No project description provided
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/shry-project/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.
Contributing to the project
Please work on your forked repository, and send a pull request to the devel branch of the original GitHub repository. After the pull request is approved and the devel branch is merged.
If you want to contribute to the project, report a bug, or ask for a new feature, please raise an issue.
How to release for maintainers
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> = v1.1.4 or v1.1.4-alpha(for pre-release)
Add and push with the new tag
# Push with tag
git tag <next-version> # e.g., git tag v1.1.4 # Do not forget "v" before the version number!
git push origin devel --tags # or to the new branch # Do not push to the mater branch!!
Make a pull request for merging the devel branch to the main branch by hand. The implemented GitHub Action checks if the automatic deploy works using test-pyPI.
Finally, do a new release with a release note on GitHub. The new release triggers an implemented GitHub Action that automatically uploads the package to PyPI (if the commit is tagged correctly, e.g., v1.1.0 or v1.1.0-alpha).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.