution in #3509

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

v2024.2.20

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. Thank you to William Khem-Marquez (@SteakEnthusiast) for the discovery and responsible disclosure of this issue.

🐛 Bug Fixes

Revert back TransformedStructure.__getattr__ by @mjwen in #3617
Fixed Incar object to allow for ML_MODE vasp tag by @davidwaroquiers in #3625
Add missing MPSCANRelaxSet.yaml parameters and alphabetize by @Andrew-S-Rosen in #3615
Fix bader_analysis_from_path using warning as file path and reinstate test by @janosh in #3632

🛠 Enhancements

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

🧹 House-Keeping

Refactors + types + fix doc string returns to use Google format by @janosh in #3620

🚀 Performance

Speeding up get_nn_info in local_env.py by @ftherrien in #3635

💥 Breaking Changes

Lobsterenv improvements by @naik-aakash in #3624

🤷‍♂️ Other Changes

Fix URL joining in OptimadeRester by @rdamaral in #3613
Create a CODEOWNERS by @Andrew-S-Rosen in #3616
Adds support for an MSONAtoms class that's an MSONable form of an ASE Atoms object by @Andrew-S-Rosen in #3619
Lobster io improvements by @naik-aakash in #3627

New Contributors

@jinlhr542 made their first contribution in #3572
@rdamaral made their first contribution in #3613
@ftherrien made their first contribution in #3635

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

v2024.2.8

🐛 Bug Fixes

Fix Vasprun.get_potcars search method; tweak fake POTCARs by @esoteric-ephemera in #3587

🛠 Enhancements

Aims input sets by @tpurcell90 in #3482
Add SiteCollection.reduced_formula property by @janosh in #3610
Add Entry.(formula|reduced_formula) by @janosh in #3611
VASP IO copy() methods by @janosh in #3602

📖 Documentation

Adding FHI-aims inputs developers by @tpurcell90 in #3592

🧹 House-Keeping

chore: fix a typo by @VsevolodX in #3609

🧪 Tests

Add tests for the New Vasp input sets by @Zhuoying in #3576

🏥 Package Health

Switch macOS wheel building to new M1 runners by @janosh in #3596

🤷‍♂️ Other Changes

Fix text formatting in bug_report.yaml by @Andrew-S-Rosen in #3589
Minor update to avoid deprecation warning by @kavanase in #3601

New Contributors

@VsevolodX made their first contribution in #3609

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

v2024.1.26

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

Pass file IO modes as kwarg by @janosh in #3560
Remove deprecated (to|from|as|get)_string methods by @janosh in #3561

🧪 Tests

Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests by @esoteric-ephemera in #3491
Add test for NEBAnalysis.get_plot() by @janosh in #3570
tests/io/aims use numpy.testing.assert_allclose and pytest.MonkeyPatch by @janosh in #3575

💥 Breaking Changes

Breaking: remove single-use PolarizationLattice which inherited from Structure (antipattern) by @janosh in #3585

🤷‍♂️ Other Changes

Standardise and update VASP input sets by @utf in #3484

New Contributors

@DanielYang59 made their first contribution in #3528
@minhsueh made their first contribution in #3529
@exenGT made their first contribution in #3422
@wladerer made their first contribution in #3502
@tomdemeyere made their first contribution in #3555
@lhycms made their first contribution in #3512

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

v2023.12.18

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

QCInput: add docstrings for svp and pcm_nonels by @rkingsbury in #3522

🚀 Performance

Avoid redirects in MPRester requests by @tschaume in #3496

🧪 Tests

Fix weak __str__ tests across pymatgen by @janosh in #3472
Test improvements by @janosh in #3497

🏷️ Type Hints

ruff automatic type annotations by @janosh in #3498

New Contributors

@kyledmiller made their first contribution in #3467

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

v2023.11.12

🐛 Bug Fixes

Hot fix: pymatgen package missing potcar-summary-stats.json.bz2 by @janosh in #3468

🛠 Enhancements

Add Composition.charge and charge_balanced properties by @janosh in #3471

v2023.11.10

🐛 Bug Fixes

Fix LobsterMatrices calculated incorrectly by @naik-aakash in #3407
Fix test_relax_chgnet by @janosh in #3417
Breaking: return sum of Species with matching Element in Composition.__getitem__ by @janosh in #3427
Update inputs.py by @RedStar-Iron in #3430
Fix lattice velocities formatting by @gpetretto in #3433
Fix lobsterin dict inheritance and treat \t in lobsterins correctly by @JaGeo in #3439
Fix BSPlotterProjected.get_elt_projected_plots by @janosh in #3451
Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms by @kaifengZheng in #3426
Write test-created files to temporary directory, don't pollute test dir by @janosh in #3454
Issue stronger warning if bader is run without the AECCARs by @janosh in #3458
Fix Vasprun not interpreting float overflow as nan by @tawe141 in #3452
Aims bug fixes by @tpurcell90 in #3466

🛠 Enhancements

Add LobsterMatrices parser to lobster.io.outputs by @naik-aakash in #3361
Propagate site labels in SymmetrizedStructure() by @stefsmeets in #3423
Add lattice velocities to Poscar by @gpetretto in #3428
Add summary_stats key to Vasprun.potcar_spec by @esoteric-ephemera in #3434
Deprecate CifParser.get_structures() in favor of new parse_structures in which primitive defaults to False by @janosh in #3419
FHI-aims IO Parsers by @tpurcell90 in #3435

🧹 House-Keeping

Rename Poscar.from_file() check_for_POTCAR to check_for_potcar by @janosh in #3406
Remove warning in cohp module by @JaGeo in #3418
Drop black for ruff format by @janosh in #3420
Refresh OPTIMADE aliases and update docstrings by @ml-evs in #3447
Use convenience exports from pymatgen/core/__init__.py where no risk of circular imports by @janosh in #3461
Move needlessly function-scoped imports to module scope by @janosh in #3462
Module-scoped imports by @janosh in #3464

🤷‍♂️ Other Changes

Create jekyll-gh-pages.yml by @shyuep in #3410
Make from_(str|file) (static->class)methods by @janosh in #3429

New Contributors

@RedStar-Iron made their first contribution in #3430
@tawe141 made their first contribution in #3452
@tpurcell90 made their first contribution in #3435

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.10.11...v2023.11.10

v2023.10.11

🐛 Bug Fixes

Fix outdated setup.py find_namespace_packages and add test_egg_sources_txt_is_complete by @janosh in #3374
release.yml add option to publish to TestPyPI by @janosh in #3375
Fix wrong unit=eV in get_band_(skewness|kurtosis) doc string by @janosh in #3383
Further updating POTCAR validation / identification by @esoteric-ephemera in #3392
MatPESStaticSet.yaml set LMAXMIX: 6 by @janosh in #3400
Fix type annotations in phonon/ and lammps/ by @ab5424 in #3401
Fix OBAlign(includeH=False, symmetry=False) can't take keywords by @janosh in #3403

🛠 Enhancements

New class to handle NcICOBILIST.lobster files by @QuantumChemist in #2878
Add inplace: bool=True arg to Structure.apply_strain() by @janosh in #3376
Add Structure.to_(conventional|primitive|cell) methods by @janosh in #3384
Add SiteCollection.to_ase_atoms() by @janosh in #3389
Add mode: Literal["w", "a", "wt", "at"] = "w" keyword to CifWriter.write_file() by @janosh in #3399

📖 Documentation

Add docs/fetch_pmg_contributors.py script by @janosh in #3387

🧹 House-Keeping

Fix ruff FURB violations by @janosh in #3382
Remove deprecated module pymatgen/util/convergence.py by @janosh in #3388
Remove pylint: disable comments by @janosh in #3390
Fix ruff N806 by @janosh in #3394

🧪 Tests

Update incar_parameters.json to allow ISIF=8 by @matthewkuner in #3381
Add test_potcar_summary_stats() by @janosh in #3395
Mirror atomate2 fix and improve MPScanRelaxSet.test_kspacing edge case coverage by @janosh in #3396

💥 Breaking Changes

Breaking: snake_case FiestaInput keywords and class attributes by @janosh in #3386
Ion: default hydrates=False in reduced_formula by @rkingsbury in #3350

🏷️ Type Hints

Add type annotations to io/lammps by @ab5424 in #3379
Add type annotations to phonon by @ab5424 in #3393

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.10.4...v2023.10.11

v2023.10.4

🐛 Bug Fixes

Fix missing potcar_summary_stats.json.gz in setup.package_data by @janosh in #3372
Bug fixes for MPRester and packaged data by @shyuep

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.10.3...v2023.10.4

v2023.10.3

🐛 Bug Fixes

Revert openbabel.OBAlign() in molecule_matcher.py to use positional args for includeH, symmetry by @janosh in #3353
Fix MPMD set bug by @MichaelWolloch in #3355
Fix TestMPResterNewBasic + AseAtomsAdaptor test errors and TransformedStructure.from_snl overwriting hist variable by @janosh in #3362
Fix TypeError: can only join an iterable with AECCAR in VolumetricData.write_file by @chiang-yuan in #3343

🛠 Enhancements

Don't rely on jsanitize in Atoms <--> Structure object interconversion by @Andrew-S-Rosen in #3359
Breaking: New method of POTCAR validation by @esoteric-ephemera in #3351
Add alias .to_file() for .to() method of structures and molecules by @QuantumChemist in #3356

🧹 House-Keeping

Chargemol minor refactor by @janosh in #3357
Breaking typo fix: Targe(tt->t)edPenaltiedAbundanceChemenvStrategy by @janosh in #3360
Fix undiscovered tests by @janosh in #3369

🏥 Package Health

Bump min numpy to v1.25.0 by @janosh in #3352

New Contributors

@esoteric-ephemera made their first contribution in #3351
@QuantumChemist made their first contribution in #3356

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.9.25...v2023.10.3

v2023.9.25

New basic MPRester implemented that supports the most common use cases without having to install mp-api. mp-api is no longer a dependency of pymatgen.
Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and get_ax_fig_plt->get_ax_fig plus no longer return plt
Misc bug fixes.

v2023.9.10

🐛 Bug Fixes

Fix code comment in ASE adapter by @Andrew-S-Rosen in #3298
Fix IndexError when parsing Hessian from Gaussian frequency job by @janosh in #3308

🛠 Enhancements

Add an input arg check for Kpoints.automatic_density_by_lengths by @Andrew-S-Rosen in #3299

🏥 Package Health

Remove pydantic < 2 from setup.py and bump monty in requirements.txt by @Andrew-S-Rosen in #3303
Move py.typed to package root by @Andrew-S-Rosen in #3307
Consistent casing setup->setUp across test classes by @janosh in #3305

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10

🛠 Enhancements

Add an input arg check for Kpoints.automatic_density_by_lengths by @Andrew-S-Rosen in #3299

🏥 Package Health

Remove pydantic < 2 from setup.py and bump monty in requirements.txt by @Andrew-S-Rosen in #3303
Move py.typed to package root by @Andrew-S-Rosen in #3307
Consistent casing setup->setUp across test classes by @janosh in #3305

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10

v2023.9.2

Add Lattice property params_dict by @janosh in #3239
Generate SupercellTransformation from minimum boundary distance by @JiQi535 in #3238
More concise test_from_boundary_distance by @janosh in #3242
Breaking: remove deprecated keyword properties from Species by @janosh in #3243
Typo in Docs for PeriodicsSite by @jmmshn in #3249
Fix Vasprun.converged_electronic check if ALGO=CHI in INCAR by @janosh in #3250
Breaking: Have plot methods return plt.Axes object, not matplotlib module by @janosh in #3237
Fix ruff D212 by @janosh in #3251
Fix some Kpoints generated using wrong mesh types by @matthewkuner in #3245
read mag from OSZICAR by @chiang-yuan in #3146
Use numpy.testing.assert_allclose over assert np.allclose by @janosh in #3253
Don't let tests pollute the pymatgen repo by @janosh in #3255
Update compatibility.md by @mbercx in #3260
Google-style doc string return types by @janosh in #3258
Quasi-RRHO Thermochemistry Analysis Module by @arepstein in #2028
Add keyword check_occu: bool = True to CifParser.get_structures() by @jonathanjdenney in #2836
Fix bug in feff inputs.py by @kaifengZheng in #3256
Cancel concurrent CI runs to save budget by @janosh in #3263
Fix Procar.get_projection_on_elements for structures with multiple same-element ionic sites by @Na-Kawa in #3261
Fix TestMPScanStaticSet.test_as_from_dict() by @janosh in #3266
Bump activesupport from 7.0.6 to 7.0.7.2 in /docs by @dependabot in #3267
Fix TestMPStaticSet using MPRelaxSet in test_user_incar_kspacing and test_kspacing_override by @janosh in #3268
Fix nelectrons not updating when replacing species in Molecule by @janosh in #3269
Add properties to Structure and Molecule by @gpetretto in #3264
Fix CifParser.get_structures(check_occu=False) by @janosh in #3272
Add PotcarSingle.__repr__ by @janosh in #3273
__str__ to __repr__ by @janosh in #3274
Ion: handle dissolved gas formulas by @rkingsbury in #3275
Add VASP input set MatPESStaticSet by @SophiaRuan in #3254
Fix test_valid_magmom_struct() error message regex by @janosh in #3276
fix tests of MatPESStaticSet by @SophiaRuan in #3281
Breaking: bump minimum Python version to 3.9 by @janosh in #3283
Breaking: Update AseAtomsAdaptor to handle Structure.properties/Molecule.properties by @Andrew-S-Rosen in #3270
Slightly relax the constraint satisfy condition of get_primitive_structure() by @fyalcin in #3285
[WIP] add custodian modified incar settings to incar and modify tests by @SophiaRuan in #3284
Add keyword bandgap_tol: float = 1e-4 to MPScanRelaxSet by @janosh in #3287
np.(arange->linspace) in io/vasp/optics.py get_delta, get_setp and epsilon_imag by @LucasGVerga in #3286
MatPESStaticSet restore GGA tag removal if xc_functional.upper() == "R2SCAN" by @janosh in #3288
Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 by @dependabot in #3294
Bump cython from 3.0.0 to 3.0.2 by @dependabot in #3292
Bump scipy from 1.11.1 to 1.11.2 by @dependabot in #3291
Bump plotly from 5.11.0 to 5.16.1 by @dependabot in #3289
Bump joblib from 1.3.1 to 1.3.2 by @dependabot in #3290
Bump mp-api from 0.33.3 to 0.35.1 by @dependabot in #3293
xyz.iter() -> iter(xyz) by @janosh in #3228
Deprecate overlooked from/as_..._string methods by @janosh in #3295

