Bump pymatgen from 2024.3.1 to 2024.10.29

[dependabot]

Bumps pymatgen from 2024.3.1 to 2024.10.29.

Release notes

Sourced from pymatgen's releases.

v2024.10.29

• 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 nest directories. Also, supports non-object string returns.
• Bug fix for parsing of BSE vaspruns.xml.

v2024.10.22

• 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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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.

... (truncated)

Commits

• 5404615 Update docs
• 5dd8c74 Update changelog.
• 7719515 VaspDoc.get_incar_tags: Use Mediawiki API (#4141)
• 91a5b65 Fixed execution of packmol in relative path. (#4145)
• c600ffc Bump rexml from 3.3.6 to 3.3.9 in /docs (#4147)
• a3dfc8e Update changelog.
• 6311a81 Merge branch 'master' of github.com:materialsproject/pymatgen
• 89969ba Rename VaspDir to PMGDir and move it to pymatgen.io.common since it is
• e85d73b Silly me, just use relative_to in pathlib.
• 22b6a7f Fix VaspDir.files.
• Additional commits viewable in compare view

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Superseded by #248.