Changelog

2024.11.13

  • CP2K fixes (@janosh)
  • Fix borg.hive.SimpleVaspToComputedEntryDrone.assimilate ValueError when core file missing (@DanielYang59)
  • Revert breaking analysis.local_env default_op_params/cn_opt_params rename (@DanielYang59)
  • Added new Flag for AutoOxiStateDecorationTransformation (@jmmshn)
  • Fixed execution of packmol in relative path. (@davidwaroquiers)
  • Improve element mismatch handling with POTCAR for Poscar.from_file/str (@DanielYang59)
  • Preprocess Structure Reduction Before Bulk Match (@lan496)
  • Add min “thickness” check in CifParser to filter invalid structure which leads to infinite loop (@DanielYang59)

2024.10.29

  • VaspDir has been renamed and moved to pymatgen.io.common.PMGDir for more general support of all IO classes. Note that this is a backwards incompatible change. It should not affect many users since VaspDir was introduced only in the last one week.
  • Fixed execution of packmol in relative path. (@davidwaroquiers)
  • VaspDoc.get_incar_tags: Use Mediawiki API (@yantar92)
  • Fix comment pass in Kpoints constructors (@DanielYang59)

v2024.10.27

  • Bug fix for parsing of dielectric calculations from vasprun.xml.

v2024.10.25

  • VaspDir now supports nested directories. Also, supports returning strings where a parser is not defined.
  • Bug fix for parsing of BSE vaspruns.xml.

v2024.10.21

  • New pyamtgen.io.vasp.VaspDir class for easy navigation of VASP directories as pymatgen objects.
  • Fix gaussian input parser (@sio-salt)
  • Fix: preserve site properties over cell transform (@Lattay)
  • Make Incar keys case insensitive, fix init Incar from dict val processing for str/float/int (@DanielYang59)
  • Fix: Preserve PBC info in AseAtomsAdaptor (@jsukpark)
  • Migrate ext.COD from mysql to REST API (@DanielYang59)
  • Fix: Parsing bugs in io.pwscf.PWInput (@jsukpark)
  • Fix arg passing in inverse property of SymmOp (@DanielYang59)
  • Add support for use_structure_charge keyword in FHI-aims input generator (@ansobolev)
  • Fix: savefig in pmg.cli.plot (@DanielYang59)
  • Fix: Volumetric data and XDATCAR parsing for monatomic structures (@esoteric-ephemera)
  • Support to aims format from Structure instance (@ansobolev)
  • Fix: Bugfix for Ion CO2(aq) reduced formula (@rkingsbury)
  • Replace deprecated ExpCellFilter with FrechetCellFilter (@ab5424)

v2024.10.3

  • Enable parsing of “SCF energy” and “Total energy” from QCOutput for Q-chem 6.1.1+. (@Jaebeom-P)
  • Fix dict equality check with numpy array (@DanielYang59)
  • Fix usage of strict=True for zip in cp2k.outputs (@DanielYang59)
  • Fix bug with species defaults (@tpurcell90)
  • SLME Bug Fixes (@kavanase)

v2024.9.17.1

  • Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @yang-ruoxi for fixing.)

v2024.9.17

  • Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @yang-ruoxi for fixing.)

v2024.9.10

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

🛠 Enhancements

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

🐛 Bug Fixes

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

💥 Breaking Changes

  • Pascal-case PMG_VASP_PSP_DIR_Error by @janosh in https://github.com/materialsproject/pymatgen/pull/4048

📖 Documentation

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

🧹 House-Keeping

  • Use strict=True with zip to ensure length equality by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4011

🚀 Performance

  • add LRU cache to structure matcher by @kbuma in https://github.com/materialsproject/pymatgen/pull/4036

🚧 CI

  • Install optional boltztrap, vampire and openbabel in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3985

💡 Refactoring

  • Make AimsSpeciesFile a dataclass by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/4054

🧪 Tests

  • Remove the skip mark for test_delta_func by @njzjz in https://github.com/materialsproject/pymatgen/pull/4014
  • Recover commented out code in tests and mark with pytest.mark.skip instead by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4027
  • Add unit test for io.vasp.help by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4020

