Bump pymatgen from 2021.3.9 to 2022.0.9

[dependabot-preview[bot]]

Bumps pymatgen from 2021.3.9 to 2022.0.9.

Release notes

Sourced from pymatgen's releases.

v2022.0.9

Features

• 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)

Changes

• Change names of high-symmetry paths (@​munrojm, #2144)
• Change default for filter_solids argument of PourbaixDiagram (@​rkingsbury, #2177)

Fixes

• 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

• 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

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)

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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 @​richardtran415 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

... (truncated)

Commits

• b789d74 Run black code formatter
• 6b6e27e Remove deprecation warnings, clarify docstrings
• c8562d4 Update version and changelog
• e002483 Merge pull request #2177 from rkingsbury/pourbaix_updates
• 15a857c proper type checking bugfix per shyamd
• 5fb8b2b python 3.8 hinting fix
• b244025 docstring correction
• d2550da lint with black, add type hinting to PourbaxiDiagram
• 443df01 default to filter_solids=True; deprecate as_dict kwarg
• 9d1737d fix bug introduced by e8028b0cfe783f8628c9090da07ff6e435244f6c
• Additional commits viewable in compare view

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Superseded by #9.