v2023.8.10

fix estimate_nbands function by @matthewkuner in #3149
Add CifParser.get_structures(on_error='warn') by @janosh in #3175
ruff . --fix by @janosh in #3176
AseAtomsAdaptor: Retain tags property when interconverting Atoms and Structure/Molecule by @Andrew-S-Rosen in #3151
Fix a bug in pwscf.py. The proc_val function modifies string values. by @pablogalaviz in #3172
Delete commented out print statements by @janosh in #3178
lots of from_string should be classmethod by @njzjz in #3177
Extend lobsterenv for coop/cobi by @naik-aakash in #3050
BUG: fix setting zero magmoms by @lbluque in #3179
Prefer pymatviz interactive plotly version of periodic table heatmap if available by @janosh in #3180
Better Composition repr by @janosh in #3182
Breaking: Return True for Element in Composition if Species.symbol matches Element by @janosh in #3184
Revert LMAXMIX "fix" added in #3041 by @janosh in #3189
Add bader_exe_path keyword to BaderAnalysis and run bader tests in CI by @janosh in #3191
Unskip and fix packmol tests by @janosh in #3195
Propagate labels through various Structure operations by @stefsmeets in #3183
Delete variable self assignments by @janosh in #3196
Improve Structure tests by @janosh in #3197
Test class XYZ edge cases by @janosh in #3206
Fix EnergyAdjustment.__repr__ by @janosh in #3207
Markdownlint by @janosh in #3209
Fix codecov by @janosh in #3210
Update pytest-split durations by @janosh in #3211
Fix GitHub language statistics after test files migration by @janosh in #3214
Fix automatic_density_by_lengths and add tests for it by @janosh in #3218
Prefer len(structure) over structure.num_sites by @janosh in #3219
Add PhaseDiagram method get_reference_energy by @janosh in #3222
Fix isomorphic for molecular graphs by @rohithsrinivaas in #3221
Add Structure.elements property by @janosh in #3223
Add keyword in_place: bool = True to SiteCollection.replace_species by @janosh in #3224
list offending elements in BVAnalyzer.get_valences error message by @janosh in #3225
Add Entry.elements property by @janosh in #3226
Move PymatgenTest.TEST_FILES_DIR attribute into module scope by @janosh in #3227
f-string path construction everywhere, no need for os.path.join(...) by @janosh in #3229
speed up bader_caller and chargemol_caller by @chiang-yuan in #3192
Fix ruff PYI041 and ignore PYI024 by @janosh in #3232
Deprecate get_string() methods in favor of get_str() by @janosh in #3231
Structure/Molecule.to() now always return same string written to file by @janosh in #3236

New Contributors

@matthewkuner made their first contribution in #3149
@pablogalaviz made their first contribution in #3172
@rohithsrinivaas made their first contribution in #3221

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.7.20...v2023.08.10

v2023.7.20

Unreadable string concat ops to f-string by @janosh in #3162
Revert mp-api<0.34.0 pin by @janosh in #3165
Fix CI error "pdentries_test.csv" not found by @janosh in #3168
Fix issues with labels by @stefsmeets in #3169

v2023.7.17

Cython 3.0 support.
PR #3157 from @mattmcdermott magnetic-analyzer-fix. Fixes bug briefly mentioned in #3070, where recent spin property changes resulted in the MagneticStructureEnumerator failing. This is apparently due to creating structures where only some Species.spin properties are defined, causing CollinearMagneticStructureEnumerator` to fail.
PR #3070 from @mattmcdermott magnetic-enumerator-fix. To summarize: changes to default magnetic moments introduced in #2727 now mean that structures with only partially defined magnetic moments (e.g., on half the sites) cannot be successfully analyzed by SpaceGroupAnalyzer. This was encountered when performing magnetic ordering enumeration, as the previous default behavior for MagOrderingTransformation does not implicitly yield spins of 0 on the nonmagnetic sites. This has now been fixed.

v2023.7.14

Emergency bug fix release to remove use of sys.path in pymatgen.io.ase package.
Fix "Incompatible POTCAR" error on ComputedEntries with oxidation states.
New global config variable PMG_POTCAR_CHECKS provides means to disable all POTCAR checking.

v2023.7.11

Use joblib to speed up expensive enumeration energy computations.
Minor cleanups.

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.
PR #3111 from @xjf729 fix-MoleculeGraph-draw_graph
PR #3030 from @lbluque Remove superfluous structure argument docstring from SQSTransformation init
PR #3031 from @kavanase Quick fix to allow direct initialisation of the DictSet class.
PR #3015 from @lbluque Optimized cython code in find_points_in_spheres, getting ~5x faster runtime.

v2023.6.23

PR #3062 from @Andrew-S-Rosen asefix Closes #3061. @JaGeo
PR #3030 from @lbluque master Remove superfluous structure argument docstring from SQSTransformation init
PR #3031 from @kavanase master This is a quick fix to allow direct initialisation of the DictSet class, which was possible before but broke in #2972 due to the Yb_2 check querying self.CONFIG, which is only defined if DictSet was being initialised from a subclass and not directly.
PR #3015 from @lbluque neighbors Optimized cython code in find_points_in_spheres, getting ~5x faster runtime.

v2023.5.31

Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" #3022
Unignore ruff PD011 #3020
Tweak variable names #3019
MaterialsProjectCompatibility issue silencable deprecation warning #3017
Optimize cython find_points_in _spheres #3015
Cp2k 2.0 #2672
Added methods to compute and compare DOS fingerprints #2772
Breaking: Overhaul class PymatgenTest #3014
Fix ValueError when structure.selective_dynamics has type np.array #3012
Clean up #3010
Update .pytest-split-durations #3005
Lookup MPRester API key in settings if None provided as arg #3004
Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) #3003
Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None #3002
Species parse oxi state from symbol str #2998
Re-export SiteCollection + DummySpecies from pymatgen.core #2995
Orbital-resolved icohplist #2993
Hide all type-hint-only imports behind if TYPE_CHECKING #2992
Add type hints for pymatgen.io.ase module #2991
Enable ruff doc rules in CI #2990
Suspected Typo Fix in pymatgen.io.vasp.optics #2989
Doc strings #2987
Fix average error #2986
Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports #2981
Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) #3022
fix unwanted x margins in get_elt_projected_plots_color (closes #562) #562
Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) #2756
add doc str explaining need for class ElementBase (closes #2999) #2999
Update docs. 3e3c31c <https://github.com/materialsproject/pymatgen/commit/3e3c31c8d342c84f2c6bbb961c321e458b9accb9>_
ruff set isort.split-on-trailing-comma = false c0ec534 <https://github.com/materialsproject/pymatgen/commit/c0ec53452c3dc87c6cca5edc1c6b2b6218f15569>_

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 <https://newscenter.lbl.gov/2023/04/17/meet-the-autonomous-lab-of-the-future> 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 #2968and #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
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

v2023.3.23

Misc bug fixes.
Enable Structure relaxations with TrajectoryObserver (@janosh)
Breaking: Rename gen_sl_transform_matrices->gen_sl_transform_matrices (#2894)

v2023.3.10

PR #2882 substrate-optimizations for speed up (@mkhorton)
Fix very fragile POTCAR parsing.

v2023.2.28

69a548e210 revert adding ubuntu-latest to release job matrix
e63cab3620 add 3.11 to release job python-versions
c03dacb94d use cibuildwheel to build linux wheels (#2800)
fe2597d92e Merge setup.cfg into pyproject.toml (#2858)
40cbf1d7c4 del class AtomicFile, _maketemp(), ask_yesno() from pymatgen/util/io_utils.py (#2860)
0b16987f2c fix reduced formula in Ion (#2864)

v2023.2.22

PR #2848 from @ml-evs ml-evs/update_optimade_aliases Currently OptimadeRester defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means they will not be used if the user provides their own filtered list of aliases, without doing some extra work. This PR refreshes the vendored list of aliases (which should be much more stable now since their initial addition 2 years ago), and also adds the option to refresh the aliases on initialization of the class. This currently affects the pymatgen OPTIMADE tutorials at https://github.com/Materials-Consortia/optimade-tutorial-exercises.

v2023.1.30

PR #2806 from @samblau qchem
- Major changes to Q-Chem IO (inputs.py and outputs.py) to accommodate differences and new features in version 6+
- Additional parsing capabilities for HOMO/LUMO, dipoles, NBO info (hyperbonds and 3C bonds) in outputs.py
- Utility for processing a parsed binary Hessian scratch file
- Overdue updates to default values in sets.py and new defaults associated with differences and new features in Q-Chem 6+
PR #2814 from @jmmshn patch_dos

Added Convenience to obtain the normalized CompleteDos object

Added tests to make sure calling it multiple time still only gives one result.

v2023.1.20

Passthrough kwargs support for Structure.from_file and Structure.from_str
Allow the frac_tolerance to be specified for rounding coordinates in CifParser.
PR #2803 from @amkrajewski add_weightbasedfunctions When working with metallic alloys, weight-fraction-based notations such as Ti64 / Ti-6V-4Al or NiTiNOL60 / Ni-40Ti are commonly employed in both industrial specifications and scientific literature. Regardless of the numerous downsides of this situation, including errors in scientific experiments or NLP-parsing when they are mistaken for atomic fractions or chemical formulas, being able to create a Composition object from them (under correct interpretation) would be a useful pymatgen feature.
- Composition class method to initialize it from a dictionary of weight fractions
- Composition property giving a dictionary of weight fractions
- concise tests for the two above were added QChem: translate DMSO name in smd_solvent

v2023.1.9

PR #2792 from @JaGeo bug_fix
PR #2773 from @ab5424 cbar
PR #2776 from @MichaelWolloch master
PR #2762 from @MichaelWolloch master
PR #2774 from @dgaines2 fix-poscar
PR #2667 from @nwinner volumetric-data-patch
PR #2764 from @naik-aakash lobster_lsodos
PR #2215 from @rkingsbury cmirs
PR #2742 from @materialsproject pip-dependabot
PR #2741 from @materialsproject resurrect-req-txt
PR #2735 from @njzjz patch-1

v2022.11.7

PR #2724 from @janosh: raise ValueError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries
PR #2720 by @utf: Fix tensor mapping
PR #2562 from @sudarshanv01: In case the Fock-matrix and eigenvalues are requested by the user (though the flags scf_final_print or scf_print), outputs.py now allows parsing both these quantities.

v2022.11.1

Order of kwargs fmt and filename in Structure.to() swapped for ease of use (note: this can break codes that do not use these options as kwargs).
@yuzie007 Parse "Atomic configuration" in POTCAR (52 and 54). Useful for estimating a reasonable NBANDS value.
EnumerateStructureTransformation now supports m3gnet_relax or m3gnet_static options.

v2022.10.22

Allow env settings to override .pmgrc.yaml (@janosh)
Add EntryLike type (@janosh)
Update spglib to 2.0+.
@cnncnnzh Method to plot the atom-resolved phonon band structures.
@jmmshn More Flexible reproduction of VASP's optical code
@Ameyanagi Fix the sorting of the FEFF IO module to create ATOMS input.
@JaGeo Extend the ThermalDisplacementMatrices class to read cif files in P1 format.
@rkingsbury Changes to FEFF I/O to support the use of non-periodic input structures.
@jmmshn Merge Waverder and Wavederf
@jmmshn Set the structure_charge while parsing Potcar

v2022.9.21

@chunweizhu fix the bugs when running TEMCalculator
@munrojm Support for new MPRester.

v2022.9.8

@janosh Add AirssProvider.as_dict
@gpetretto Outcar parsing optimization.
@ScottNotFound Adds res file io to handle results from airss searches
@janosh Fixes the AttributeError currently raised when passing disordered structures to methods like get_cn() and get_bonded_structure() of CrystalNN and other NearNeighbors subclasses.
@naik-aakash Added new option standard_with_comp_range for generating lobsterin files using vasp

v2022.8.23

Structure Graphs from Lobster Data (@JaGeo)
Added 'get_orbit_and_generators'-method to SpaceGroup class (@nheinsdorf)
Class to handle Thermal displacements matrices (@JaGeo)
Change default number of significant digits to write VASP POSCAR (@henriquemiranda)
Misc bug fixes.

v2022.7.25

Implemented sufficient methods for new MPRester to cover about 70-80% of common use cases.

v2022.7.24.1

Implementation changed to allow seamless use of MPRester regardless of whether new or old API key is used.

v2022.7.24

Initial implementation of MPRester2 with new API support. Basic functionality for now.

v2022.7.19

This will be the final release with the pymatgen.analysis.defects module included in the standard pymatgen package. This release will include the older defects code by default, but can also be replaced with the newer defects code through installation of pymatgen-analysis-defects.

Subsequent versions of pymatgen will require the additional installation of pymatgen-analysis-defects <https://github.com/materialsproject/pymatgen-analysis-defects>_ for all defect-related functionality via pip install pymatgen-analysis-defects.

Relevant imports will still be from the pymatgen.analysis.defects namespace but the code will now be maintained and developed in this separate repository.

There will be significant changes to the defects code to support new functionality.Existing PyCDT users should use this version of pymatgen or older. Any questions about this change should be directed to Jimmy-Xuan Shen, @jmmshn.

For more information about other pymatgen "add-on" packages, please see this page in our documentation <https://pymatgen.org/addons.html>_.

Preparation for the removal of the defects module, PR #2582 by @jmmshn

v2022.7.8

Welcome to new contributors @naveensrinivasan, @xivh, @dgaines2, @yang-ruoxi, @cajfisher and @mjwen!

