Change Log#

v3.2.2#

  • Consolidate SnB/doped INCAR defaults and remove redundant settings.

  • Ensure backwards compatiblity in defect folder name handling.

  • Fix bug in get_site_magnetizations.

v3.2.1#

  • Update CLI config handling.

  • Remove shakenbreak.vasp module and use doped VASP file writing functions directly.

  • Add INCAR/KPOINTS/POTCAR file writing tests. test_local.py now deleted as these tests are now automatically run in test_input.py/test_cli.py if `POTCAR`s available.

v3.2.0#

  • Following the major release of doped v2.0, now compatible with the new pymatgen defects code (pymatgen>2022.7.25), this update:

    • Allows input of doped DefectsGenerator object to Distortions

    • Updates the tutorials to reflect the current recommended workflow of generating defects with doped and then applying ShakeNBreak, no longer requiring separate virtual environments šŸŽ‰

v3.1.0#

  • Update dependencies, as hiphive=1.2 has been released, making ShakeNBreak compatible with `python=3.11`šŸŽ‰

v3.0.0#

  • Switch to semantic versioning

  • Update rattling functions to handle primitive bulk materials as well as supercells.

  • Add check to snb-run if there are multiple `OUTCAR`s present with one or less ionic steps, and if this is also the case for the current run -> warn the user.

  • Small fixes, formatting and docs updates.

v23.06.23#

  • Add snb-mag function, and automatically check the magnetisation from ISPIN = 2 OUTCAR files when continuing relaxations with snb-run (and change to ISPIN = 1 if magnetisation is negligible).

  • Update handling of minimum distances and oxidation states, to deal with single-atom primitive unit cells and systems where pymatgen cannot guess the oxidation state (e.g. single-elements, intermetallics etc).

  • Docs updates

v23.06.03#

  • Make parsing of `DefectEntry`s more robust.

  • Update dependencies (now supporting python=3.10 due to numba updates)

  • Refactor CITATION.cff to CITATIONS.md

  • Update docs, formatting and cleanup.

v23.04.27#

  • Update numpy requirement to numpy>=1.21.2 to fix numpy.typing.NDArray import error.

  • Add News & Views free-to-read link to docs

v23.04.26#

  • Updates to snb-run (copy job from parent directory if present, switch to ALGO = All if poor electronic convergenceā€¦)

  • Make format_defect_name() more robust

  • Update docs and README.md with published article links

  • Formatting and cleanup

  • Make oxidation state guessing more efficient (previously was causing bottleneck with large cells)

  • Fix oxidation state guessing for rare elements

  • Add note to Tips docs page about bulk phase transformation behaviour

  • Refactor to json rather than pickle

v23.02.08#

  • Change numpy version requirement in docs/requirements.txt to numpy>=1.21 to work with numpy.typing.NDArray.

v23.02.02#

  • Refactor Distortions() class to take in DefectEntry objects as input, rather than Defect objects, to be

compatible with pymatgen-analysis-defects. - Fix ticks and ticklabels in plots

v23.01.25#

  • Specify pandas version in requirements.txt to equal or higher than 1.1.0

  • Refactor snb-regenerate to execute when no arguments are specified (rather than showing help message)

v23.01.7#

  • Add ā€˜Studies using ShakeNBreakā€™ and ā€˜How to Citeā€™ to readme and docs.

v22.12.2#

  • Add JOSS badge to docs

v22.12.1#

  • Minor updates to paper.md and paper.bib

v22.11.29#

Main changes: - Add example notebook showing how to generate interstitials and apply SnB to them. - Fix typo in example notebook and docs. - Add comment about font installation to Installation guide. - Update paper.md with suggestions from editor.

v22.11.18#

Add docs plots.

v22.11.18#

Docs tutorial update.

v22.11.17#

Main changes:

  • Refactor Distortions() to a list or simple-format dict of Defect objects as input. Same for Distortions.from_structures()

  • Update defect naming to {Defect.name}_s{Defect.defect_site_index} for vacancies/substitutions and {Defect.name}_m{Defect.multiplicity} for interstitials. Append ā€œaā€, ā€œbā€, ā€œcā€ etc in cases of inequivalent defects

  • Make ShakeNBreak compatible with most recent pymatgen and pymatgen-analysis-defects packages.

  • Update legend format in plots and site index/multiplicity labelling, make default format png.

  • Update default charge state setting to match pymatgen-analysis-defects oxi state + padding approach.

  • A lot of additional warning and error catches.

  • Miscellaneous warnings and docs updates.

v22.11.7#

Main changes:

  • Refactor ShakeNBreak to make it compatible with pymatgen>=2022.8.23. Now Distortions takes in pymatgen.analysis.defects.core.Defect objects.

  • Add Distortions.from_dict() and Distortions.from_structures() to generate defect distortions from a dictionary of defects (in doped format) or from a list of defect structures, respectively.

v22.11.1#

Main changes:

  • Update rattling procedure; stdev be automatically set to 10% bulk bond length and seed alternated for different distortions (set to 100*distortion_factor) to avoid rare ā€˜stuck rattleā€™ occurrences.

  • Refactor pickle usages to JSON serialisation to be more robust to package (i.e. pymatgen) updates.

  • Update snb-regenerate to be more robust, can be continually rerun without generating duplicate calculations.

  • Update snb-run to consider calculations with >50 ionic steps and <2 meV energy change as converged.

  • Minor changes, efficiency improvements and bug fixes.

v22.10.14#

Just bumping version number to test updated GH Actions pip-install-test workflow.

v22.10.13#

Main changes:

  • Updated defect name handling to work for all conventions

  • More robust snb-generate and plotting behaviour

  • Add CLI summary GIF to docs and README

  • Updated snb-run behaviour to catch high-energies and forces error to improve efficiency

  • Many miscellaneous tests and fixes

  • Docs updates

v22.9.21#

Main changes:

  • Fonts now included in package_data so can be installed with pip from PyPI

  • Refactoring distortion_plots plot saving to saving to defect directories, and preventing overwriting of previous plots

  • Miscellaneous tests and fixes

  • Add summary GIF to docs and README

  • Handling for partial oxidation state input

  • Setting EDIFFG = -0.01 and local_rattle = False as default

v22.9.2#

Main changes:

  • Update CLI commands (snb-parse, analyse, plot and groundstate can all now be run with no arguments within a defect folder)

  • Update custom font

  • Update groundstate() tests

  • Update plotting

v22.9.1#

Main changes:

  • Test for pip install

  • Automatic release and upload to pypi

  • Add ShakeNBreak custom font, and automatise its installation

  • Update ShakeNBreak default INCAR for VASP relaxations

  • Formatting

v1.0.1#

Main changes:

  • Docs formatting

  • Update pymatgen version to v2022.7.25, while refactoring to be compatible with v2022.8.23 takes place.

v1.0#

Release with full code functionality (CLI and Python), pre JOSS submission.

v0.2#

Release with final module architecture of the code. Implemented command-line interface and I/O to codes other than VASP.

v0.1#

First release with full functionality present, except CLI and I/O to codes other than VASP.

v0.0#

Initial version of the package.

Added#

  • Script files:

    • BDM

    • distortions

    • energy_lowering_distortions

    • plot_BDM

    • analyse_defects

    • champion_defects_rerun