Bump pymatgen-core from 2026.5.18 to 2026.8.13

[dependabot]

Bumps pymatgen-core from 2026.5.18 to 2026.8.13.

Release notes

Sourced from pymatgen-core's releases.

v2026.8.13

• PR #123 The enumlib_caller module docstring notes Enumlib.jl, a from-scratch Julia reimplementation of enumlib that is a drop-in replacement for enum.x (unchanged struct_enum.in/out contract, makeStr.py reused; this module's own test suite passes against it). EnumlibAdaptor emits an advisory UserWarning recommending it when the resolved enum.x is not Enumlib.jl; detection probes enum.x --version at most once per command path and never raises, so enumeration behavior is unchanged. (by @​glwhart)
• PR #99 Locpot and Elfcar store collinear spin-polarized data under spin_up/spin_down keys, matching what VASP actually writes for these files (two direct spin channels) instead of mislabeling them with CHGCAR's total/diff (total/magnetization) convention. Legacy total/diff access keeps working through warning-backed deprecated aliases. VolumetricData gains a data_key argument selecting the primary grid, is_soc is now detected from the diff_x/diff_y/diff_z keys instead of len(data) >= 4, and linear_add/scale invalidate cached spin data. Fixes materialsproject/pymatgen#4307. (by @​DanielYang59)
• PR #121 Accelerate FermiDos.get_e_h_concs (and thus get_doping and get_fermi) by 3–10×: trapezoid weights are precomputed once in __init__ (turning each integration into a dot product) and the Fermi-Dirac integrand is truncated beyond ~40 k_BT from the Fermi level where its contribution is negligible. Results identical to within ~1e-12 relative error. (by @​kavanase)
• PR #114 Fix hkl_transformation computing matrix-element denominators via int(1 / i), which is wrong for fractions other than 1/n (e.g. the 2/3 in R-decentering). The sign convention changes from "at most one negative index" to "first nonzero index positive" (as in #101), so the returned hkl may differ between equivalent representations, e.g. now (1, -1, -2) where (-1, 1, 2) was returned before. New uvw_transformation transforms direct-lattice [uvw] vectors using the same machinery with the transposed inverse matrix. (by @​Sanftperlig)
• PR #117 Fix Vasprun parsing of vasprun.xml from MD simulations using MLFF (ML_LMLFF), which store steps as top-level tags rather than <calculation> blocks: ionic_step_skip/ionic_step_offset now parse the full file and subsample md_data, nionic_steps is taken from md_data when present, and converged_electronic returns True for MLFF runs (no electronic steps exist). Fixes materialsproject/pymatgen#4200. (by @​DanielYang59)
• PR #111 SlabGenerator.gen_possible_terminations is now a public method (previously an inner function of get_slabs). Termination positions are computed with a PBC-aware circular mean over each cluster instead of relying on atom order, and the siteless case is handled. (by @​Sanftperlig)
• PR #113 generate_all_slabs forwards the cell parameter (added to get_symmetrically_distinct_miller_indices in #101) so it can actually be used. (by @​Sanftperlig)