New: Partial periodic boundary conditions, PR #2429 by @gpetretto
New: Element.from_name(), PR #2567 by @rkingsbury
New: Materials Project input set for absorption calculations, PR #2320 by @yang-ruoxi
Enhancement: compressed LAMMPS and XYZ files in pymatgen.io.lammps, PR #2538 by @ab5424
Enhancement: remove vertical lines from VoltageProfilePlotter.get_plotly_figure(), PR #2552 by @acrutt
Enhancement: chemical potential plot background color changed, PR #2559 @jmmshn
Enhancement: ability to change voronoi_distance_cutoff in ChemEnv, PR #2568 by @JaGeo
Enhancement: Ion.oxi_state_guesses will use correct charge by default, PR #2566 by @rkingsbury
Enhancement: Remove not converged warning for VASP AIMD runs, PR #2571 by @mjwen
Fix: generation of continuous line-mode band structures, PR #2533 by @munrojm
Fix: duplicate site properties for magnetic moments hwen using AseAtomsAdaptor, PR #2545 by @Andrew-S-Rosen
Fix: bug in Grüneisen parameter calculation, PR #2543 by @ab5424
Fix: allow a comment on final line of KPOINTS file, PR #2549 by @xivh
Fix: for Composition.replace with complex mappings, PR #2555 by @jacksund
Fix: Implement equality method and fix iter for InputSet, PR #2575 by @rkingsbury
Fix: use negative charge convention for electron in "update_charge_from_potcar", PR #2577 by @jmmshn
Fix: ensure charge is applied to initial and final structures parsed from vasprun.xml, PR #2579 by @jmmshn
Chore: Set permissions for GitHub actions, PR #2547 by @naveensrinivasan
Chore: Included GitHub actions in the Dependabot config, PR #2548 by @naveensrinivasan
Documentation: fix typos in pymatgen.symmetry.analyzer docstrings, PR #2561 by @dgaines2
Documentation: clarification about usage of InputFile, PR #2570 by @orionarcher
Documentation: Improve messages and warnings, PR #2572 and PR #2573 by @cajfisher
Documentation: fix typo, PR #2580 by @janosh

Notice: functionality from pymatgen.analysis.defects will be incorporated into a separate add-on package in the future, see deprecation notice.

v2022.5.26

Q-Chem updates to NBO and new geometry optimizer, PR #2521 by @samblau
Bug fix for VolumetricData, PR #2525 by @jmmshn
Bug fix for MPRester, PR #2531 by @janosh

v2022.5.19

Added option for additional criteria to be passed to MPRester.get_entries_in_chemsys (@shyuep).

v2022.5.18.1

Initial support for parsing ML MD runs from vasprun.xml (@shyuep).

v2022.5.18

Bug fix for sulfide_type. Sometimes symmetry analysis fails because of tolerance issues. A fallback to analyze all sites.

v2022.5.17

PR #2518 from @JaGeo. Fixed wrong line in ICOHPLIST.lobster being read to assess whether orbitalwise interactions are included in these files.
PR #2520 from @Andrew-S-Rosen. Adds a new property to the PointGroupAnalyzer: the rotational symmetry number.
PR #2522 from @jmmshn. Fixes PD JSON serialization.
PR #2514 from @qianchenqc. Replaced the IALGO tag with ALGO as recommended in the vasp documentation https://www.vasp.at/wiki/index.php/IALGO.
PR #2404 from @nheinsdorf. Added a method that gets all the neighbors up a maximum distance for a Structure, and groups these 'bonds' according to their symmetry.
PR #2509 from @jacksund Fix NMR Set.

v2022.4.26

Fix dipole units in recent vasp versions (at least 6.3, maybe even before) (@fraricci)
Removed complex numbers from the definition of WSWQ (@jmmshn)
MP database version logging is now no longer logged in the .pmgrc.yaml but rather in the .mprester.log.yaml. This avoids the MPRester constantly rewriting a config file and causing users' pymatgen to completely fail.

v2022.4.19

Fix for discharged and charged entries in conversion battery. (@peikai)pylint in .pre-commit-config.yaml.
Allow skipping of structure reduction in StructureMatcher.group_structures (@lan496)
Return NotImplemented for composition comparison methods. (@janosh)
BSPlotter bug fixes (@fraricci)
Misc bug fixes and deprecation fixes.

v2022.3.29

Major update to CP2K module, PR #2475 from @nwinner
Bug fix to remove problematic import, PR #2477 from @mkhorton

v2022.3.24

Emergency bugfix release to fix circular import (@janosh)

v2022.3.22

Support kwargs for ASE adaptor. (@Andrew-S-Rosen)
Fix for cation error in Lobster analysis. (@JaGeo)
Major revampt of Abstract interface for Input classes in IO. (@rkingsbury)
Orbital-projected band center, band filling, band center, skewness, kurtosis, etc. (@Andrew-S-Rosen)
Misc cleanups. (@janosh)

v2022.3.7

Add VASP WSWQ file parsing, PR #2439 from @jmmshn
Improve chemical potential diagram plotting, PR #2447 from @mattmcdermott
Update to Lobster calculation settings, PR #2434 from @JaGeo master
Allow non-integer G-vector cut-off values when parsing WAVECAR, PR #2410 from @Andrew-S-Rosen
Fix for Structure.from_file when file is in YAML format from @janosh fix-structure-from-yml
Update of linter configuration, PR #2440 from @janosh
Update to ChemEnv citation, PR #2448 from @JaGeo
Type annotation fix, PR #2432 from @janosh
Documentation fix for Structure.apply_operation, PR #2433 from @janosh
Add caching to compatibility classes as speed optimization, PR #2450 from @munrojm

This release was previously intended for v2022.2.25.

Important note: an update to a library that pymatgen depends upon has led to the ~/.pmgrc.yml configuration file being corrupted for many users. If you are affected, you may need to re-generate this file. This issue should now be fixed and not re-occur.

v2022.2.10

Require Cython during setup. (@jonringer)

v2022.2.7

Critical bug fix for pmgrc.yaml being overwritten in MPRester in a non-standard way.
Change in config file for Lobster basis. Removed the 2p orbitals for Be as they led to problems in our computations and probably should be optional during the projection. (@JaGeo)
Return None for ISPIN=1 for Vasprun('vasprun.xml').complete_dos.spin_polarization.

v2022.2.1

Chargemol caller for partial atomic charge analysis (@Andrew-S-Rosen)
ASEAtomAdaptor: (1) Updates to magmom support, (2) Oxidation states support, (3) Charges are now passed (@Andrew-S-Rosen)
Cleanup of deprecated methods. (@janosh)
Bigfix for gzipped DOSCAR (@JaGeo)
Updates for QChem Support (@samblau)
QuantumEspresso k-grid fix input fix. (@vorwerkc)
Entry.__repr__() now outputs name where available. (@janosh)
Fixes to Vasprun.final_energy to report e_0_energy (the desired energy quantity) for VASP 6+. (@Andrew-S-Rosen)
Outcar().final_energy now prints out e_0_energy (also called "energy(sigma->0)" in the OUTCAR) rather than energy_fr_energy (also called "free energy TOTEN" in the OUTCAR). This is to be consistent with Vasprun().final_energy and because it is generally the desired quantity. Outcar now has two new attributes: .final_energy_wo_entrp and final_fr_energy, which correspond to e_wo_entrp and e_fr_energy, respectively. (@Andrew-S-Rosen)
Improved parsing of coupled cluster calculations in QChem (@espottesmith).

v2022.1.24

Misc bug fixes, e.g., handling of yaml files and type check for MAGMOM flag.

v2022.1.20

Unicode fixes (@janosh)
YAML deprecation fixes. (@janosh)
ASE adaptor support for charge, spin multiiciplity and site properties of molecules. (@Andrew-S-Rosen).
New keyword option (keep_site_properties) in various structure.symmetry.analyzer functions to keep the site properties on the sites after a transformation. (@Andrew-S-Rosen)
Bug fixes for Lobster module (@JaGeo).
SCAN / GGA(+U) mixing scheme (@rkingsbury). Mixing scheme code lives in the new file mixing_scheme.py and is implemented as a Compatibility class.
Fix for parsing of QuantumExpresso files due to new format (@vorwerkc)

v2022.1.9

Formal support for Python 3.10.
Misc refactoring and bug fixes. No new functionality.

v2022.1.8

First proper new release of 2022 formalizes the switch back to date-based versioning introduced as a temporary measure last year.
Numpy version pinned to 1.22.0. This is necessary to avoid binary incompatibility.
With the numpy version, py37 support is dropped.
ASE io improvements (e.g., magnetic moments and selective dynamics transfer). @Andrew-S-Rosen
New automatic k-point generation scheme, automatic_density_by_lengths, which allows the user to specify a density of k-points in each dimension (rather than just for the entire volume). @Andrew-S-Rosen
Build improvements to dynamically generate C code by running Cython on pyx files rather than having hard-generated .c files.

v2022.0.17

Welcome to new contributor @e-kwsm!

More robust smart fermi method by @utf in #2303
Replace-species by @janosh in #2291
Add warning if improper ALGO is used for hybrid calculations by @Andrew-S-Rosen in #2298
Wrap supercell to unit cell when performing change of setting by @jmmshn in #2300
Clearer handling of the MAGMOM flag in pymatgen.io.vasp.sets by @Andrew-S-Rosen in #2301
Add warning if LASPH != True for meta-GGA/hybrid/vdW/+U by @Andrew-S-Rosen in #2297
Add ability to request additional OPTIMADE fields by @ml-evs in #2315
Add missing elements to MPScanRelaxSet PBE .54 potentials by @Andrew-S-Rosen in #2316
Fix write Trajectory XDATACAR with variable lattice by @gpetretto in #2310
Fix small cutoff neighbor by @chc273 in #2277
Add Composition.replace() by @janosh in #2284
Ion bugfixes and enhancements by @rkingsbury in #2287
Fix oddly split strings and a few typos by @janosh in #2285
InsertionElectrode bug fix and documentation update by @acrutt in #2257
Remove accidentally tracked files and unset executable flag by @e-kwsm in #2296
Update DOI URLs by @e-kwsm in #2295
Documentation update: Fix missing Outcar attributes and update elemental_dos_dos string by @Andrew-S-Rosen in #2293
Documentation update for CutOffDictNN by @ltalirz in #2278

v2022.0.16

Fix to allow PhaseDiagram to be JSON-serializable with computed data cached (@mkhorton, #2276)
Temporarily revert #2239 pending investigation into slow-down in some nearest neighbor finding routines. This does not affect the behavior of any of these classes.

v2022.0.15

Welcome to new contributors @blokhin, @pzarabadip, @ml-evs, @wuxiaohua1011, @janssenhenning and @penicillin0. A reminder to all new contributors to ensure your information is accurate at https://pymatgen.org/team.html so that you are acknowledged appropriately by filling out the linked form.

Breaking change in PhaseDiagram serialization which will affect any users of BasePhaseDiagram which has now been removed (@shyuep, 2b9911d)
Speed up nearest-neighbor routines & structure graph generation (@ltalirz, #2239)
Add two more pre-defined OPTIMADE aliases (@blokhin, #2242)
Refactor interface_reactions module, adding support for Plotly (@mattmcdermott, #2233)
Update NOMAD access in MPRester (@wuxiaohua1011, #1958)
General improvements to Phase Diagram code (@CompyRhys, #2263, #2264, #2268)
Improve appearance of periodic table heatmap (@penicillin0, #2272)
Small improvements to battery classes (@jmmshn, #2262)
Fix for Composition.chemical_system to match expected behavior for compositions with oxidation states (@CompRhys, #2249)
Fix for bad param in OPTIMADE response fields (@ml-evs, #2244)
Fix for issue in parsing bandOverlaps.lobster file (@pzarabadip, #2237)
Fix for Moladaptor (@orioncohen, #2269)
Fix for incorrect Potcar hash warnings (@mkhorton, #2273)
Type hint and correct documentation of Structure.remove_site_properties (@kmu, #2256)
Type hint improvements across pymatgen (@janosh, #2241, #2247, #2261)
Add pymatgen-io-fleur addon to addons page (@janssenhenning, #2232)

v2022.0.14

Update OPTIMADE interface to allow querying multiple providers, this changes the method signature of OptimadeRester and so is considered a backwards incompatible change (@mkhorton, #2238)

v2022.0.13

New feature to plot chemical potential diagrams (@mattmcdermott, #2218), see ArXiv:2104.05986 for example
Numerous updates to LOBSTER support for new version and including handling COBICAR, SitePotentials and MadelungEnergies (@JaGeo, #2228)
Updates and fixes for LAMMPS CombinedData (@htz1992213, #2191)
Bug fix for Bader caller (@nwinner, #2230)
Documentation fix for Composition (@CompRhys, #2231)

v2022.0.12

@chc273 Major bugfix for cython handling of fractional coordinates wrapping.
@mattmcdermott Bug fix for entry_ID phase diagram plotting bug described in this Issue: #2219
@FCMeng Fix for PWSCF to distinguish same element with different oxidation state, which might have different pseudopotentials.
@gmatteo fix minor bug when reading Structure from a netcdf4 file with hdf5 groups

v2022.0.11

New features to handle Grüneisen parameters (@JaGeo, @ab5424, @gpetretto, #2190)
New option to return SymmetrizedStructure in CifParser (@mkhorton, 0d9a455)
Fix for SubstrateAnalyzer (@shyamd, #2198)
Fix for BandFillingCorrection (@kavanase, #2193)

v2022.0.10

Add spin-dependent eigenvalue band properties (@Andrew-S-Rosen, #2187)
Bug fix for settings loading (@ardunn, #2186)

v2022.0.9

Significant new functionality for handling interfaces between structures (@shyamd, #2149)
Add input/output for CREST (@arepstein, #2020)
Add RadialSiteDistortionTransformation (@nwinner, #2108)
Add Q-Chem NBO functionality (@samblau, #2174)
Change hkl annotation format in diffraction plots (@flaviu-gostin, #2143)
Add space group to print output of SymmetrizedStructure (@CompRhys, #2139)
Better error handling in QCOutput (@rkingsbury, #2147, #2165, #2135)
Add progress bar for applying compatibility scheme (@CompRhys, #2136)
Allow combining data with multiple molecule IDs in LAMMPS (@htz1992213, #2157)
Update EDIFF in DFPT input set to be consistent with atomate (@utf, #2172)
Change names of high-symmetry paths (@munrojm, #2144)
Change default for filter_solids argument of PourbaixDiagram (@rkingsbury, #2177)
Fix to improve precision in FermiDos, NOTE: this can result in significant changes in some instances (@nwinner, #2109)
Fix for handling of Exceptions (@kmu, #2150)
Fix for PourbaixEntry (@JosephMontoya-TRI, #2148)
Fix for loading of settings from file when environment variables also set (@ardunn, #2164)
Fix equation for calculation of k-spacing in SCAN sets, NOTE: this now results in a lower k-point density (@ab5424, #2163)
Fix for parsing of VASP vasprun.xml when ALGO=CHI (@KazMorita, #2171)
Documentation update for MP2020 corrections scheme (@rkingsbury, #2141)
Documentation update for SCAN sets (@janosh, #2140)
Documentation update for using CifWriter (@755452800, #2156)

v2022.0.8

PR #2130 @rkingsbury ensures that energy corrections applied to each anion have unique names (e.g., N vs. Cl vs. Br).
PR #2133 @rkingsbury adds support for custom vdW radii to QCInput and QChemDictSet. These radii are used in the construction of PCM cavities and when calculating charges.
PR #2123 from @gpetretto fixes bug in get_conventional_standard_structure method of the SpacegroupAnalyzer for triclinic crystals.
PR #2134 from @ab5424 supports zopen in parsing lammps logs
PR #2132 from @htz1992213 speeds up LammpsData.as_string for non-hybrid data with large coeff sections and adds as_lammpsdata method to CombinedData
PR #2129 from @CifLord improves analysis of surface symmetry of slabs.
PR #2117 from @nwinner contains bug fixes for bader caller.

