Package to generate and analyse distorted defect structures, in order to identify ground-state and metastable defect configurations.
ShakeNBreak (SnB)
ShakeNBreak is a defect structure-searching method employing chemically-guided bond distortions to
locate ground-state and metastable structures of point defects in solid materials. Docs here!
Main features include:
VASP, CP2K, Quantum-Espresso, CASTEP & FHI-aims)VASP)The code currently supports VASP, CP2K, Quantum-Espresso, CASTEP & FHI-aims. Code contributions to support additional solid-state packages are welcome.
ShakeNBreak can be installed using pip:
pip install shakenbreak
Alternatively if needed, it can also be installed from conda with:
conda install -c conda-forge shakenbreak
If using VASP, in order for ShakeNBreak to automatically generate the pseudopotential input files (POTCARs), your local VASP pseudopotential directory must be set in the pymatgen configuration file $HOME/.pmgrc.yaml as follows:
PMG_VASP_PSP_DIR: <Path to VASP pseudopotential top directory>
Within your VASP pseudopotential top directory, you should have a folder named POT_GGA_PAW_PBE
which contains the POTCAR.X(.gz) files (in this case for PBE POTCARs). Please refer to the doped Installation docs if you have
difficulty with this.
The font Montserrat (Open Font License) will be installed with the package, and will be used by default for plotting.
For development work, ShakeNBreak can also be installed from a copy of the source directory:
ShakeNBreak source code using the command: git clone https://github.com/SMTG-Bham/ShakeNBreak
cd ShakeNBreak
pip install -e .
This command tries to obtain the required packages and their dependencies and install them automatically.
ShakeNBreak can be used through a Python API, as exemplified in the SnB Python API tutorial, with more info available on the docs.
Alternatively, the code can be used via the command line:
The functions provided include:
snb-generate: Generate distorted structures for a given defectsnb-generate_all: Generate distorted structures for all defects present in the specified/current directorysnb-run: Submit geometry relaxations to the HPC schedulersnb-parse: Parse the results of the geometry relaxations and write them to a yaml filesnb-analyse: Generate csv files with energies and structural differences between the final configurationssnb-plot: Generate plots of energy vs distortion, with the option to include a colorbar to quantify structural differencessnb-regenerate: Identify defect species undergoing energy-lowering distortions and test these distortions for the other charge states of the defectsnb-groundstate: Save the ground state structures to a Groundstate directory for continuation runsMore information about each function and its inputs/outputs are available from the CLI section of the docs or using -h help option (e.g. snb -h).
We recommend at least looking through the tutorials when first starting to use ShakeNBreak, to familiarise yourself with the full functionality and workflow.
ShakeNBreak is built to natively function using pymatgen Defect objects (docs available here) and be compatible with the most recent version of pymatgen.
If you are receiving pymatgen-related errors when using ShakeNBreak, you may need to update pymatgen and/or ShakeNBreak, which can be done with:
pip install --upgrade pymatgen shakenbreak
ShakeNBreak can take pymatgen Defect objects as input (to then generate the trial distorted structures),
but also can take in pymatgen Structure objects, doped defects or structure files
(e.g. POSCARs for VASP) as inputs. As such, it should be compatible with any defect code
(such as doped, pydefect,
PyCDT, PyLada,
DASP, Spinney,
DefAP, PyDEF...) that generates these files.
Please let us know if you have any issues with compatibility, or if you would like to see any additional features added to ShakeNBreak to make it more compatible with your code.
Please use the Issue Tracker to report bugs or request new features.
Contributions to extend this package are very welcome! Please use the "Fork and Pull" workflow to do so and follow the PEP8 style guidelines.
See the Contributing Documentation for detailed instructions.
Unit tests are in the tests directory and can be run from the top directory using unittest.
Automatic testing is run on the master and develop branches using Github Actions. Please run tests and add new tests for any new features whenever submitting pull requests.
ShakeNBreak has benefitted from feedback from many members of the Walsh and Scanlon research groups who have used / are using it in their work, including Adair Nicolson, Xinwei Wang, Katarina Brlec, Joe Willis, Zhenzhu Li, Jiayi Cen, Lavan Ganeshkumar, Daniel Sykes, Luisa Herring-Rodriguez, Alex Squires, Sabrine Hachmioune and Chris Savory.
ShakeNBreakShakeNBreak is made available under the MIT License.
If you use it in your research, please cite:
You may also find this Preview paper useful, which discusses the general problem of defect structure prediction:
BibTeX entries for these papers are provided in the CITATIONS.md file.
ShakeNBreak is compatible with Python 3.9 - 3.12 and requires the following open-source python packages:
FAQs
Package to generate and analyse distorted defect structures, in order to identify ground-state and metastable defect configurations.
We found that shakenbreak demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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