3.4.3

• Efficient oxidation state guessing using doped functions, along with handling of mixed-valence systems by @hwbng
• Explicitly set charge in CP2K output files.
• Minor bugfixes and robustness updates.

3.4.2

• Add polarons distortion tutorial; https://shakenbreak.readthedocs.io/en/latest/ShakeNBreak_Polaron_Workflow.html
• Update to use efficiency functions from latest doped.
• Use tqdm progress bar for distortion generation.

3.4.1

• Updated handling of Dimer distortions:
  • The default dimer bond lengths are now set to match known covalent bond lengths (e.g. for O-O, S-S,
    O-N etc), or failing that, the sum of their covalent radii (rather than prev hard default of 2 Å).
  • Alternatively, dimer bond lengths can be specified by the user, both in the distortions functions
    and in the higher level shakenbreak.input functions/classes (i.e. in Distortions).
• Added distort_and_rattle convenience function to distortions, to easily apply the SnB distortions
  and rattling (where rattling is not applied to the bond-distorted atoms) to a given structure. Useful for
  power users.
• Minor code streamlining and simplification in inputs/distortions.

3.4.0

• Major efficiency updates:
  • Uses _scan_sm_stol_till_match and turbo-charged StructureMatcher methods from doped
v3, speeding up structure matching (e.g. in snb-regenerate for identifying distinct defect
    geometries) by >~3 orders of magnitude.
  • Uses caching in atomic displacement calculations (for "disp"/"max_dist" metrics)
  • Use efficient Voronoi analyzer from doped v3 for multiplicity determination.
  • More efficient (and cleaner) plotting with many defects/distortions
• Add Dimer to default distortions grid output for vacancies, following discussions and testing for
  cation vacancies in oxides.
• Miscellaneous:
  • All snb-xxx functions now auto-detect if running within a defect folder or in a top-level
    directory (i.e. auto --all behaviour).
  • Handling of gzipped OUTCAR.gz files for energy parsing.
  • For (rare) cases of degenerate choices of NNs to distort in terms of distance, but non-degenerate
    combinations (e.g. distorting 2 NNs of a square coordination, could be cis or trans choices),
    the choice is made deterministically; choosing the combination with the shortest distances between
    distorted NNs (i.e. the cis choice).
  • Greater verbosity control
  • Some code cleanup and formatting, and robustness updates

3.3.6

• Add py.typed to properly detect type hints by @Andrew-S-Rosen
• snb-run updates to improve efficiency

3.3.5

• Enforce doped>=2.4.4 requirement.

3.3.4

• Make oxidation state guessing more efficient.
• Update Quantum Espresso and FHI-aims IO functions to work with new (and old) ASE release.
• Minor updates to ensure compatibility with recent pymatgen release.
• Allow unrecognised defect names when plotting.

3.3.3

• Add verbose option to more parsing/plotting functions for better control of output detail.
• Improve effiency & robustness of oxidation state handling.
• Miscellaneous efficiency (e.g. memory reduction) and robustness updates.
• Improved GitHub Actions test efficiency.

3.3.1

• distortion_metadata.json for each defect now saved to the individual defect folders (as well as the
  combined total distortion metadata in the top level folder) – more likely to be retained by the user
  when scping around etc.
• Minor updates:
  • Refactor _format_defect_name to format_defect_name from doped (now a public function)
  • Update snb-run to avoid possible 'file exists' warning
  • Update tutorials/notebooks to specify vasp_nkred_std to streamline workflow
  • Remove unnecessary tutorials folder with duplicate tutorial notebook (to reduce workload).
  • Add Binder/Colab buttons to run tutorials in the cloud from docs
  • Default verbosity updates (quieten some unnecessary info messages)
  • Make distortion_metadata overwriting/combining more robust and less (unnecessarily) verbose
• Bugfix of snb-run from v3.3.0: If max number of electronic steps (NELM) threshold was reached
  in an ionic step, it would be falsely recognised as converged (due to unconverged being in the
  OUTCAR). This would only affect snb-run behaviour in some cases with v3.3.0, and if so the
  user should be warned anyway with Bond_Distortion_X not fully relaxed when later running
  snb-parse/snb-plot/snb-groundstate. Now fixed. To double check, one can update
  ShakeNBreak and just re-run snb-run, and any affected distortions will be correctly determined as
  unconverged and be re-submitted.

3.3.0

• Add Dimer distortion as a targeted distortion for dimer reconstructions. It pushes two of the defect NN to a distance of 2 Å.
• Add option distorted_atoms to the Distortion class to allow users to specify the indexes of the atoms to distort.
• Update tests to check the new functionality.
• Update get_homoionic_bonds to detect homoionic bonds between different cations/anions (rather than just bonds between the same element)
• Fix issue with snb-generate when no defect name was specified (by adding unrelaxed=True when calling get_defect_name_from_entry)
• Update functions that read OUTCARs to be able to read OUTCAR.gz files too
• Update energies parsing to still work when all distortions are high energy, but warn the user about this (i.e. only Unperturbed)
• Update snb-run to add early-on detection of distortions that are stuck in high energy basins and rename them to "High_Energy" to avoid continuing their relaxation
• Miscellaneous efficiency improvements and bug fixes