v2026.7.31

• New MatPESRelaxSet in pymatgen.io.vasp.sets: same settings as MatPESStaticSet but performs a full relaxation of ionic positions and cell (ISIF=3, IBRION=2, NSW=99) with a force-based convergence criterion (EDIFFG=-0.02), so DFT calculations can be performed to match MatPES MLIPs. (by @​shyuep)
• PR #110 Improve R-centering in SpacegroupAnalyzer. get_conventional_to_primitive_transformation_matrix now returns a positive-determinant (spglib-style, no reflection component) matrix for R-centered groups; get_primitive_standard_structure reorients rhombohedral lattices to the Setyawan/Curtarolo convention while keeping fractional coordinates instead of rebuilding sites and rechecking periodic equivalence; the unused international_monoclinic argument is deprecated (passing it emits a DeprecationWarning). Behavior change: the R-centering transformation matrix differs from the previous negative-determinant one, so primitive rhombohedral cells may come out with a different (equivalent) orientation. (by @​Sanftperlig)
• PR #97 Setters for Structure.frac_coords and Structure.cart_coords with length validation, enabling e.g. whole-structure translation via struct.frac_coords += vector. (by @​Sanftperlig)
• PR #105 SlabGenerator and generate_all_slabs gain allow_smaller_than_ouc (default False): with primitive=True, primitivization may reduce the slab below the oriented unit cell and its lattice may diverge from the OUC's. Slab.scale_factor is now corrected for LLL reduction, primitivization, and c-axis changes (solved from the parent lattice → slab lattice relation instead of the base-OUC scaling), and Slab.oriented_unit_cell preserves the input class (Structure vs IStructure). (by @​Sanftperlig)
• PR #109 Remove ENAUG from MP24RelaxSet, MPSCANRelaxSet, and MatPESStaticSet YAML configs and from MVLSlabSet, since VASP ignores/deprecates ENAUG when PREC=Accurate. (by @​DanielYang59)
• PR #112 Fix latexify_spacegroup/unicodeify_spacegroup subscripting only the single digit after _, so screw-axis symbols like P2_12_12_1 render as P2₁2₁2₁ instead of absorbing multi-digit runs. (by @​minhsueh)
• PR #102 Fix BSPlotterProjected crash when orbital summation is not enabled (sum_morbs=None). (by @​ShengLin1001)
• PR #106 Correct the get_symmetrically_distinct_miller_indices overload signatures and docstring default introduced in #101. (by @​Sanftperlig)

v2026.7.27

• PR #101 Overhaul get_symmetrically_distinct_miller_indices. A new cell argument (input, conventional, primitive, conv_np, prim_2conv) makes the treatment of centered cells explicit instead of implicit; sorting is now fully deterministic (smaller max |h|,|k|,|l| first, then smaller sum of |h|,|k|,|l|, then larger h, k, l); indices with gcd > 1 are skipped up front and fewer SpacegroupAnalyzer instances are built; a crystal-family helper was added to SpacegroupAnalyzer and the return type is now inferred from whether hkil or hkl is requested. Behavior change: trigonal cells are no longer implicitly primitivized (the default cell="input" uses the lattice as given), and the representative index chosen for a symmetry-equivalent set may differ. (by @​Sanftperlig)
• PR #103 Remove deprecated functions/classes/methods whose deadlines fell in 2025: StructureGraph/MoleculeGraph with_empty_graph, with_edges, with_local_env_strategy (use the from_* constructors); BrunnerNN_reciprocal, BrunnerNN_relative, BrunnerNN_real; IStructure.ntypesp (use n_elems); the CP2K aliases V_Hartree_Cube, MO_Cubes, E_Density_Cube, Xc_Functional, Kpoint_Set, Band_Structure; JDFTx to_dict() (use as_dict()); and DictSet (use VaspInputSet). BaderAnalysis's parse_atomic_densities argument is now a no-op that emits a DeprecationWarning and will be removed on 2026-12-31. (by @​DanielYang59)
• PR #100 Oszicar ionic-step parsing now goes through _vasprun_float, so VASP overflow markers such as T= ****** yield nan with a warning instead of raising ValueError (fixes materialsproject/pymatgen#4537). (by @​DanielYang59)

v2026.7.24

• PR #95 Outcar table parsing now detects a truncated table (header present but no matching footer, e.g. an OUTCAR cut off mid-write) and emits a warning while returning the partial data, instead of hanging. (by @​DanielYang59)
• PR #92 Coordinate helpers handle empty/siteless inputs: IStructure/Structure coordinate accessors always return a 2D array even with no sites, and get_all_distances returns an empty array when either coordinate set is empty (previously errored on siteless/empty structures). (by @​Sanftperlig)
• PR #93 Replace hand-computed degree/radian conversions (180.0 / pi, pi / 180.0) with math.radians/math.degrees (and np.deg2rad/np.rad2deg for arrays) across lattice, interface, and operations. (by @​Sanftperlig)