v2022.0.7

Improved Gaussian Cube I/O (@nwinner, #2121)
Updated van der Waals radii (@rkingsbury, #2122)
Update MaterialsProject2020Compatibility for multi-anion systems (@rkingsbury, #2128)
Fixes and improvements to Q-Chem parsing (@samblau, #2125)
Bug fix for isseus with hard-coded path in MaterialsProject2020Compatibility (@CompRhys, #2124)
Bug fix for DOS serialization (@zooks97, #2119)
Bug fix for XDATCAR lattice parsing (@nkeilbart, #2115)
Documentation link fix (@adam-kerrigan, #2127)

v2022.0.6

Feature to calculate Selling vectors and distances between Lattices (@bwjustus, #1888)
XPS Spectrum class added (@shyuep, #2110, see galore <https://github.com/SMTG-UCL/galore>_)
Updated MaterialsProject2020Compatibility for formation energy correction (@rkingsbury, #2106)
Bug fix for detecting broken bonds in slab generation (@fyalcin, #2015)
Bug fix for electrodes (@jmmshn, #2101)
Documentation improvement for get_conventional_standard_structure (@tom-wood, #2100)

v2022.0.5

Bug fix to remove possibility of duplicate edges in StructureGraph (@mkhorton, #2095)

v2022.0.4 / v2021.3.9

Element now has ionization_energies, ionization_energy and electron_affinity properties.
Extensive documentation has been added on pymatgen compatibility and the new namespace architecture! We have also released a template repo <https://github.com/materialsproject/pymatgen-addon-template>_ to help new developers write add-ons for pymatgen! Check out our :doc:contributing page</contributing> for details.

v2022.0.3

Another bug fix release! Now SETTINGS have been moved to pymatgen.core.

v2022.0.2 (Yanked)

Bug fix release for missing package data files in v2022.0.1

v2022.0.1 (Yanked)

pymatgen, pymatgen.ext, pymatgen.io and pymatgen.analysis are now namespace packages. Note that this does not affect normal usage of pymatgen from v2022.0.0. All imports remain the same. However, it does allow developers to write "add-ons" to these subpackages. A full documentation with examples and templates is in the works to guide developers on how to write these packages.

v2022.0.0 (Yanked)

This is the new version of pymatgen going forward. Root-level imports have been removed. Please see https://pymatgen.org/compatibility.html on how to update your code for compatibility with v2022.

v2021.3.5

Backwards incompatible changes in v2021.3.4 have been removed. Instead another semantic version v2022.0.0 has been released. Future critical bug fixes will be backported to v2021.x.x, but the main line of development will occur on v2022.0.0 onwards.

v2021.3.4 (Yanked)

Backwards incompatible: Pymatgen root imports have been removed from v2021.3.4 in preparation for a change to a more modular, extensible architecture that will allow more developers to contribute.

If your existing code uses from pymatgen import <something>, you will need to make modifications. The easiest way is to use an IDE to run a Search and Replace. First, replace any from pymatgen import MPRester with from pymatgen.ext.matproj import MPRester. Then, replace from pymatgen import with from pymatgen.core import. Alternatively, if you are using a Mac command line, you can do::

find . -name '.py' | xargs sed -i "" 's/from pymatgen import MPRester/from pymatgen.ext.matproj import MPRester/g' find . -name '.py' | xargs sed -i "" 's/from pymatgen import/from pymatgen.core import/g'

From a Linux command line, you can do::

find . -name '.py' | xargs sed -i 's/from pymatgen import MPRester/from pymatgen.ext.matproj import MPRester/g' find . -name '.py' | xargs sed -i 's/from pymatgen import/from pymatgen.core import/g'

This should resolve most import errors and only a few more modifications may need to be done by hand.

Specifically, the following "convenience imports" have been removed in favor of their canonical import::

from pymatgen import Composition # now "from pymatgen.core.composition import Composition" from pymatgen import Lattice # now "from pymatgen.core.lattice import Lattice" from pymatgen import SymmOp # now "from pymatgen.core.operations import SymmOp" from pymatgen import DummySpecie, DummySpecies, Element, Specie, Species # now "from pymatgen.core.periodic_table ..." from pymatgen import PeriodicSite, Site # now "from pymatgen.core.sites ..." from pymatgen import IMolecule, IStructure, Molecule, Structure # now "from pymatgen.core.structure ..." from pymatgen import ArrayWithUnit, FloatWithUnit, Unit # now "from pymatgen.core.units ..." from pymatgen import Orbital, Spin # now "from pymatgen.electronic_structure.core ..." from pymatgen import MPRester # now "from pymatgen.ext.matproj ..."

v2021.3.3

Backwards incompatible: pymatgen.SETTINGS have been moved to pymatgen.settings.SETTINGS. In general, this should not lead to many breakages since most of these settings are used within pymatgen itself.
Backwards incompatible: pymatgen.loadfn and get_structure_from_mp have been removed since no one was using them.
critic2_caller has been refactored. (@samblau)
Improved hash for Composition (@CompRhys)
Fixes Outcar parsing for VASP 6.2.0. (@MichaelWolloch)
Allow None for Gaussian functional, bset, charge and multiplicity (@eimrek)

v2021.2.16

Add a new interface to OPTIMADE-compliant APIs in pymatgen.ext.optimade (@mkhorton, #2066)
Addresses missing text file, all_cg.txt, in package
Note that a previous released increased the suggested minimum numpy version and suggested minimum Python version
Previous release also dropped support for aconvasp since this the interface has not been maintained

v2021.2.14

Misc bug fixes.

v2021.2.12

Misc bug fixes.

v2021.2.8.1

Patch release to restore CompositionError to preserve backwards compatibility.

v2021.2.8

Addition of new job types to Q-Chem IO (@espottesmith, #2055), note metal_edge_extender has been moved into local_env for this change
Improvements to string utils, new Stringify mixin with to_pretty_string(), to_latex_string(), to_unicode_string(), to_html_string() (@shyuep)
Improvements to build system (@shyuep, @ltalirz, see #2046)
Entry is now immutable, removing "in_place" option for normalize (@mkhorton, @mattmcdermott, #2060)
Bug fix for co-ordination geometry finder (@davidwaroquiers, #2035)
Bug fix for GibbsComputedStructureEntry (@mattmcdermott)

v2021.1.28

Ability to read Lobster wavefunctions (@JaGeo, #2034)
Method to estimate number of bands for VASP calculation (@rwoodsrobinson, #2044)
Q-Chem cube file plotting and improvements to output parsring (@samblau, #2032)
Improvements to PhaseDiagram hashing and equality checking (@CompRhys, #2014)
Improvements to pymatgen import speed (@mkhorton, #2031)
Bug fix for k-path generation (@munrojm, #2037)
Bug fix for parsing of core potentials from VASP (@utf, #2033)

v2020.12.31

End of 2020 release with minor bug fixes for cli scripts.

v2020.12.18

New IsayevNN nearest-neighbor algorithm (@utf, #2011)
Improvements to electrode objects (@jmmshn, #2016)
Improvements to Element and PhaseDiagram (@jmmshn, #2005)
Bug fix to increase minimum version of setuptools which was causing incompatible versions of numpy to be installed for some users (@shyuep, see issue #2010)
Bug fix to VASP run type detection (@rkingsbury, #2007)

v2020.12.3

Site insertion algorithm based on charge density (@jmmshn, #1997)
Allow calculation of Fermi level from occupancies in VASP calculation (@rkingsbury, #2000)
Improvement to legibility of 3D phase diagram plots (@bayesfactor, #1999)
Improvement to allow general input for exciting (@vorwerkc, #1975)
Improvements to code formatting (@mkhorton, #2008)
Bug fix for VASP run type detection (@rkingsbury, #1996)

v2020.11.11

Bug fix for PhononBandStructureSymmLine. (@gpetretto)
Improved robustness in ABINIT input generation. (@gpetretto)
Other minor bug fixes.

v2020.10.20

Cp2K support (@nwinner)
Better BSPlotter (@fraricci)
Better deprecation warnings.
Bug fix for Py3.9 support.
Bug fix for neutron diffraction get_plot.

v2020.10.9

Cube parsing and Cube integration to Bader (@nwinner, #1967)
Improvements to PhaseDiagram (@CompRhys, #1899)
Improvements to VASP sets to calculate NGX/Y/Z, NGX/Y/ZF (@jmmshn, #1959)
Changes to MPRelaxSet, default to low spin for Co (@shyuep, #1976)
Changes to MPScanSet (@rkingsbury, #1952)
Rename of Specie to Species, Specie will be retained for backwards compatibility (@shyuep, #1963)
Bug fix for VASP sets (@utf, #1979)
Bug fix for PDPlotter (@mattmcdermott, #1973)
Bug fix for EnergyAdjustment (@rkingsbury, #1960)

v2020.9.14

New Plotly backend for PhaseDiagram plotting (@mattmcdermott, #1936)
New reporting and logging of Materials Project database version in MPRester (@mkhorton, #1945)
Improvements and bug fixes with mcsqs integration (@rwoodsrobinson, #1942)
Improvements to PackmolRunner (@rkingsbury, #1947)
Improvements to ComputerEntry (@rkingsbury, #1948)
Improvements for MPScanSet (@rkingsbury, #1940)
Bug fix for Surface and Composition (@gpetretto, #1937)
Bug fix for EwaldSummation serialization (@lbluque, #1932)
Bug fix for SeeK k-path (@Ian496, #1930)
Fix for deprecation warning in MPRester (@rkingsbury, #1951)

v2020.8.13

New GibbsComputedStructureEntry (@mattmcdermott, #1921)
Changes to MPScanRelaxSet and new MPScanStaticSet (@rkingsbury, #1917)
Changes to LobsterSet (@JaGeo, #1928)
Bug fix and change for MPRelaxSet (@mkhorton, 9eb3ac2)
Bug fix for JMolNN (@utf, #1920)
Bug fix for Element valences (@rkurchin, #1926)
Bug fix for BabelMolAdaptor (@smheidrich, #1924)
Bug fix for Gaussion IO (@eimrek, #1918)

v2020.8.3

Change neighbor-finding algorithm extension to C instead of C++ for better cross-platform robustness (@chc273)
Add I/O for JARVIS Atoms (@knc6)

v2020.7.18

Add validation and extrapolation for stitching XAS (@yimingcheng)
Better error handling and possibly verbose warning to get_structure_by_material_id

v2020.7.16

Bug fix for boltztrap2 spin support. (@fraricci)

v2020.7.14

EwaldSummation is now MSONable (@lbluque).
Fix for QChem freq parsing (@samblau)
Much improved linting and workflows.

v2020.7.10

Bug fix: serialization of slabs (@utf)
Bug fix: enumlib url (@wsyxbcl)
Bug fix: change in tolerance for Lattice comparison (@mbjumar)
Bug fix: k-path division by zero (@mfherbst)
New: support for openbabel 3.0 (@orioncohen)

v2020.7.3

Make Slabs properly serializable in as_dict. Fixes #1892.
Fixes for Critic2Caller (@yuuukuma)
Add cost data for He, H, Ar, Ne, Kr, Tc (@computron)
Parse scientific notation in OUTCAR (possibly without spaces in between)
Spin support for boltztrap2 (@fraricci)
New static method to generate basis functions Lobster (@JaGeo)
SLME and spillage analysis (@knc6)

v2020.6.8

New: Support for parsing WAVECARS with spin-orbit coupling (@mturiansky, #1861)
New: Support to convert WAVECAR to wannier90 UNK files (@mturiansky, #1861)
New: Site-weighted XAS spectrum (@yimingchen95, #1837)
Fixed: Elfcar serialization (@ayushgupta, #1859)
Fixed: Units in label for phonon plot (@ab5424, #1857)
Fixed: StructureMatcher serialization (@lbluque, #1850)
Fixed: Comment string in KPOINTS file (@Andrew-S-Rosen, #1842)
Fixed: parsing of dielectric function in VASP output (@computron, #1836)

v2020.4.29

Improved SQS caller. (@rwoodsrobinson)
VolumetricData speedup (@mturiansk)
Misc bug fixes

v2020.4.2

New high-symmetry k-path algorithm (@munrojm, @kt-latimer)
New TEM diffraction calculator (@welltemperedpaprika, @thefrankwan, @shyamd)
New plotly plotting option for Wulff shapes (@CifLord)
Improvements to SQS caller (@rwoodsrobinson)
Various bug fixes and improvements (@mfherbst, @chc273, @jacksund, @espottesmith, @hongyi-zhao, @montoyjh, @dongsenfo, @dynikon) including significant BrunnerNN, EconNN fixes (@utf), see individual pull requests for details.

v2020.3.13

Added angle_tolerance to CifWriter.
Change default float precision in CifWriter to 8. Adds float_prec kwarg to allow setting of arbitrary precision.
Rudimentary pymatgen.io.vasp.help.VaspDoc class for obtaining help from VASP wiki.
Massive documentation cleanup.
Reorganization of Entry, ComputedEntry (@ayushsgupta).
Bug fix for PourbaixDiagram (@montoyjh).
Read WAVECAR from gamma-point only VASP executable. (@bernstei)

v2020.3.2

New MonteCarloRattleTransformation and phonopy integration (@utf)
New structure connectivity features in Chemenv analysis (@davidwaroquiers)
Bug fixes (@CifLord, @chc273, @JaGeo, @dskoda, @rkingsbury, @jmmshn, @espottesmith, @gVallverdu, @yimingchen95, @fraricci)

v2020.1.28

Plugin architecture for pymatgen.
Improvements to pymatgen.analysis.xas.spectrum.XAS class. (@yiming)
Fixes for ISYM uniform bug and auto-NEDSO (@fraricci)
Improvements to ReactionDiagram.
Chemenv improvements (@davidwaroquiers)
Misc bug fixes.

v2020.1.10

New connectivity analysis in Chemenv (@davidwaroquiers)
Improvements to DOSPlotter (@uthpalah)
Improvements to writing VASP input sets (@rkingsbury)
Bug fix for PhaseDiagram (@montoyjh)

v2019.12.22

Improvements to reaction calculator (@mattmcdermott)
VASP input set for SCAN from Materials Project, MPScanSet (@rkingsbury)
Bug fixes and documentation improvements (@LindaHung-TRI, @rkingsbury, @kwaters4, @rwoodsrobinson, @JaGeo, @nishiyamat, @smheidrich)

v2019.12.3

Respect KSPACING in INCAR.
Bug fixes.

