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Project description
SHRY (Suite for High-throughput generation of models with atomic substitutions implemented by python) is a tool for generating unique ordered structures corresponding to a given disordered structure.
How to cite
Please cite the following paper:
SHRY: Application of Canonical Augmentation to the Atomic Substitution Problem, G.I. Prayogo*, A. Tirelli, K. Utimula, K. Hongo, R. Maezono, and K. Nakano*, J. Chem. Inf. Model., 62, 2909-2915 (2022), DOI:10.1021/acs.jcim.2c00389
Installation
SHRY can be obtained from PyPI
pip install shry
For Windows Users
For Windows users, if you don’t have Python already, you can try, for example, installing Python from the Microsoft store following instructions on this page.
Then install SHRY just like above within PowerShell or your favourite terminal.
pip install shry
Development
If you prefer to install from source, instead follow the procedures below.
git clone https://github.com/giprayogo/SHRY.git
cd SHRY
pip install -e .
Quick use
Preparation of an input file (a CIF file)
You can prepare a CIF file with partial occupations.
# label element x y z occupation
Sm1 Sm 0.000 0.00 0.00 1.000
Fe1 Fe 0.250 0.25 0.25 0.400
Nb1 Nb 0.250 0.25 0.25 0.600
Fe2 Fe 0.278 0.50 0.00 1.000
SHRY will automatically stop if the total occupancy of a site is either less or more than 1.0. To simulate vacancies, create a pseudo atom with species X.
Check total symmetry-inequivalent structures
You can readily check the number of total symmetry-inquivalent structures using the following command.
shry --count-only STRUCTURE_CIF
This operation is based on Polya enumeration and takes much less time than a proper generation.
Creating supercell
Sometimes a supercell is required to fit in finer concentrations. SHRY accepts either 3-digit (diagonal) or 9-digit (non-diagonal) format to specify the supercell’s scaling matrix. For example a 2x2x1 supercell can be specified by either
shry -s 2 2 1 --count-only STRUCTURE_CIF
or
shry -s 2 0 0 0 2 0 0 0 1 --count-only STRUCTURE_CIF
Generating unique structures
Finally, you can generate symmetry-inequivalent structures using the following command:
shry -s 2 2 1 STRUCTURE_CIF
The generated symmetry-inequivalent structures are saved in sliceXX directories.
Additional information
For additional information, you can use the help command:
shry -h
or you can refer to the documentation.
Documentation
The documentation is available here.
How to release
Merge devel to master
git checkout master
git merge devel
Check the next-version version
# Confirm the version number via `setuptools-scm`
python -m setuptools_scm
e.g., 1.1.4.dev28+gceef293.d20221123 -> <next-version> = 1.1.5
Add and push a new tag
# Push with tag
git tag <next-version>
git push origin master --tags
An implemented Github action automatically uploads the package to testPyPI and PyPI (if the commit is tagged correctly, e.g., v1.1.0).
Finally, do a new release with a release note on Github
Contributing to the project
If you want to contribute to the project, report a bug, or ask for a new feature, please raise an issue.
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