Bump pymatgen from 2022.0.17 to 2022.8.23

[dependabot]

Bumps pymatgen from 2022.0.17 to 2022.8.23.

Release notes

Sourced from pymatgen's releases.

v2022.8.23

• Structure Graphs from Lobster Data (@​JaGeo)

v2022.7.25

No release notes provided.

v2022.7.24.1

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

Note that a further announcement will be made about the future of MPRester. Until then, users of MPRester are advised to consult the Materials Project documentation: https://docs.materialsproject.org/downloading-data/differences-between-new-and-legacy-api

v2022.7.24

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

Note that a further announcement will be made about the future of MPRester. Until then, users of MPRester are advised to consult the Materials Project documentation: https://docs.materialsproject.org/downloading-data/differences-between-new-and-legacy-api

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 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.

• 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!

What's Changed

• 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 @​arosen93
• Fix: bug in Grüneisen parameter calculation, PR #2543 by 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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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

... (truncated)

Commits

• 2b56a75 Update docs
• 410998c Update docs.
• ec603e7 Merge pull request #2633 from utf/fix-circular-import
• 8b2bb60 Fix circular import
• 0abcca9 Merge pull request #2631 from arosen93/rosen-depre
• eb0de13 Fix deprecation warning on gaussian_filter1d
• 5a1f04a Merge pull request #2620 from nheinsdorf/master
• cd01652 Merge pull request #2623 from JaGeo/lobster_graph2.0
• f21e87c Merge pull request #2629 from janosh/doc-str-JmolNN-min_bond_distance
• 11e380c document kwarg min_bond_distance of JmolNN
• Additional commits viewable in compare view

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Superseded by #232.