🧹 Linting

  • Fix failing ruff PT001 on master by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4003
  • Fix fixable ruff rules by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4015
  • Fix S101, replace all assert in code base (except for tests) by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4017
  • Fix ruff PLC0206 and PLR6104 by @janosh in https://github.com/materialsproject/pymatgen/pull/4035

🏥 Package Health

  • Drop Python 3.9 support by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4009
  • Avoid importing namespace package pymatgen directly by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/4053

🏷️ Type Hints

  • Set kpoints in from_str method as integer in auto Gamma and Monkhorst modes by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3994
  • Improve type annotations for io.lobster.{lobsterenv/outputs} by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3887

🤷‍♂️ Other Changes

  • VaspInputSet.write_input: Improve error message by @yantar92 in https://github.com/materialsproject/pymatgen/pull/3999

New Contributors

  • @yantar92 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3999
  • @kbuma made their first contribution in https://github.com/materialsproject/pymatgen/pull/4036

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.8.9…v2024.9.10

v2024.8.9

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

🎉 New Features

  • Add multiwfn QTAIM parsing capabilities by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3926

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

  • Replace expired BoltzTraP link by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3929
  • Correct method get_projection_on_elements docstring under Procar class by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3945

🧹 House-Keeping

  • Split VASP input sets into submodules by @janosh in https://github.com/materialsproject/pymatgen/pull/3865

🚧 CI

  • Install some optional dependencies in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3786

💡 Refactoring

  • Fix Incar check_params for Union type by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3958

🏥 Package Health

  • build against NPY2 by @njzjz in https://github.com/materialsproject/pymatgen/pull/3894

🏷️ Type Hints

  • Improve types for electronic_structure.{bandstructure/cohp} by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3873
  • Improve types for electronic_structure.{core/dos} by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3880

🤷‍♂️ Other Changes

  • switch to attr access interface for transformation matrix by @tsmathis in https://github.com/materialsproject/pymatgen/pull/3964
  • Fix import sorting by @janosh in https://github.com/materialsproject/pymatgen/pull/3968
  • Don’t run issue-metrics on forks by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3962
  • Enable Ruff rule family “N” and “S” by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3892

New Contributors

  • @danielzuegner made their first contribution in https://github.com/materialsproject/pymatgen/pull/3915
  • @tsmathis made their first contribution in https://github.com/materialsproject/pymatgen/pull/3964
  • @jsukpark made their first contribution in https://github.com/materialsproject/pymatgen/pull/3931

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.7.18…v2024.8.8

v2024.8.8

🎉 New Features

  • Add multiwfn QTAIM parsing capabilities by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3926

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

  • Replace expired BoltzTraP link by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3929
  • Correct method get_projection_on_elements docstring under Procar class by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3945

🧹 House-Keeping

  • Split VASP input sets into submodules by @janosh in https://github.com/materialsproject/pymatgen/pull/3865

🚧 CI

  • Install some optional dependencies in CI by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3786

💡 Refactoring

  • Fix Incar check_params for Union type by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3958

🏥 Package Health

  • build against NPY2 by @njzjz in https://github.com/materialsproject/pymatgen/pull/3894

🏷️ Type Hints

  • Improve types for electronic_structure.{bandstructure/cohp} by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3873
  • Improve types for electronic_structure.{core/dos} by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3880

🤷‍♂️ Other Changes

  • switch to attr access interface for transformation matrix by @tsmathis in https://github.com/materialsproject/pymatgen/pull/3964
  • Fix import sorting by @janosh in https://github.com/materialsproject/pymatgen/pull/3968
  • Don’t run issue-metrics on forks by @ab5424 in https://github.com/materialsproject/pymatgen/pull/3962
  • Enable Ruff rule family “N” and “S” by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3892

New Contributors

  • @danielzuegner made their first contribution in https://github.com/materialsproject/pymatgen/pull/3915
  • @tsmathis made their first contribution in https://github.com/materialsproject/pymatgen/pull/3964
  • @jsukpark made their first contribution in https://github.com/materialsproject/pymatgen/pull/3931