v2019.11.11

Extend grosspop class (@Jageo)
Add option to VaspInputSet to write output with POTCAR.spec
Add sort_structure option to Poscar.
Added ability to make gaussian input file without a geometry (@WardLT)
Misc big fixes.

v2019.10.16

Major refactoring of ABINIT IO to remove workflow-based packages (@gmatteo)
Use caching in MinimumVIRENN class. (Alex Ganose)
Changes to Lobster module and lobsterset (@jageo)
Eigenval object for EIGENVAL output file (@mturiansky)

v2019.10.4

Fix compile args.

v2019.10.3

Faster get_all_neighbors based on @chc273's improvements. get_all_neighbors now returns a Site-like object with nn_distance, image and index attributes. Much easier to use.
Bug fix for XCrySDen parser (@stevetorr)
Added optional mid_struct to direct interpolation (@jmmshn)

v2019.10.2

IRSpectra class (@henriquemiranda)
Much faster get_neighbors written in Cython (@chc273).
VolumetricData allows for sum or subtraction of data with different structures, with warnings.

v2019.9.16

Updates to annotation, docstrings, etc. Linting service now provided on Github Actions as well as CircleCI.

v2019.9.12

Massive updates to type annotations, especially for core classes.
pycodestyle, pydocstyle and mypy will henchforth be enforced for all new PRs.

v2019.9.8

Supplemental release to address missing incar_parameters.json

v2019.9.7

New fast Pourbaix algorithm (@montoyjh)
VASP Incar parameter checking (@CifLord)
New VASP input set for Lobster, read support for GROSSPOP file (@JaGeo)
New CombinedData class for LAMMPS (@htz1992213)
Improvements to molecule fragmenter (@samblau)
Various bug fixes and improvements (@dongsenfo, @shyuep, @ardunn, @nathan-diodan, @rkingsbury, @kmu)

v2019.8.23

pycodestyle now enforced, except on tests. Developers should install pycodestyle and the pre-commit hook (copy pre-commit to .git/hooks) provided in the repo to check before commits. CI now checks for code style and PRs must pass pycodestyle.
chemsys str input now allowed in get_entries_in_chemsys (@rkingsbury)
ComputedEntry and subclasses now support a normalize().
Speed improvements in fragmeter using igraph. (@samblau)

v2019.8.14

Update DOSCAR from lobster (@JaGEO)
PerturbStructureTransformation (@rees-c)
Misc bug fixes.

v2019.7.30

Bug fixes (@shyuep, @mfherbst)
More type hint annotations (@shyuep)
Improvements to BabelMolAdaptor (@smheidrich)
Convenience Transformations for AdsorbateSiteFinder (@mkhorton)

v2019.7.21

Add CubicSupercellTransformation and PerturbedSupercellsTransformation (@rees-c, @utf)
Add interface for ShengBTE (@rees-c, @utf)
Add interface for Vampire (@ncfrey)
Improved Lobster interface (@JaGeo)
Bug fixes (@sthartman, @dwinston, @utf)
New functionality for calculation of Heisenberg exchange parameters (@ncfrey)
Improvements to Miller indices handling and Lattice (@CifLord)

v2019.7.2

Improvements to grain boundary transformations and Rester (@Tinaatucsd)
Improvements to AdsorbateSiteFinder (@oxana-a)
Improvements to Waveder support (@JRSuckert)
Improvements to run type detection (@darnoceloc)
Add XAS data to Rester (@yimingchen95)
Fix to ATAT input/output (@dongsenfo)
Initial support for Prismatic input (@mkhorton)

v2019.6.20

New interface class (@sivonxay, @kylebystrom, @shyamd)
Updates to SlabGenerator (@CifLord)
Updates to PiezoTensor (@dongsenfo)
Add support for parsing on-site density matrix to Outcar (@mkhorton, @mhsiron, @clegaspi)
Fixes for magnetic space groups (@simonward86)
Fixes for Lobster class (@JaGeo)
Fix for FEFF (@stevetorr)
Fix for Waveder (@JRSuckert)

v2019.6.5

Linear scaling get_all_neighbors. Tested to be faster for > 100 atoms (@chc273).
Lobsterin class to handle input for Lobster (@JaGeo).
Strict options for composition parsing (@mkhorton).
Bug fix for CovalentBondNN.get_bonded_structure (@lan496).

v2019.5.28

New VASP Input Set "from previous" interface (@utf)
ELFCAR support (@mkhorton)
Improvements to plotting of band structures and densities of states (@ShuaishuaiYuan)
Convenience functions added to Composition including chemical system convention (@mkhorton)
Various bug fixes (@mkhorton, @utf)
Improvements to MEGNET API (@shyuep)
Improvements to Structure interpolation (@mturiansky)

v2019.5.8

Numerous updates and improvements to defect classes (@dbroberg)
New API for MEGNET models, see http://megnet.crystals.ai (@shyuep)
Update to NMR symmeterization (@dongsenfo)
Change CIF indexing (@kmu)
Add BoltzTraP mode to NonSCF input sets (@utf)

v2019.5.1

Small speeds to Structure.get_all_neighbors.
Big fixes for gulp_caller. (@kmu)
Plot fatbands from Lobster. (@jageo)
Speed up get_ir_mesh (@utf)
Parsing of plasma frequencies from Outcar.
Miscellaneous bug fixes.

v2019.4.11

Improvements to MimimumDistanceNN (@jmmshn)
Improvements to Lobster. (@JaGeo)
Implement a metal warning for ISMEAR < 1 and NSW > 0.
Misc bug fixes to input sets, including detection of metal systems and checking for standardization.

v2019.3.27

Bug fixes for OrderDisorderComparator (@utf), custom k-points in MPNonSCFSet (@dyllamt), battery app (@jmmshn), MPSOCSet (@mkhorton), more
Improvements to COHP (@JaGeo)
Support to read WAVEDER files (@knc6)
Addition of van Arkel-Ketelaar triangle plots (@CifLord)
Addition of optional user agent to MPRester API calls, see documentation for more information (@dwinston)

v2019.3.13

Streamlined Site, PeriodicSite, Molecule and Structure code by abandoning immutability for Site and PeriodicSite.
VaspInput class now supports a run_vasp method, which can be used to code runnable python scripts for running simple calculations (custodian still recommended for more complex calculations.). For example, the following is a kpoint convergence script that can be submitted in a queue

.. code-block:: pycon

from pymatgen import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet


VASP_CMD = ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "16", "vasp"]


def main():
    mpr = MPRester()
    structure = mpr.get_structures("Li2O")[0]
    for k_dens in [100, 200, 400, 800]:
        vis = MPRelaxSet(structure,
            user_kpoints_settings={"reciprocal_density": k_dens})
        vi = vis.get_vasp_input()
        kpoints = vi["KPOINTS"].kpts[0][0]
        d = f"Li2O_kpoints_{kpoints}"

        # Directly run vasp.
        vi.run_vasp(d, vasp_cmd=VASP_CMD)
        # Use the final structure as the new initial structure to speed up calculations.
        structure = Vasprun(f"{d}/vasprun.xml").final_structure


if __name__ == "__main__":
    main()

Many pymatgen from_file methods now support pathlib.Path as well as strings.
Misc bug fixes.

v2019.2.28

Type hints now available for core classes.
New pymatgen.util.typing module for useful types.
Misc bug fixes.

v2019.2.24

New EntrySet class for easy manipulation of entries to grab subsets, remove non-ground-states, etc. Makes it easier to grab a large set of entries and work with sub chemical systems. Also MSONable for caching.
Performance improvements in core classes and Poscar (@ExpHP).
New/changed methods for IcohpCollection and Completecohp

v2019.2.4

New Trajectory class for MD simulations (@sivonxay)
Lattice.get_vector_along_lattice_directions (@blondgeek)
Misc bug fixes.

v2019.1.24

Python 3 only!
Improvements to local environment code including VESTA bond emulation (@utf)
Update Cohp analysis (@JaGEO)
Updates to Boltztrap2 (@fraricci)

v2019.1.13

Pymatgen is now Py3 ONLY. If you need Py27 support, please use versions < 2019.1.1.
PARCHG parsing from WAVECAR (@mturiansky)
Improvements to defect generation algorithms (@dbroberg)
Simplifications to COHP plotting (@JaGeo)

v2018.12.12

Support for IUPAC ordering of elements in Composition formulae (@utf)
Various bug fixes including returning integer miller indices, catching negative values in Composition and fixes to graph analysis (@utf), fix to Composition serialization (@jmmshen), defect analysis (@HanmeiTang), removing sites in surfaces (@yiming-xu), and fix to support the new PROCAR format in VASP (@dkorotin)
PMG_MAPI_ENDPOINT environment variable added to support different endpoints for the Materials Project REST interface (@mkhorton)

v2018.11.30

MPRester.query now supports bulk queries for large scale requests. (@dwinston)
MVLRelax52Set which uses VASP 52 pseudopotentials. (@HanmeiTang)
EPH calculations in ABINIT (@gmatteo)
New ScaleToRelaxedTransformation (@CifLord)
New dimensionality finder, and consolidation of existing algorithms (@utf)
New dopant predictor built on structure predictor (@utf)
Misc bug fixes (@HanmeiTang, @utf, @tamuhey, @mkhorton, @yiming-xu, @CifLord)

v2018.11.6

Ionic radius based CrystalNN (@computron)
InterfacialReactivity (@dbroberg)
Misc bug fixes

v2018.10.18

New bond fragmenter and bond dissociation analysis modules (@samblau)
Improvements to MoleculeGraph (@espottesmith)
Fix: bug in triclinic tensor conversion to IEEE standard (@montoyjh)
Fix: insertion battery summary dictionary format (@jmmshn)
Speed improvements to certain tests (@shyuep, @samblau)

v2018.9.30

Fix: increased cut-off to VoronoiNN to avoid scipy crash (@utf)
Fix: Outcar parsing issues with certain values of electrostatic potential (@sivonxay)
Fix: bug in EnumlibAdaptor/EnumerateStructureTransformation involving incorrect stoichiometries in some instances (#1286) (@shyuep)
Fix: fractional coordinate finite precision errors in CifParser, now also includes additional warnings for implicit hydrogens (@mkhorton)
New features and improvements to GBGenerator (@ucsdlxg, @shyuep)
New analysis options in StructureGraph, speed up tests (@mkhorton)
New utility function to pretty print disordered formulae, along with a ordered-to-disordered structure transformation (@mkhorton)
Ability to use pymatgen's StructureMatcher against AFLOW's library of crystallographic prototypes (@mkhorton)
Make Chgcar serializable to/from dict for database insertion (@jmmshn)

v2018.9.19

Fix to composition handling in MolecularOrbitals (@dyllamt)
Fix to allow mixed compressed/uncompressed loading of VASP band structures (@ajjackson)
New features and fixes to chemenv analysis module (@davidwaroquiers)
Fix to include structure predictor data with pip/conda-installed pymatgen (@shyamd)
Fixes to Defect objects, including allowing rotational supercell transformations (@dbroberg)
Fix to BSDOSPlotter to correctly fill in parts of DOS (@fraricci)
Added '@' notation parsing in Composition (@tamuhey)
BibTex reference extraction updated in CifParser to support ICSD CIFs (@shyamd)
Various updates to speed up and fix test suite (@shyuep, @fraricci)
Improvements to BoltzTraP 2 support (@shyuep, @fraricci)

v2018.9.12

Use boltztrap2 (@fraricci)
Refactoring of tensor code to core (@montoyjh)
Support for new Lobster version (@JaGeo)
Misc bug fixes

v2018.8.10

Bug fix for pymatgen.analysis.gb and pymatgen.io.lammps.

v2018.8.7

Massive refactoring of LAMMPS support. (@adengz)
Allow kwargs passthrough for Structure.to.
Updates to ABINIT support (@gmatteo)
GrainBoundaryTransformation class. (@Tinaatucsd)

v2018.7.15

Grain boundary generator (Xiangguo Li @ucsdlxg)
Massive updates to defect code and new DefectTransformation (@shyamd)
Bug fix for OUTCAR parsing with more than one space in electrostatic potential.
get_fermi_interextrapolated to support wider range of input doping (@albalu)
Update to cython compile to support Py3.7.
Update VoronoiNN cutoff dynamically (@computron)

v2018.6.27

Improved local_env and MoleculeGraph (@WardLT, @espottesmith)
Improve BabelMolAdaptor with conformer search and other functions (@Qi-Max)
Improved surface analysis (@CifLord)

v2018.6.11

Updates to ABINIT support for 8.1.3
Updates to Interface analyzer.
Fix bug in deserialization of ComputedStructureEntry.
Misc bug fixes.

v2018.5.22

Misc bug fixes.

v2018.5.21

Bug-fix for missing HHI data file.
Misc bug fixes.

v2018.5.14

Dash docs now available for pymatgen. See pymatgen.org "Offline docs" section for details.
Better CrystalNN. (Anubhav Jain)
Fixes for elastic module. (Joseph Montoya)

v2018.5.3

Improvements to qchem (@samblau).
Improvements to nwchem to support tddft input and parsing (@shyuep).
Improvements to CrystalNN (@computron).
Add methods for getting phonon BS, DOS, and DDB output (@dwinston).

v2018.4.20

Neutron diffraciton calculator (Yuta)
Non-existent electronegativity (e.g., He and Ne) are now returned as NaN instead of infinity.
CifParser now handles Elements that are in all caps, which is found in some databases. (Gpretto)
Improvements to local_env (Anubhav Jain)
Improvements to Qchem ()
Inputs sets for NMR (Shyam)
New ChargeDensityAnalyzer class to find interstitial sites from charge density (Hanmei)

v2018.4.6

Updated Debye temperature formulation (Joey Montoya)
Add bandgap option for FermiDos for scissoring (Alireza Faghaninia)
Improved Pourbaix code (Joey Montoya)
Local env code improvements (Nils)

v2018.3.22

Bug fixes to structure, phase diagram module, enumlib adaptor, local env analysis.

v2018.3.14

ReactionDiagram for calculating possible reactions between two compositions.
Misc bug fixes for EnumlibAdaptor and MagOrderingTransformation

v2018.3.13

Support for VESTA lattice vector definitions.
GaussianOutput read now bond_orders of a NBO calculations (@gVallverdu)
Bug fixes to phonons, abinit support.

v2018.3.2

Various algorithms for nearest neighbor analysis (Hillary Pan)
Cleanup of local_env modules (Nils)
Enhancements to surface packages (Richard)
Misc bud fixes

v2018.2.13

Improved chemenv parameters and bug fixes (David Waroquiers).
Improved Qchem IO (Shyam).
Improved interfacial reactions.
local_env update (Nils).
Improved ABINIT support (@gmatteo).
Misc bug fixes.