v2026.7.16

• PR #68 Refactor IStructure/IMolecule {from_file,from_str,to} onto a new pymatgen.io.registry module. Each pymatgen.io.<format> self-registers a StructureFormat/MoleculeFormat handler; built-in formats stay lazily imported (no added from pymatgen.core import Structure import cost) and third parties can plug in via the pymatgen.io.structure_formats/pymatgen.io.molecule_formats entry-point groups. User-facing behavior (aliases, filename-inference priority, error wording, kwarg warnings, default-to-JSON) is preserved; aims/fleur get fallback shims. (by @​shyuep)
• PR #62 Add static XCrySDen XSF support (MOLECULE/POLYMER/SLAB/CRYSTAL, plus DATAGRID/BANDGRID blocks) with round-trip writing; XSF extras are stored as flat structure properties (grids/…, bands/…). CONVCOORD and animated XSF remain unsupported. (by @​hheei)
• PR #81 Vaspwave.get_chgcar() now reads HDF5 charge-augmentation occupancies (/charge/aug_occupancies_*) into Chgcar.data_aug, so legacy CHGCAR augmentation sections round-trip through Chgcar.write_file(). (by @​hheei)
• PR #69 Extend INCAR list tokenization to accept scientific notation (e.g. ROPT = 1e-3 1e-3 1e-3), which previously parsed as 1 -3 1 -3 1 -3. (by @​kavanase)
• PR #82 Further vectorize the Ewald summation (_calc_recip, _calc_real_and_point); ~10× speedup on 100+-atom systems. (by @​Bud-Macaulay)
• PR #72 Preserve pbc through structure transformations. IStructure.__mul__/make_supercell and other ops that build a new Lattice no longer silently reset pbc to (True, True, True). (by @​deepanshuaggarwal51)
• PR #88 Overhaul standard-cell handling in SpacegroupAnalyzer: get_primitive_standard_structure now correctly detects rhombohedral lattices and handles disordered structures, builds the standard cell once, returns float64, and adds an angle check to get_conventional_standard_structure (fixes materialsproject/pymatgen#4679). (by @​Sanftperlig)
• PR #76 Rescale magmoms when CifParser expands symmetry-equivalent sites from .mcif files whose magnetic cell has unequal-length crystal axes (moment components are converted to Cartesian before applying the operation). (by @​lan496)
• PR #87 VolumetricData.from_cube now honors the grid origin on line 3 instead of discarding it, fixing incorrectly positioned structures for cube files with a nonzero origin (fixes #4607). (by @​mminotaki)
• PR #77 Re-allow generation of Slabs from disordered structures (regressed by #24 using .species instead of .species_and_occu). (by @​Sanftperlig)
• PR #78 Forward the reduce kwarg to recursive IStructure.get_primitive_structure calls so SlabGenerator finds smaller slabs when primitive=True (regressed by #24). (by @​ThomasWarford)
• PR #67 Do not require projections in HighSymmKPath.get_continuous_path (they are not a required field of BandStructureSymmLine). (by @​esoteric-ephemera)
• PR #85 Classify a run as HSE06 for HFSCREEN in [0.2, 0.21] rather than exactly 0.2, matching common 0.207/0.208 usage. (by @​kavanase)
• PR #64 Use trapezoidal integration for FermiDos DOS integration (more accurate carrier concentrations) and add get_e_h_concs() to expose individual electron/hole concentrations. (by @​kavanase)
• PR #90 Use math.tau for full-precision 2π and prefer math.* over np.* for scalar ops (fixes #89). (by @​Sanftperlig)
• PR #91 Raise an explicit ValueError("xyz only supports ordered sites.") when exporting disordered sites to .xyz, instead of a cryptic AttributeError. (by @​Sanftperlig)
• PR #73 Fix get_projected_plots_dots returning a non-Axes ax for single-row/column subplot layouts and a repeated-condition typo. (by @​mias0356)
• PR #74 Fix _get_projections_by_branches_patom_pmorb plotting Spin.up projections in place of Spin.down. (by @​mias0356)
• PR #52 Fix get_projected_plots_dots_patom_pmorb empty-subplot layout and integer-division of row count for num_columns != 2. (by @​mias0356)
• Volumetric I/O. VolumetricData.parse_file for CHGCAR/LOCPOT/ELFCAR is now backed by a Cython fast-float parser (vendored single-header fast_float C port). Roughly 6× faster than the prior _plain_loadtxt path on real fixtures and ~11× with parallel scaling experiments on multi-GB inputs (sequential path is what ships).