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.7.18…v2024.8.8

v2024.7.18

  • Fix setuptools for packaging (#3934)
  • Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (#3900)
  • Add electronic structure methods for Species (#3902)
  • Migrate spglib to new SpglibDataset format with version 2.5.0 (#3923)
  • SpaceGroup changes (#3859)
  • Add MD input set to FHI-aims (#3896)

v2024.6.10

  • Fix bug in update_charge_from_potcar (#3866)
  • Fix bug in VASP parameter parsing (@mkhorton)
  • Add strict_anions option to MaterialsProject2020Compatibility (@mkhorton)
  • Slightly more robust MSONAtoms handling (@Andrew-S-Rosen)
  • Bug fix: handle non-integer oxidation states in Species (@esoteric-ephemera)
  • Revert change that removed test structure files from pymatgen source.

v2024.6.4

🐛 Bug Fixes

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

🛠 Enhancements

  • Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] by @janosh in https://github.com/materialsproject/pymatgen/pull/3858

📖 Documentation

  • Clarify argument shift for SlabGenerator.get_slab by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3748

🚧 CI

  • Add CI run without 'optional' deps installed by @janosh in https://github.com/materialsproject/pymatgen/pull/3857

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.31…v2024.6.4

2024.5.31

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

  • Imperative get_... method and @property doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3802
  • Doc string standardization by @janosh in https://github.com/materialsproject/pymatgen/pull/3805

🧹 House-Keeping

  • Add types for core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc) by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3829
  • Move test structures out of util directory by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3831

🧪 Tests

  • Improve type annotations for core.(trajectory/units) by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3832

🏷️ Type Hints

  • More type annotations by @janosh in https://github.com/materialsproject/pymatgen/pull/3800
  • Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3814
  • Guard TYPE_CHECKING only imports by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3827
  • Improve type annotations and comments for io.cif by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3820
  • Improve type annotations for core.structure by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3837

🤷‍♂️ Other Changes

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

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.1…v2024.5.31

v2024.5.1

🐛 Bug Fixes

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

📖 Documentation

  • Add note to documentation for usage of CrystalNN by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3764
  • Update to average Grüneisen documentation by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3773
  • Format doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3790
  • Imperative doc strings by @janosh in https://github.com/materialsproject/pymatgen/pull/3792

🧹 House-Keeping

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

🚧 CI

  • Officially support Python 3.12 and test in CI by @janosh in https://github.com/materialsproject/pymatgen/pull/3685

🏥 Package Health

  • Remove gulp from package data, code base and CI tests by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3789

🏷️ Type Hints

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

🤷‍♂️ Other Changes

  • add get_string->get_str alias for Poscar by @timurbazhirov in https://github.com/materialsproject/pymatgen/pull/3763
  • Fix ruff FURB192 by @janosh in https://github.com/materialsproject/pymatgen/pull/3785

New Contributors

  • @timurbazhirov made their first contribution in https://github.com/materialsproject/pymatgen/pull/3763
  • @AntObi made their first contribution in https://github.com/materialsproject/pymatgen/pull/3784

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.4.13…2024.5.1

v2024.4.13

Hot fix release for v2024.4.12 to be yanked on PyPI due to https://github.com/materialsproject/pymatgen/issues/3751.

🐛 Bug Fixes

  • Revert mistaken Cohp.has_antibnd_states_below_efermi rename by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3750
  • Fix typing_extension ImportError in downstream packages by @janosh in https://github.com/materialsproject/pymatgen/pull/3752
  • Update some of the OPTIMADE aliases by @ml-evs in https://github.com/materialsproject/pymatgen/pull/3754

🧹 House-Keeping

  • Remove duplicate ruff rule in pyproject.toml by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3755

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.4.12…v2024.4.13

v2024.4.12

🎉 New Features

  • Add pymatgen.io.openff module by @orionarcher in https://github.com/materialsproject/pymatgen/pull/3729

🐛 Bug Fixes

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

🛠 Enhancements

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

🚧 CI

  • Migrate CI dependency installation from pip to uv by @janosh in https://github.com/materialsproject/pymatgen/pull/3675
  • Prevent GitHub Actions from running docs-related CI on forks by @lan496 in https://github.com/materialsproject/pymatgen/pull/3697

