Change Log#
v3.3.6#
Add py.typed to properly detect type hints by @Andrew-S-Rosen
snb-run updates to improve efficiency
v3.3.5#
Enforce
doped>=2.4.4
requirement.
v3.3.4#
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.
v3.3.3#
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.
v3.3.2#
Add
verbose
options toio.parse_energies()
andsnb-parse
, also used insnb-plot
andsnb-analyse
, and set toFalse
by default to reduce verbosity of certain SnB CLI commands.Use
doped
functions to make oxi-state guessing (and thus defect initialisation) more efficient.Miscellaneous efficiency and robustness updates.
Testing updates.
v3.3.1#
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 ``scp``ing around etc.- Minor updates:
Refactor
_format_defect_name
toformat_defect_name
from doped (now a public function)Update
snb-run
to avoid possible ‘file exists’ warningUpdate tutorials/notebooks to specify
vasp_nkred_std
to streamline workflowRemove 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
fromv3.3.0
: If max number of electronic steps (NELM
) threshold was reached in an ionic step, it would be falsely recognised as converged (due tounconverged
being in theOUTCAR
). This would only affectsnb-run
behaviour in some cases withv3.3.0
, and if so the user should be warned anyway withBond_Distortion_X not fully relaxed
when later runningsnb-parse
/snb-plot
/snb-groundstate
. Now fixed. To double check, one can updateShakeNBreak
and just re-runsnb-run
, and any affected distortions will be correctly determined as unconverged and be re-submitted.
v3.3.0#
Add Dimer distortion as a targeted distortion for dimer reconstructions. It pushes two of the defect NN to a distance of 2 A.
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
v3.2.3#
Ensure the sorted pymatgen Structure is created for the VASP input (fixes a rare bug in v3.2.1 and v3.2.2 where for certain structures the order of elements in the POSCAR was not properly sorted, which is usually fine, but messed with the ROPT INCAR setting).
Plotting format updates (make legend frame more transparent to make datapoints behind it easier to see).
Update tests
Update docs (note about handling AFM systems)
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 🎉
v3.1.0#
Update dependencies, as hiphive=1.2 has been released, making ShakeNBreak compatible with `python=3.11`🎉
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 convergence…)
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 ‘Studies using ShakeNBreak’ and ‘How to Cite’ 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 ofDefect
objects as input. Same forDistortions.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 “a”, “b”, “c” etc in cases of inequivalent defectsMake
ShakeNBreak
compatible with most recentpymatgen
andpymatgen-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 andseed
alternated for different distortions (set to 100*distortion_factor) to avoid rare ‘stuck rattle’ occurrences.Refactor
pickle
usages toJSON
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