... (truncated)

Changelog

Sourced from pymatgen-core's changelog.

v2026.8.13

• PR #123 The enumlib_caller module docstring notes Enumlib.jl, a from-scratch Julia reimplementation of enumlib that is a drop-in replacement for enum.x (unchanged struct_enum.in/out contract, makeStr.py reused; this module's own test suite passes against it). EnumlibAdaptor emits an advisory UserWarning recommending it when the resolved enum.x is not Enumlib.jl; detection probes enum.x --version at most once per command path and never raises, so enumeration behavior is unchanged. (by @​glwhart)
• PR #99 Locpot and Elfcar store collinear spin-polarized data under spin_up/spin_down keys, matching what VASP actually writes for these files (two direct spin channels) instead of mislabeling them with CHGCAR's total/diff (total/magnetization) convention. Legacy total/diff access keeps working through warning-backed deprecated aliases. VolumetricData gains a data_key argument selecting the primary grid, is_soc is now detected from the diff_x/diff_y/diff_z keys instead of len(data) >= 4, and linear_add/scale invalidate cached spin data. Fixes materialsproject/pymatgen#4307. (by @​DanielYang59)
• PR #121 Accelerate FermiDos.get_e_h_concs (and thus get_doping and get_fermi) by 3–10×: trapezoid weights are precomputed once in __init__ (turning each integration into a dot product) and the Fermi-Dirac integrand is truncated beyond ~40 k_BT from the Fermi level where its contribution is negligible. Results identical to within ~1e-12 relative error. (by @​kavanase)
• PR #114 Fix hkl_transformation computing matrix-element denominators via int(1 / i), which is wrong for fractions other than 1/n (e.g. the 2/3 in R-decentering). The sign convention changes from "at most one negative index" to "first nonzero index positive" (as in #101), so the returned hkl may differ between equivalent representations, e.g. now (1, -1, -2) where (-1, 1, 2) was returned before. New uvw_transformation transforms direct-lattice [uvw] vectors using the same machinery with the transposed inverse matrix. (by @​Sanftperlig)
• PR #117 Fix Vasprun parsing of vasprun.xml from MD simulations using MLFF (ML_LMLFF), which store steps as top-level tags rather than <calculation> blocks: ionic_step_skip/ionic_step_offset now parse the full file and subsample md_data, nionic_steps is taken from md_data when present, and converged_electronic returns True for MLFF runs (no electronic steps exist). Fixes materialsproject/pymatgen#4200. (by @​DanielYang59)
• PR #111 SlabGenerator.gen_possible_terminations is now a public method (previously an inner function of get_slabs). Termination positions are computed with a PBC-aware circular mean over each cluster instead of relying on atom order, and the siteless case is handled. (by @​Sanftperlig)
• PR #113 generate_all_slabs forwards the cell parameter (added to get_symmetrically_distinct_miller_indices in #101) so it can actually be used. (by @​Sanftperlig)