v2018.1.29

Improvements to local_env (Nils)
Term symbols for Element (Weike Ye).
Timeout for enumlib (Horton).

v2018.1.19

Phonon plotting and analysis improvements (Guido Petretto).
Voronoi site finder (Hanmei Tang)
Some bug fixes for Gaussian (Marco Esters)
Misc improvements.

v2017.12.30

Added detailed Shannon radii information and method.
Magoms for lanthanides (Weike Ye)
Chemenv improvements (David Waroquiers)
Ewald summation improvements (Logan Ward)
Update to ABINIT support (G Matteo)

v2017.12.16

Add optical absorption coefficient method
Improve plot_element_profile

v2017.12.15

Deprecated methods cleanup for 2018. Note that this may break some legacy code. Please make sure you update your code!
Better dielectric parsing for VASP 5.4.4 to include both density-density and velocity-velocity functions.
Orbital-resolved COHPs support (Macro Esters)
Convenient plot_element_profile method in PDPlotter.
Input set for SCAN functional calculations.
Misc bug fixes and code improvements.

v2017.12.8

Pymatgen no longer depends on pyhull.
MPRester method to get interface reaction kinks between two reactants.
Misc improvements.

v2017.12.6

Support for HDF5 output for VolumetricData (CHGCAR, LOCPOT, etc.).
Support for Crystal Orbital Hamilton Populations (COHPs) (@marcoesters)
REST interface for Pourbaix data
Support for optical property parsing in Vasprun.
Improvements to LammpsData
Misc bug fixes.

v2017.11.30

Fix for severe enumlib_caller bug. This causes enumerations not to be carried out properly due to bad accounting of symmetry of ordered sites. It results in too few orderings.
New method to extract clusters of atoms from a Molecule based on bonds.

v2017.11.27

Improvements to FEFF
MPRester now supports surface data.
Improvement to DiscretizeOccupanciesTransformation.

v2017.11.9

Massive rewrite of LAMMPSData to support more functionality (Zhi Deng)
Misc bug fixes.

v2017.11.6

Better exception handling in EnumlibAdaptor and EnumerateStructureTransformation.
Allow bypassing of ewald calculation in EnumerateStructureTransformation.
get_symmetry_operations API convenience method for PointGroupAnalyzer.
New DiscretizeOccupanciesTransformation to help automate ordering of disordered structures.
Fix POTCAR check for POSCAR.
Minor updates to periodic table data.
Misc bug fixes.

v2017.10.16

Added many more OPs and made normalization procedure more robust (Nils Zimmermann)
Molecular orbitals functionality in Element (Maxwell Dylla)
Improvements in chemenv (David Waroquiers)
Add I/O for ATAT’s mcsqs lattice format (Matthew Horton)

v2017.9.29

critic2 command line caller for topological analysis (M. Horton)
Refactor coord_util -> coord.

v2017.9.23

Gibbs free energy of a material with respect to Pourbaix stable domains.
Phonopy io now supports structure conversions.
EnumerateStructureTransformation now implements a useful occupancy rounding.
MVLNPTMDSet
Improved PDPlotter options.
Misc bug fixes.

v2017.9.3

VDW support (Marco Esters)
Bug fix release.

v2017.9.1

Massive refactoring of PhaseDiagram. Now, PDAnalyzer is completely defunct and all analysis is carried out within PhaseDiagram itself, e.g., pd.get_e_above_hull as opposed to PDAnalyzer(pd).get_e_above_hull.
Refactoring of structure prediction. Now in pymatgen.analysis.structure_prediction.
New core Spectrum object and associated pymatgen.vis.plotters.SpectrumPlotter.
Parsing energies from gen_scfman module in Qchem 5 (Brandon Wood)
Improvements to LAMMPSData, vasp IO.

v2017.8.21

Minor bug fixes.

v2017.8.20

Input sets for GW and BSE calculations (Zhenbin Wang) and grain boundary calculations (Hui Zheng). Input sets now support overriding of POTCAR settings.
Haven ratio calculation (Iek-Heng Chu).
LAMMPS io updates (Kiran Matthews).
Oxidation state guessing algorithms based on ICSD data (Anubhav Jain).
New local_env module for local environment analysis. (Nils Zimmerman).
pymatgen.util.plotting.periodic_table_heatmap (Iek-Heng Chu).
Improvements to surface code for tasker 3 to 2 reconstructions.
pymatgen.analysis.interface_reactions.py for analyzing interfacial reactions (Yihan Xiao).

v2017.8.16

PointGroupAnalyzer now allows for symmetrization of molecules. (@mcocdawc)
QuasiharmonicDebyeApprox with anharmonic contribution. (Brandon)
Improvements to LAMMPS io. (Kiran)
Misc bug fixes.

v2017.8.14

Fixes and minor improvements to elastic, bader and defect analyses.

v2017.8.4

Major refactoring and improvements to lammps io. (Kiran)
Major improvements to BaderAnalysis. (Joey and Zhi)
Major improvements to Magmom support in cifs, SOC calculations, etc. (Matthew Horton)
Add remove_site_property function. Add magmom for Eu3+ and Eu2+.
BoltztrapAnalyzer/Plotter support for seebeck effective mass and complexity factor (fraricci)

v2017.7.21

Misc bug fixes to elastic (J. Montaya),
Decrease default symprec in SpacegroupAnalyzer to 0.01, which should be sufficiently flexible for a lot of non-DFT applications.

v2017.7.4

Bug fixes for oxide corrections for MP queried entries, and pickling of Potcars.
Default to LPEAD=T for LEPSILON=T.

v2017.6.24

New package pymatgen.ext supporting external interfaces. Materials Project REST interface has been moved to pymatgen.ext.matproj. Backwards compatibility will be maintained until 2018.
Two new interfaces have been added: i) Support for John Hopkin's Mueller group's efficient k-point servelet (J Montaya). ii) Support for Crystallography Open Database structure queries and downloads. (S. P. Ong). See the examples page for usage in getting structures from online sources.

v2017.6.22

Speed up pmg load times.
Selective dynamics parsing for Vasprun (Joseph Montaya)
Allow element radius updates in get_dimensionality (Viet-Anh Ha).
Dielectric function parse for vasp 5.4.4 (Zhenbin Wang).
Parsing for CIF implicit hydrogens (Xiaohui Qu).

v2017.6.8

Switch to date-based version for pymatgen.
Electronegativities now available for all elements except for He, Ne and Ar, which are set to infinity with a warning.
Bond lengths are now set to sum of atomic radii with warning if not available.
Bug fixes to boltztrap, symmetry for trigonal-hex systems, etc.

v4.7.7

Magnetic symmetry and CIF support. (Horton)
Improved PWSCF Input file generation.
Misc bug fixes.

v4.7.6

Fix serious bug in PointGroupAnalyzer that resulted in wrong point groups assigned to non-centered molecules.
Useful get_structure_from_mp at the root level for quick retrieval of common structures for analysis.
More efficient kpoint grids.
Misc bug fixes.

v4.7.5

MultiXYZ support (Xiaohui Xu)
Misc bug fixes and cleanup.

v4.7.4

New ferroelectric analysis module (Tess).
Magmom support and MagSymmOp (Matthew Horton).
Improved CIF Parsing.

v4.7.3

Sympy now a dependency.
Massive improvements to elastic package. (Joseph Montoya)
Symmetrized structures now contain Wyckoff symbols.
More robust CIF parsing and MITRelaxSet parameters (Will).

v4.7.2

Support for Abinit 8.2.2, including support for DFPT calculations. (Matteo)

v4.7.1

Pathfinder speedup
Minor bug fix for plots.

v4.7.0

Improvements to BSDOSPlotter.
Enhancements to Phase diagram analysis and reaction calculator.
Enhancements to surface slab and adsorption. (Richard and Joey)
Support NpT ensemble in diffusion analysis.

v4.6.2

Improve Spacegroup class support for alternative settings. Add a get_settings class method.
Improvements to FEFF support.
Improvements to EOS class.

v4.6.1

Phonon bandstructure plotting and analysis. (Guido Petretto)
New capabilities for performing adsorption on slabs. (Joey Montoya)
Remove pathlib dependency.

v4.6.0

Improve support for alternative settings in SpaceGroup.
Fix respect for user_incar_settings in MPNonSCFSet and MPSOCSet
Support for argcomplete in pmg script.
Speed ups to Ewald summation.
Add functionality to parse frequency dependent dielectric function.
Improvements to Bolztrap support.

v4.5.7

PMG settings are now prefixed with PMG_ to ensure proper namespacing.
Improve error output in command line bader caller.
Add Py3.6 classifier.
Misc bug fixes.

v4.5.6

Minor bug fix.
Fixed elastic energy density

v4.5.5

Fix bad reading of pmgrc.
Gaussian opt section added allowing for torsion constraints
Update spglib.

v4.5.4

BSDOSPlotter (Anubhav Jain)
Fixes to defect analysis (Bharat)
intrans as an input to BoltztrapAnalyzer. Allows for scissor operation.
Pmg is now continuously tested on win-64/py35 using Appveyor!

v4.5.3

Added an alternative interstitial finder that works with a grid-based structure-motif search. (Nils Zimmermann)
Optional possibility to specify that the saddle_point in the NEB should have a zero slope. (David Waroquiers)
Read intensity and normal modes for Gaussian. (Germain Salvato Vallverdu)
Minor bug fixes.

v4.5.2

Minor bug fix for POTCAR settings.

v4.5.1

You can now specify a different default functional choice for pymatgen by setting PMG_DEFAULT_FUNCTIONAL in .pmgrc.yaml. For use with newer functional sets, you need to specify PBE_52 or PBE_54 for example.
Switch to ISYM 3 by default for HSE.
Updates to FEFF>
Misc bug fixes and startup speed improvements.

v4.5.0

Major speed up of initial load.
Collection of misc changes.

v4.4.12

Fix for dynamic numpy import.

v4.4.11

Update to new version of spglib.

v4.4.10

Minor fixes for proper gzipped structure file support and MVLSlabSet.

v4.4.9

Dependency cleanup. Now, basic pymatgen requires on much fewer packages.
Fixed reading of POSCAR files when more than 20 types of atoms.
Misc bug fixes.

v4.4.8

Cleanup of entry points and dependencies.

v4.4.7

Update to spglib 1.9.7.1
Proper use of dependency markers for enum34.

v4.4.6

Update to spglib 1.9.6, which fixes some bugs and is Windows compatible.

v4.4.5

Bug fix for SubstitutionProb.

v4.4.4

Bug fix for electronic structure plotter.

v4.4.3

Bug fix for Diffusion Analyzer.

v4.4.2

Bug fix for BS serialization.
Cleanup dependencies.

v4.4.1

Massive updates to FEFF support (Kiran Mathews).
Bug fixes in band structure plotting.

v4.4.0

Much more Pythonic API for modifying Structure/Molecule species. Now, strings, slices, and sequences should magically work, in addition to the previous API of simple int indices. Examples::

s[0] = "Fe" s[0] = "Fe", [0.5, 0.5, 0.5] # Replaces site and fractional coordinates. s[0] = "Fe", [0.5, 0.5, 0.5], {"spin": 2} # Replaces site and fractional coordinates and properties. s[(0, 2, 3)] = "Fe" # Replaces sites 0, 2 and 3 with Fe. s[0::2] = "Fe" # Replaces all even index sites with Fe. s["Mn"] = "Fe" # Replaces all Mn in the structure with Fe. s["Mn"] = "Fe0.5Co0.5" # Replaces all Mn in the structure with Fe: 0.5, Co: 0.5, i.e.,creates a disordered structure!
Massive update to internal representation of Bandstructure objects for memory and computational efficiency.
Bug fixes to CIF parsing in some edge cases. (Will Richards).

v4.3.2

Massive speedup of Bandstructure, especially projected band structures, parsing.
Massive update to pmg cli script, with new query functions as well as a more rational command structure.
Updates to ChemEnv.
Misc bug fixes.

v4.3.1

Upgrade monty and spglib requirements for bug fixes.
Updates to feff support (Kiran).

v4.3.0

Massive update to elastic module. (Joey Montaya)
Pathfinder algorithm for NEB calculations. (Ziqing Rong)
Wheels for Windows and Mac Py27 and Py35.

v4.2.5

Bug fix for BSPlotter.

v4.2.4

Bug fix for kpoint weight calculation for Monkhorst meshes.

v4.2.3

Minor cleanup.
Simplified installation. enumlib and bader can now be installed using pmg setup --install.

v4.2.2

Global configuration variables such as VASP_PSP_DIR and MAPI_KEY are now stored in "~/.pmgrc.yaml". If you are setting these as environmental variables right now, you can easily transition to the new system using::
```
pmg config --add VASP_PSP_DIR $VASP_PSP_DIR MAPI_KEY $MAPI_KEY
```
This new scheme will provide greater flexibility for user-defined global behavior in pymatgen, e.g., tolerances, default input sets for transmuters, etc., in future.
Beta of k-point weight calculator.
Use default MSONable as and from_dict for all transformations.

v4.2.1

New DopingTransformation that implements an automated doping strategy.
Updated MIC algorithm that is a lot more robust (Will Richards).
Major update to chemenv package (David Waroquiers)

v4.2.0

Fix important bug in minimum image distance computation for very skewed cells.
Major refactoring of WulffShape code.
Misc bug fixes for elastic tensor and other codes.

v4.1.1

Major refactoring of WulffShape and lammps support.

v4.1.0

Wulff shape generator and analysis.
Minor bug fixes.

v4.0.2

Fix kpoint reciprocal density.

v4.0.1

Minor bug fix release.

v4.0.0

Massive update with many deprecated methods removed. Note that this may break backwards incompatibility!
Support for ABINIT 8.
Improved sulfide compatibility.

v3.7.1

Fix deprecation bug.

v3.7.0

Last version before pymatgen 4.0, where deprecated modules will be removed!
Massive update to LAMMPS (Kiran Matthews).
New input sets with a different interface that replaces old input sets.
Massive update to elastic properties.

v3.6.1

Massive cleanup to Boltztrap interface (Anubhav Jain)
Refactor of piezoelectric analysis to use tensor base class (Joey)
More robust CIF parsing.

v3.6.0

Pymatgen now uses spglib directly from Togo's website. Spglib is no longer bundled as a dependency.
Improved support for velocities in Poscar (Germaine Vallverdu)
Backwards incompatible change in Born charge format in Outcar.
Fixes for Lammps input serialization

v3.5.3

Misc refactorings and bug fixes, especially for Outcar and Boltztrap classes.