📖 Documentation

  • Reformat docstrings to Google style and add type annotations by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3694
  • Breaking: all plot methods return plt.Axes by @janosh in https://github.com/materialsproject/pymatgen/pull/3749

🧹 House-Keeping

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

🚀 Performance

  • Dynamic __hash__ for BalancedReaction by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3676

🧪 Tests

  • Clean up tests 2 by @janosh in https://github.com/materialsproject/pymatgen/pull/3716
  • Remove unnecessary unittest.TestCase subclassing by @janosh in https://github.com/materialsproject/pymatgen/pull/3718

🔒 Security Fixes

  • Avoid using exec in code by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3736
  • Avoid using eval, replace manual offset in enumerate and rename single letter variables by @DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3739

🏷️ Type Hints

  • Self return type on from_dict methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3702
  • Return self from Structure methods replace, substitute, remove_species, remove_sites by @janosh in https://github.com/materialsproject/pymatgen/pull/3706
  • Self return type on Lattice methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3707

🤷‍♂️ Other Changes

  • os.path.(exists->isfile) by @janosh in https://github.com/materialsproject/pymatgen/pull/3690

New Contributors

  • @JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3679
  • @uliaschauer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3734

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.3.1…v2024.4.12

v2024.3.1

What’s Changed

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

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

🧹 House-Keeping

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

🧪 Tests

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

🏷️ Type Hints

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

🤷‍♂️ Other Changes

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

New Contributors

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

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

v2024.2.23

🐛 Bug Fixes

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

🛠 Enhancements

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

🧪 Tests

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

🤷‍♂️ Other Changes

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

New Contributors

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

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

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

🛠 Enhancements

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

🧹 House-Keeping

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

🚀 Performance

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

💥 Breaking Changes

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

🤷‍♂️ Other Changes

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

New Contributors

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

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

v2024.2.8

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

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

🧹 House-Keeping

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

🧪 Tests

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

🏥 Package Health

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

🤷‍♂️ Other Changes

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

New Contributors

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

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

v2024.1.26

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

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

🧪 Tests

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

💥 Breaking Changes

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

🤷‍♂️ Other Changes

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

New Contributors

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

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

v2023.12.18

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

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

🚀 Performance

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

🧪 Tests

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

🏷️ Type Hints

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

New Contributors

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

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

v2023.11.12

🐛 Bug Fixes

  • Hot fix: pymatgen package missing potcar-summary-stats.json.bz2 by @janosh in https://github.com/materialsproject/pymatgen/pull/3468

🛠 Enhancements

  • Add Composition.charge and charge_balanced properties by @janosh in https://github.com/materialsproject/pymatgen/pull/3471

v2023.11.10

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

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

🤷‍♂️ Other Changes

  • Create jekyll-gh-pages.yml by @shyuep in https://github.com/materialsproject/pymatgen/pull/3410
  • Make from_(str|file) (static->class)methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3429

New Contributors

  • @RedStar-Iron made their first contribution in https://github.com/materialsproject/pymatgen/pull/3430
  • @tawe141 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3452
  • @tpurcell90 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3435

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

v2023.10.11

🐛 Bug Fixes

🛠 Enhancements

📖 Documentation

🧹 House-Keeping

🧪 Tests

💥 Breaking Changes

🏷️ Type Hints

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

v2023.10.4

🐛 Bug Fixes

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

v2023.10.3

🐛 Bug Fixes

🛠 Enhancements

🧹 House-Keeping

🏥 Package Health

New Contributors

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

🛠 Enhancements

🏥 Package Health

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

🛠 Enhancements

🏥 Package Health

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

v2023.9.2

v2023.8.10

New Contributors

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

v2023.7.20

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 https://github.com/materialsproject/pymatgen/pull/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!

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

  1. Cp2K support (@nwinner)
  2. Better BSPlotter (@fraricci)
  3. Better deprecation warnings.
  4. Bug fix for Py3.9 support.
  5. 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

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

v2019.10.4

  1. 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.vaspput 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

  1. Consistent use of unicode throughout pymatgen.
  2. Minor bug fixes.

v3.0.1

  1. Minor bug fixes for cifio.
  2. 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.
© Copyright 2011, Materials Project