v2026.7.31

• New MatPESRelaxSet in pymatgen.io.vasp.sets: same settings as MatPESStaticSet but performs a full relaxation of ionic positions and cell (ISIF=3, IBRION=2, NSW=99) with a force-based convergence criterion (EDIFFG=-0.02), so DFT calculations can be performed to match MatPES MLIPs. (by @​shyuep)
• PR #110 Improve R-centering in SpacegroupAnalyzer. get_conventional_to_primitive_transformation_matrix now returns a positive-determinant (spglib-style, no reflection component) matrix for R-centered groups; get_primitive_standard_structure reorients rhombohedral lattices to the Setyawan/Curtarolo convention while keeping fractional coordinates instead of rebuilding sites and rechecking periodic equivalence; the unused international_monoclinic argument is deprecated (passing it emits a DeprecationWarning). Behavior change: the R-centering transformation matrix differs from the previous negative-determinant one, so primitive rhombohedral cells may come out with a different (equivalent) orientation. (by @​Sanftperlig)
• PR #97 Setters for Structure.frac_coords and Structure.cart_coords with length validation, enabling e.g. whole-structure translation via struct.frac_coords += vector. (by @​Sanftperlig)
• PR #105 SlabGenerator and generate_all_slabs gain allow_smaller_than_ouc (default False): with primitive=True, primitivization may reduce the slab below the oriented unit cell and its lattice may diverge from the OUC's. Slab.scale_factor is now corrected for LLL reduction, primitivization, and c-axis changes (solved from the parent lattice → slab lattice relation instead of the base-OUC scaling), and Slab.oriented_unit_cell preserves the input class (Structure vs IStructure). (by @​Sanftperlig)
• PR #109 Remove ENAUG from MP24RelaxSet, MPSCANRelaxSet, and MatPESStaticSet YAML configs and from MVLSlabSet, since VASP ignores/deprecates ENAUG when PREC=Accurate. (by @​DanielYang59)
• PR #112 Fix latexify_spacegroup/unicodeify_spacegroup subscripting only the single digit after _, so screw-axis symbols like P2_12_12_1 render as P2₁2₁2₁ instead of absorbing multi-digit runs. (by @​minhsueh)
• PR #102 Fix BSPlotterProjected crash when orbital summation is not enabled (sum_morbs=None). (by @​ShengLin1001)
• PR #106 Correct the get_symmetrically_distinct_miller_indices overload signatures and docstring default introduced in #101. (by @​Sanftperlig)

v2026.7.27

• PR #101 Overhaul get_symmetrically_distinct_miller_indices. A new cell argument (input, conventional, primitive, conv_np, prim_2conv) makes the treatment of centered cells explicit instead of implicit; sorting is now fully deterministic (smaller max |h|,|k|,|l| first, then smaller sum of |h|,|k|,|l|, then larger h, k, l); indices with gcd > 1 are skipped up front and fewer SpacegroupAnalyzer instances are built; a crystal-family helper was added to SpacegroupAnalyzer and the return type is now inferred from whether hkil or hkl is requested. Behavior change: trigonal cells are no longer implicitly primitivized (the default cell="input" uses the lattice as given), and the representative index chosen for a symmetry-equivalent set may differ. (by @​Sanftperlig)
• PR #103 Remove deprecated functions/classes/methods whose deadlines fell in 2025: StructureGraph/MoleculeGraph with_empty_graph, with_edges, with_local_env_strategy (use the from_* constructors); BrunnerNN_reciprocal, BrunnerNN_relative, BrunnerNN_real; IStructure.ntypesp (use n_elems); the CP2K aliases V_Hartree_Cube, MO_Cubes, E_Density_Cube, Xc_Functional, Kpoint_Set, Band_Structure; JDFTx to_dict() (use as_dict()); and DictSet (use VaspInputSet). BaderAnalysis's parse_atomic_densities argument is now a no-op that emits a DeprecationWarning and will be removed on 2026-12-31. (by @​DanielYang59)
• PR #100 Oszicar ionic-step parsing now goes through _vasprun_float, so VASP overflow markers such as T= ****** yield nan with a warning instead of raising ValueError (fixes materialsproject/pymatgen#4537). (by @​DanielYang59)

v2026.7.24

• PR #95 Outcar table parsing now detects a truncated table (header present but no matching footer, e.g. an OUTCAR cut off mid-write) and emits a warning while returning the partial data, instead of hanging. (by @​DanielYang59)
• PR #92 Coordinate helpers handle empty/siteless inputs: IStructure/Structure coordinate accessors always return a 2D array even with no sites, and get_all_distances returns an empty array when either coordinate set is empty (previously errored on siteless/empty structures). (by @​Sanftperlig)
• PR #93 Replace hand-computed degree/radian conversions (180.0 / pi, pi / 180.0) with math.radians/math.degrees (and np.deg2rad/np.rad2deg for arrays) across lattice, interface, and operations. (by @​Sanftperlig)