v3.5.2

Minor update to DerivedInputSet interface.

v3.5.1

New derived input sets for generating inputs that depende on previuos calculations. Old input sets deprecated.

v3.5.0

Chemical environment analysis package (David Waroquiers).
Piezoelectric property analysis (Shayam).
Cythonize certain expensive core functions. 5-10x speedup in large structure matching (Will Richards).
New NMR parsing functionality for Outcar (Xiaohui Qu).
Improved io.lammps (Kiran Mathews).
Update to spglib 1.9.2.
Element properties now return unitized float where possible.
Bug fix for get_primitive_standard affecting rhombohedral cells (important for band structures).
Vasprun.final_energy now returns corrected energy with warning if it is different from final electronic step.

v3.4.0

10-100x speed up to Structure copying and Site init, which means many functionality has seen significant speed improvement (e.g., structure matching).
Convenience method Structure.matches now perform similarity matching for Structures.
Bugfix for band gap determination.

v3.3.6

Update to use enum.x instead of multienum.x.
Minor robustness fixes to VaspInputSet serialization.
Add a reciprocal density parameter to vasp sets.
Minor bug fixes to Vasprun parsing.

v3.3.5

StructureMatcher can now work with ignored species.
Added interpolation failure warnings and smooth tolerance for scipy.interpolate.splrep in bandstructures (Tess).
Added DiffusionAnalyzer.get_framework_rms_plot.
Complete rewrite of Procar class to use NDarray access and zero-based indexing.
OrderParameters class for analysis of local structural features (Nils Zimmermann).
Bug fixes for Procar, MPRester and SpaceGroup 64.
Added Github templates for contributing to pymatgen.

v3.3.4

Procar now supports parsing of phase factors.
Miscellaneous bug fixes.

v3.3.3

Bug fixes for Poscar.
Fix Kpoints pickling.

v3.3.2

Bug fixes for pymatgen.io.abinit
Other minor big fixes.

v3.3.1

Minor bug fix release for pickle and elastic constants.

v3.3.0

Updated and checked for Python 3.5.* compatibility.
Element, Spin, Orbital and various other Enum-like classes are now actually implemented using Enum (with enum34 dependency for Python < 3.4).
Speed up Site creation by 20% for ordered sites, with cost in terms of slightly slower non-ordered Sites. Since ordered Sites is the far more common case, this gives significant boost for large scale manipulations of structures.
Alternative, more pythonic syntax for creating supercells via simply Structure 3 or Structure (3, 1, 1).
zeo++ fixes.
More stable incar settings for MITMDVaspInputSet.

v3.2.10

Fix missing scripts
Improvements to units module.
Speed up EwaldSummation.

v3.2.9

Major PD stability improvements, especially for very high dim hulls with lots of entries.
Improvements to Ewald summation to be close to GULP implementation.
Deprecate physical constants module in favor of scipy's version.
Remove many pyhull references to use scipy's ConvexHull implementation.
Bug fix for sulfide correction.

v3.2.8

Make pyhull optional.
Sulfur correction added to MaterialsProjectCompatibility for more accurate sulfide formation energies.
ADF io support. (Xin Chen)
Bug fixes for spacegroup subgroup testing.

v3.2.7

Add warning for limited subgroup testing functionality in Spacegroup.

v3.2.6

Extensive support for elasticity tensor analysis (Joseph Montoya).
Misc bug fixes and performance improvements.
Add support for QChem4.3 new format of Batch jobs

v3.2.5

Improved potcar setup via "pmg setup", with MAPI setup.
Support for new POTCARs issued by VASP.
Improvements to ABINIT support.
Improvement to Boltztrap support, e.g., scissor band gap, etc.
Vasprun now issues warning when unconverged run is detected.

v3.2.4

GaussianOutput can now parse frequencies, normal modes and Cartesian forces (Xin Chen).
Support for Aiida<->pymatgen conversion by the Aiida development team (Andrius Merkys).
Specialized BSVasprun parser that is ~2-3x faster than Vasprun.
Refactor the boltztrap package (merge a few methods together) and add several new methods (power factor, seebeck...)
Support of the new PCM format in QChem 4.3
Local environment analysis to pmg script.
Deprecate prettytable in favor of tabulate package.
Improvements to MITNEBVaspInputSet.
Misc bug fixes.

v3.2.3

Massive update to abinit support. Note that pymatgen.io.abinitio has been refactored to pymatgen.io.abinit. (Matteo, Setten)
NwOutput now supports parsing of Hessian matrices (contributed by Xin Chen)
Gaussian support now has the ability to read potential energy surface and electronic transitions computed with TD-DFT (Germain Salvato Vallverdu)
Bug fixes for CifWriter with symmetry.
Bug fixes for surface generation and reactions.
Monty requirement increased.

v3.2.1

Fix wrong U value for Ce and Eu.
Properly handle empty multiline strings in Cif
Add ability to get specific data in MPRester.get_entries. Make all get_entry methods consistent in kwargs.

v3.2.0

Force conversion to an actual list in selective dynamics and velocities in Poscar.
fix small bug in BSPlotter (wrong ylim)
Elastic tensor parsing in Outcar

v3.1.9

Fix scripts.

v3.1.7

Bug fixes for MPRester.
Ensure correct monty version requirement in setup.py.

v3.1.6

Rudimentary PWSCF output reading.
Fix ASE support.
Support for WAVEDERF and reading multiple dielectricfunctions in vasprun.xml. (Miguel Dias Costa)

v3.1.5

Move vasp.vasp*put to vasp.*puts. Also, maintain backwards compatibility with vaspio.vasp_*put

v3.1.4

Fix missing yaml files that have been moved.

v3.1.3

Major refactoring of pymatgen.io. Now, the io suffix is dropped from all io classes. i.e., it is just pymatgen.io.vasp, not pymatgen.io.vaspio. Also, all input sets have been moved within the relevant package, e.g., pymatgen.io.vasp.sets. All changes are backwards compatible for now. But deprecation messages have been included which states that the stubs will be removed in pymatgen 4.0. Pls migrate code when you see the deprecation messages.
Make Composition.anonymized_formula truly chemistry independent (No A2B2 for peroxides or A2 for diatomic gasses)
Allowing CIF data_* header to be prefixed with spaces and tabulations.

v3.1.2

HHI Resource Analysis (by Anubhav Jain).
Bug fixes for surfaces normalizatino.
Bug fix for Vasprun parsing of response function keys.
Dockerfile for generation of an image for pymatgen.
Updated requirements.txt for latest requests, scipy, numpy.

v3.1.1

Bug fixes for SpacegroupAnalyzer and SlabGenerator.
Much faster normal vec search.

v3.1.0

Much improved surface generation algorithm that provides for orthogonality constraints.
Transition state analysis tools! (beta)
Massive improvements in Outcar parsing which provides a powerful grepping syntax.
PWSCFInput generation (beta).
Reduce default SIGMA to 0.05 for MP input sets.
Update spglib to 1.7.3 as per recommendation of Togo.
Many bug fixes and efficiency improvements.

v3.0.13

Bug fix for parsing certain types of CIFs.
MPRester now has get_materials_id_references helper method.
Minor fix for Vasprun.final_energy.
Added mp_decode option to MPRester.query to allow option to not decode into pymatgen objects.
New POTCAR hash scheme to more robustly identify unique POTCARs.
Link to http://bit.ly/materialsapi for information on Materials API document schema for use with MPRester.query method.

v3.0.11

Lots of abinitio improvements (Matteo).
Added mp_decode option to MPRester.query to allow option to not decode into pymatgen objects.

v3.0.10

Fix Cartesian coord parsing in Poscar class.
Vasprun now works with non-GGA PBE runs
Misc bug fixes

v3.0.9

Major bug fixes for CIF parsing (Will Richards).
Support for {Li,Na} syntax in parse_criteria for MPRester.
Additional example notebook for ordering and enumeration.
More robust checking for oxidation states in EnumerateStructureTRansformation.
Improvements to Slab polarity checking.

v3.0.8

Massive update to abinitio (Matteo).
Improvements to OUTCAR parsing (Ioannis Petousis).

v3.0.7

Powerful Slab generation algorithms (beta!).
Improvements to DiffusionAnalyzer with constant smoothing option.
Significantly improve look of DOS plots using prettyplotlib.

v3.0.6

Cost analysis module (Anubhav Jain)
More Py3k fixes.
Extensive abinitio updates (Matteo).

v3.0.5

Completely revamped symmetry package. The finder.SymmetryFinder and pointgroup and spacegroup modules are now deprecated. Instead, all symmetry analysis is in the :module:pymatgen.symmetry.analyzer_ module. There is also a completely rewritten support for symmetry groups in :module:pymatgen.symmetry.groups_. Structure now supports a static constructor to generate a structure from a spacegroup (see examples).
BatteryAnalyzer class (Anubhav Jain) to provide for some common analysis of intercalation electrodes.
Minor bug fixes for structure_matcher, lattice, abinitio.
MOAB qadapter for abinit. (Liam Damewood)

v3.0.4

Fix missing structures json data.

v3.0.3

Updates to DiffusionAnalyzer for more fine-grained statistics.
Bug fixes and tweaks to linear assignment
Improved PymatgenTest class which provides a suite of test structures.
Speedups to Phase Diagram
Lots of improvements to Gaussian support (Nicolas Dardenne) and Abinit IO (Matteo).
Lots of Py3k minor updates.
Updated doc for Diffusion analyzer. Invert sq_disp_ions for more intuitive handling.

v3.0.2

Consistent use of unicode throughout pymatgen.
Minor bug fixes.

v3.0.1

Minor bug fixes for cifio.
Py3k updates for abinitio.

v3.0.0

Pymatgen is now completely Python 2.7 and Python 3.x compatible!
Spglib and pyhull have been updated to support Python 3.x.
Completely rewritten pure python cifio module (courtesy of William Davidson Richards) removed dependency on PyCIFRW, which has been causing many issues with installation.
Structure and Molecule now supports a very convenient to() and from_str and from_file functionality. Instead of trying to load the appropriate parser, you can output and read from the appropriate formats directly. See example usage.
~50% speedup to LinearAssignment code.
Continuous integration and contribution guidelines now include Python 3.
Backwards incompatible changes
matgenie.py has now been renamed simply "pmg" for brevity.
All deprecated methods in pymatgen 2.x have been removed. E.g., pymatgen.core.structure_modifier is no longer available.
Pymatgen classes now uses the as_dict() method protocol implemented in the Monty package. The to_dict property is now deprecated and will be removed in pymatgen v3.1.
Update main docs page examples with the new Structure to, from formats.

v2.10.6

Bug fix for np1.9 incompatibility. Now works.
Use wheel for pymatgen deployments.
matgenie.py is now renamed to pmg for faster CLI usage.
Improvements to KPOINTS automatic generation.
Simpler and faster Structure.get_all_neighbors

v2.10.5

DiffusionAnalyzer now has non-smoothed option.
Kpoints generation algorithm now guarantees minimum # of points.
Compatibility now has a proper explanation dict.
Vaspruns with NSW == 1 now checked properly for electronic conv.
make_movie now supports kwargs.

v2.10.3

MPRester.query now supports a simple but powerful string criteria syntax with support for wild cards.
Improvements to Composition - support for negative compositions, sorting etc.
Speed ups to StructureMatcher.

v2.10.2

Bug fix for Projected DOS parsing in new Vasprun.
Compatibility now has a explain method which provides a detailed outline of the changes that a Compatibility makes to an Entry.

v2.10.1

Minor fix for monty requirements in setup.py.

v2.10.0

Major update: MPRester now uses Materials API v2! Also major refactoring of MPRester.
Vastly improved Vasprun parser using cElementTree. Twice as fast, half as much code and easier to maintain.
Vast improvements to Qchem functionality (Xiaohui Qu).
Improved handling of Structure manipulations for extremely large structures (particularly in terms of memory consumption).
Bug fix for XYZ parsing for scientific notation.
Improve monty.serialization for transparent handling of JSON vs YAML. Requirements updated to monty>=0.3.3.
Update numpy requirements to 1.8+. Fixes memory leak.
Other minor bug fixes.

v2.9.14

Implements Structure.sort method. Both Structure.sort and the get_sorted_structure methods now supports all arguments supported by list .sort().
VaspInputSets configs, as well as several other configs now uses yaml. Note the new dependency on pyyaml. It is highly recommended that you install pyyaml with the libyaml C bindings.
Fix missing spglib dependency.
Use monty.serialization for transparent handling of JSON vs YAML. Requirements updated to monty>=0.3.1.

v2.9.13

Urgent bug fix for missing compatibility yamls.

v2.9.12

Defect transformations (Bharat).
Support for optical properties (Geoffroy Hautier and David Waroquiers).
Improved support for some VASP output files (XDATCAR and OSZICAR).
Refactored compatibilities now uses YAML for ease of reading.

v2.9.11

Bug fix for get_xrd_plot.
Speed up XRD calculator by allowing specification of two theta ranges.
Minor improvements to Gulp caller.

v2.9.10

Bug fix for unequal coefficients sizes in XRD.
Support for Ag radiation in XRD calculator.
Improved Procar class for extraction of information. (Germain Salvato Vallverdu)
Bug fix for extraction of GGA data from Materials API.

v2.9.9

XRDCalculator now supports disordered structures.
Minor speed ups and improvements.

v2.9.8

Initial beta version of XRD pattern calculator.
Pymatgen now uses spglib 1.6.0.
Update to Vasprun to compute static deilectric constants with DFPT in VASP. (Geoffroy Hautier)

v2.9.7

Quick bug-fix release that provides a better solution to Structure handling of properties instead of sanitizing MPRester structures.

v2.9.6

Patch to allow 1D phase diagrams (essentially finding the lowest energy phase).
Better error checking for Bandstructure KPOINTs.
Patch to sanitize structures obtained from MPRester.

v2.9.5

Bug fix for linear assignment, which may sometimes affect Structure Matcher results.
Minor improvement to the way grand canonical PDs work.

v2.9.4

Bug fix for Pourbaix Maker (Sai).
Streamline use of scratch directories for various calls. Require monty >= 0.1.2.
High accuracy mode for Zeo++ (Bharat Medasani).

v2.9.3

Bug fix release for printing TransformedStructures from Substitutor (Will Richards).
Misc improvements in BVAnalyzer, coord_utils and defects (Will Richards, David Waroquiers and Bharat Medasani).

v2.9.2

Bug fix release for DummySpecie, which failed when deserializing from json and had bad hash function.