v2026.7.16

• PR #68 Refactor IStructure/IMolecule {from_file,from_str,to} onto a new pymatgen.io.registry module. Each pymatgen.io.<format> self-registers a StructureFormat/MoleculeFormat handler; built-in formats stay lazily imported (no added from pymatgen.core import Structure import cost) and third parties can plug in via the pymatgen.io.structure_formats/pymatgen.io.molecule_formats entry-point groups. User-facing behavior (aliases, filename-inference priority, error wording, kwarg warnings, default-to-JSON) is preserved; aims/fleur get fallback shims. (by @​shyuep)
• PR #62 Add static XCrySDen XSF support (MOLECULE/POLYMER/SLAB/CRYSTAL, plus DATAGRID/BANDGRID blocks) with round-trip writing; XSF extras are stored as flat structure properties (grids/…, bands/…). CONVCOORD and animated XSF remain unsupported. (by @​hheei)
• PR #81 Vaspwave.get_chgcar() now reads HDF5 charge-augmentation occupancies (/charge/aug_occupancies_*) into Chgcar.data_aug, so legacy CHGCAR augmentation sections round-trip through Chgcar.write_file(). (by @​hheei)
• PR #69 Extend INCAR list tokenization to accept scientific notation (e.g. ROPT = 1e-3 1e-3 1e-3), which previously parsed as 1 -3 1 -3 1 -3. (by @​kavanase)
• PR #82 Further vectorize the Ewald summation (_calc_recip, _calc_real_and_point); ~10× speedup on 100+-atom systems. (by @​Bud-Macaulay)
• PR #72 Preserve pbc through structure transformations. IStructure.__mul__/make_supercell and other ops that build a new Lattice no longer silently reset pbc to (True, True, True). (by @​deepanshuaggarwal51)
• PR #88 Overhaul standard-cell handling in SpacegroupAnalyzer: get_primitive_standard_structure now correctly detects rhombohedral lattices and handles disordered structures, builds the standard cell once, returns float64, and adds an angle check to get_conventional_standard_structure (fixes materialsproject/pymatgen#4679). (by @​Sanftperlig)
• PR #76 Rescale magmoms when CifParser expands symmetry-equivalent sites from .mcif files whose magnetic cell has unequal-length crystal axes (moment components are converted to Cartesian before applying the operation). (by @​lan496)
• PR #87 VolumetricData.from_cube now honors the grid origin on line 3 instead of discarding it, fixing incorrectly positioned structures for cube files with a nonzero origin (fixes #4607). (by @​mminotaki)
• PR #77 Re-allow generation of Slabs from disordered structures (regressed by #24 using .species instead of .species_and_occu). (by @​Sanftperlig)
• PR #78 Forward the reduce kwarg to recursive IStructure.get_primitive_structure calls so SlabGenerator finds smaller slabs when primitive=True (regressed by #24). (by @​ThomasWarford)
• PR #67 Do not require projections in HighSymmKPath.get_continuous_path (they are not a required field of BandStructureSymmLine). (by @​esoteric-ephemera)
• PR #85 Classify a run as HSE06 for HFSCREEN in [0.2, 0.21] rather than exactly 0.2, matching common 0.207/0.208 usage. (by @​kavanase)
• PR #64 Use trapezoidal integration for FermiDos DOS integration (more accurate carrier concentrations) and add get_e_h_concs() to expose individual electron/hole concentrations. (by @​kavanase)
• PR #90 Use math.tau for full-precision 2π and prefer math.* over np.* for scalar ops (fixes #89). (by @​Sanftperlig)

... (truncated)

Commits

• 8c9a68b Update changelog.
• e921212 Note Enumlib.jl as a drop-in enum.x successor for EnumlibAdaptor (#123)
• d2d8cf4 Elfcar and Locpot use proper spin_up/down instead of total and diff (#99)
• 102a571 Accelerate FermiDos.get_e_h_concs (and thus get_doping) (#121)
• d7c1d8c Add SupportsIndex to getitem and many more, widen list and fix small non-...
• 96a7388 Fix incorrect determinant calculation in hkl_transformation, add `uvw_trans...
• dfac299 Set bibtexparser<2 upper pin (#116)
• c757f17 fix parsing of vasprun.xml from MD Simulations Using MLFF (#117)
• 8346561 remove xfail for vasp test (#118)
• 165b3f7 Make SlabGenerator.gen_possible_terminations a public function (#111)
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