v2.9.1

Structure/Molecule now supports Pythonic list-like API for replacing and removing sites. See :ref:quick_start for examples.

v2.9.0

Updates to support ABINIT 7.6.1 (by Matteo Giantomassi).
Vastly improved docs.
Refactoring to move commonly used Python utility functions to Monty package <https://pypi.python.org/pypi/monty>_, which is now a dependency for pymatgen.
Minor fixes and improvements to DiffusionAnalyzer.
Many bug fixes and improvements.

v2.8.10

Refactoring of qchemio module (by Xiaohui Qu).

v2.8.9

qchemio module (by Xiaohui Qu).

v2.8.8

Minor bug fix release for Structure species substitution methods.

v2.8.7

Massive update to pymatgen.io.abinitio package (by Matteo Giantomassi).
Bug fixes for StructureMatcher's group_structure.
Misc bug fixes and cleanup.

v2.8.6

Bug fix for VASP io set introduced by the default to sorting of structure sites when generating VASP input.

v2.8.4

Completely revamped Compatibility/Correction system which improves readability (Shyue Ping Ong/Anubhav Jain/Sai Jayaraman). This change is backwards compatible for the most part.

v2.8.3

Big fix release for json dumping for unitized floats.

v2.8.2

Bug fix release to improve CIF parsing for more non-standard CIF files. In particular, non-ascii characters are removed and _cgraph* fields are removed prior to parsing for better support in PyCiFRW.

v2.8.1

Bug fix release. Incorrect units assigned for ionic radii.
Improved nwchemio supports COSMO and ESP calculations (Nav Rajput).

v2.8.0

Units. Pymatgen now has a new system of managing units, defined in pymatgen.core.units. Typical energy, length, time, temperature and charge units are supported. Units subclass float, which makes the usage transparent in all functions. The value that they being are in terms of conversions between different units and addition and subtraction of different units of the same type. Some basic quantities like ionic radii and atomic masses are now returned in unitized forms for easy conversion. Please see :mod:pymatgen.core.units and the :doc:examples </examples> for a demonstration of house to use units in pymatgen.
Minor backwards-incompatible change. Structures are now sorted by default when generating VASP input files using vaspio_set. Old behavior can be obtained by setting sort_structure=False in the constructor. This is typically the desired behavior and prevents the generation of large POTCARs when atomic species are not grouped together.
Bug fix for Molecule.substitute. Earlier algorithm was not detecting terminal atoms properly.
Additional conversion tools for ABINIT (by Matteo Giantomassi).

v2.7.9

Minor bug fix release to fix pyhull dependencies to be more friendly.
Improved structure matcher that allows for more flexible matching. New matching between ordered and disordered comparator.

v2.7.7

Beta new Gulp Caller and Zeo++ interface classes (Bharat . Zeo++ is an open source software for performing high-throughput geometry-based analysis of porous materials and their voids. Please see http://www.maciejharanczyk.info/Zeopp/about.html.
Specify version of distribute to 0.6.34 for better compatibility.

v2.7.6

Support for VTK 6.x in structure visualization.
Updated install instructions for openbabel.
Preliminary pourbaix analysis (Sai Jayaratnam).

v2.7.5

Vastly improved Nwchem IO (by Shyue Ping Ong).
Much improved ABINIT support (by Matteo Giantomassi).

v2.7.4

Added basic Nwchem (http://www.nwchem-sw.org/) IO support. (by: Shyue Ping Ong).
New MoleculeMatcher class for comparing molecules by RMS. Requires openbabel with python bindings. (by: Xiaohui Qu)
New functional group substitution capability for molecules (by: Lei Cheng and Shyue Ping Ong).

v2.7.2

Minor bug fix release to fix some rare errors in very high dimensional phase diagrams. Requires new pyhull version (1.3.8).

v2.7.1

Major backwards-incompatible change. With effect from v2.7.1, the default Structure and Molecule classes are now mutable objects. All functionality in the :mod:pymatgen.core.structure_modifier has been ported over to the new mutable classes. This change was implemented because the immutability of Structure and Molecule has resulted in very awkward code to make changes to them. The main cost of this change is that Structure and Molecule can no longer be used as dict keys (hash has been set to None). However, we believe this is a minor cost given that we have rarely seen the use of Structure or Molecule as dict keys in any case. For the rare instances where such functionality is needed, we have provided the IStructure and IMolecule classes (where I indicates immutability) which will perform exactly the same way as the previous classes. With this change, the :mod:pymatgen.core.structure_modifier module is now deprecated and will be removed in a future version.
read_structure and write_structure now supports pymatgen's JSON-serialized structures.
read_mol and write_mol functions now available (analogues of read_structure and write_structure for molecules)

v2.7.0

Beta support for ABINIT input and output via pymatgen.io.abinitio (courtesy of the excellent work of Matteo Giantomassi).
Properties are now checked when comparing two Species for equality.
MaterialsProjectVaspInputSet is now renamed to MPVaspInputSet for easier typing. The old input sets have been deprecated.
New VaspInputSets for MPStatic, MPNonSCF, MITMD which supports uniform grid, bandstructure and molecular dynamics calculations. The MD input set uses MIT parameters for speed.
A beta DiffusionAnalysis class in the apps package.
A revised KPOINT grid algorithm that generates more reasonable meshes.
A guided install script is now provided for Mac and Linux users.

v2.6.6

Updates to feffio (credit: Alan Dozier)
Added detailed installation instructions for various platforms.
Support for charge and spin multiplicity in Molecule. Expanded methods available in Molecule.
Added supercell matching capabilities to StructureMatcher.
More robust creation of PhaseDiagrams to take into account potential qhull precision errors.

v2.6.5

Added a command_line caller to do Bader charge analysis using Henkelmann et al.'s algorithm.
Bug fix for POSCAR parsing when title line is an empty string.
Added rmul operator for Composition.
Vastly expanded available aliases.

v2.6.4

Bug fixes for selective dynamics in Poscar.
Improved Procar parsing to support both simple and detailed PROCARs.

v2.6.3

Added new MaterialsProject REST interfaces for submit/query/delete_snl (currently open in beta for collaborators only).
Added support for new MaterialsProject REST method get_stability.
Added aliases for PhaseDiagram, GrandPotentialPhaseDiagram, PDAnalyzer and PDPlotter in pymatgen.phasediagrams.
Improvements to StructureMatcher: stol (site - tolerance) redefined as a fraction of the average length per atom. Structures matched in fractional space are now also matched in Cartesian space and a rms displacement normalized by length per atom can be returned using the rms_dist method.

v2.6.2

Site and PeriodicSite now uses a Composition mapping type to represent the species and occupancy, instead of a standard dict.
Bug fix for reading and re-writing out of Potcars.
VaspInputSet now supports MSONable framework.
Strain cell option in StructureEditor.
Miscellaneous bug fixes and speedups.

v2.6.1

Use requests.Session in MPRester for connection pooling and code simplicity.
Support for "with" context manager in MPRester.
Updated periodic table data to correct errors in Ru, Tc and other elements.
New methods in Lattice to obtain Wigner-Seitz cell and Brillouin Zone.
Miscellaneous bug fixes and speedups.

v2.5.5

Bug fix release for cifio for rhombohedral structures.
Miscellaneous bug fixes and speedups.

v2.5.4

Vastly improved Gaussian input file parsing that supports more varieties of input specifications.
StructureNL now supports molecules as well as structures.
Updated atomic and vdw radius for Elements.
Miscellaneous bug fixes and speedups.

v2.5.3

Bug fix for StructureNotationalLanguage.
Support for LDA US potential. matgenie.py script option to generate POTCARs.
Beta version of StructureNotationLanguage, a markup format for Structure data with metadata such as authors and references. (Anubhav Jain)
Vasprun parsing now parses dielectric constant where available. (Geoffroy Hautier)
New custom ipython shell script for pymatgen.
Miscellaneous bug fixes and speedups.

v2.5.1

Bug fixes for primitive cell finder.
Remove deprecated use_external_qhull option in PhaseDiagram classes.
Miscellaneous bug fixes and speedups.

v2.5.0

Added optimization package with linear assignment class.
Improved robustness of StructureMatcher using linear assignment.
Improved primitive cell search (faster and more robust).
Cleanup of deprecated methods, including pymatgen.alchemy.materials.TransformedMaterial.undo/redo_last_transformation, pymatgen.core.site.Site.distance_and_image_old, Poscar.struct, StructureFitter and tests.
Miscellaneous bug fixes and speedups.

v2.4.3

Bug fix for StructureMatcher.
Miscellaneous speedups.

v2.4.0

New StructureMatcher that effectively replaces StructureFitter. Orders of magnitude faster and more robust. StructureFitter is now deprecated.
Vastly improved PrimitiveCellTransformation.
A lot of core methods have been rewritten to take advantage of vectorization in numpy, resulting in orders of magnitude improvement in speed.
Miscellaneous bug fixes and speedups.

v2.3.2

More utilities for working with Periodic Boundary Conditions.
Improved MPRester that supports more data and a new method of specifying the API key for heavy users via a MAPI_KEY environment variable. Please refer to the :doc:usage pages </usage> for more information.
Vastly improved POTCAR setup script in scripts directly that is now installed as part of a default pymatgen installation.
Miscellaneous bug fixes and speedups.

v2.3.1

Significant improvements to the high-level interface to the Materials API. New interface provides more options to make it easier to get structures and entries, better warnings and error handling. It uses the requests library for a cleaner API.
Bug fix for VolumetricData parsing and methods such as CHGCAR and LOCPOT. Previously, the parsing was done incorrectly because VASP actually provides data by running through the x-axis first, followed by y, then z.
Bug fix for reverse_readline so that it works for gzipped and bzipped structures (courtesy of Anubhav Jain).
Fix "lossy" composition to_dict method. Now composition.to_dict properly returns a correct species string as a key for compositions using species, instead of just the element symbols.
Miscellaneous bug fixes.

v2.3.0

Remove usage of scipy and external qhull callers. Now uses pyhull package. Please note that this change implies that the pyhull package is now a required dependency. If you install pymatgen through the usual easy_install or pip install methods, this should be taken care of automatically for you. Otherwise, please look for the pyhull package on PyPI to download and install it.
Miscellaneous bug fixes.

v2.2.6

Brand new beta bond valence analyzer based on a Maximum A Posteriori algo using data-mined ICSD data.
Speed up and improvements to core classes.
Improved structure fitter (credits to Geoffroy Hautier).
Brand new entry_tools module (pymatgen.entries.entry_tools).
Vastly improved Outcar parser based on reverse parsing that speeds up reading of OUTCAR files by orders of magnitude.
Miscellaneous bug fixes.

v2.2.4

Fixed bug in hexagonal cell KPOINTS file generation.
New RelaxationAnalyzer to compare structures.
New beta bond valence analyzer.
Miscellaneous bug fixes.

v2.2.3

New filter framework for filtering structures in pymatgen.alchemy.
Updated feff io classes to support FEFF 9.6 and other code improvements.
Miscellaneous bug fixes.

v2.2.2

Bug fix release for REST interface.
Improvements to unittests.

v2.2.1

Improvements to feffio.
Master matgenie.py script which replaces many analysis scripts.
More memory efficient parsing of VolumetricData.
Beta version of structure prediction classes.
Changes to MPRester to work with v1 release of the Materials API.
Miscellaneous bug fixes and speed improvements.

v2.2.0

Beta modules (pymatgen.io.feffio) for io for FEFF, courtesy of Alan Dozier.
New smartio module that intelligently reads structure input files based on file extension.
Spglib_adaptor module has been renamed to finder for brevity.
Upgraded spglib to version 1.2.2. Improved handling of spglib install on Mac OS X and Solaris.
Major cleanup of code for PEP8 compliance.
Cssr module now supports reading of input files.
Miscellaneous bug fixes and speed improvements.

v2.1.2

Brand new CompoundPD class that allows the plotting of phase diagrams that do not have elements as their terminal points.
Spglib is now completely integrated as part of the setup.py installation.
Major (but completely backwards compatible) refactoring of sites and vaspio.
Added a EnumerateStructureTransformation with optional dependency on the enum library by Gus Hart. This provides a robust way to enumerate derivative structures,
Implemented LLL lattice reduction algorithm. Also added option to sanitize a Structure on copy.
Bug fix for missing Compatibility file in release distribution.
Vastly improved StructureFitter which performs cell reduction where necessary to speed up fitting.
Miscellaneous bug fixes and speed improvements.

v2.0.0

Brand new module (pymatgen.matproj.rest) for interfacing with the MaterialsProject REST interface.

Useful aliases for commonly used Objects, similar in style to numpy. Supported objects include Element, Composition, Structure, Molecule, Spin and Orbital. For example, the following will now work::

import pymatgen as mg
# Elemental Si
fe = mg.Element("Si")
# Composition of Fe2O3
comp = mg.Composition("Fe2O3")
# CsCl structure
structure = mg.Structure(mg.Lattice.cubic(4.2), ["Cs", "Cl"],
                         [[0, 0, 0], [0.5, 0.5, 0.5]])

New PDAnalyzer method to generate chemical potential maps.
Enhanced POSCAR class to support parsing of velocities and more formatting options.
Reorganization of Bandstructure module. Beta support for projected bandstructure and eigenvalues in vaspio and electronic_structure.
Miscellaneous bug fixes and speed improvements.

v1.9.0

Completely new json encoder and decoder that support serialization of almost all pymatgen objects.
Simplification to Borg API utilizing the new json API.
Bandstructure classes now support spin-polarized runs.
Beta classes for battery (insertion and conversion) analysis.

v1.8.3

spglib_adaptor now supports disordered structures.
Update to support new spglib with angle_tolerance.
Changes to Borg API to support both file and directory style paths.
Speed up for COMPLETE_ORDERING algo for PartialRemoveSpecieTransformation.

v1.8.1

Revamped transmuter classes for better readability and long term support.
Much improved speed for PartialRemoveSpecieTransformations.
Misc bug fixes.

v1.8.0

Support for additional properties on Specie (Spin) and Site (magmom, charge).
Molecule class to support molecules without periodicity.
Beta io class for XYZ and GaussianInput.

v1.7.2

Bug fixes for vaspio_set and compatibility classes.

v1.7.0

Complete reorganization of modules for electronic structure.
Beta of band structure classes.
Misc improvements to vaspio classes.
Bug fixes.

v1.6.0

Beta of pymatgen.borg package implemented for high-throughput data assimilation.
Added ComputedEntry classes for handling calculated data.
New method of specifying VASP pseudopotential location using a VASP_PSP_DIR environment variable.
Bug fix for pymatgen.symmetry
Ewald sum speed up by factor of 2 or more.

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