bsym

bsym: A basic symmetry module - Published in JOSS (2017)

https://github.com/bjmorgan/bsym

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 6 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
○
Committers with academic emails
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Materials Science Physical Sciences - 34% confidence

Last synced: 4 months ago · JSON representation ·

Repository

A Basic Symmetry Module (Python)

Basic Info

Host: GitHub
Owner: bjmorgan
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 5.48 MB

Statistics

Stars: 17
Watchers: 2
Forks: 6
Open Issues: 0
Releases: 10

Created over 11 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation Codemeta Zenodo

bsym is a basic Python symmetry module. It consists of core classes that describe configuration vector spaces, their symmetry operations, and specific configurations of objects within these spaces. The module also contains an interface for working with pymatgen Structure objects, to allow simple generation of disordered symmetry-inequivalent structures from a symmetric parent crystal structure.

Usage examples are provided in the documentation API documentation is here.
Source code is available at https://github.com/bjmorgan/bsym.

Installation

pip install bsym

Or download the latest release from GitHub, and install cd bsym python setup.py install

Or clone the latest development version git clone git@github.com:bjmorgan/bsym.git and install the same way. cd bsym python setup.py install

Tests

Manual tests can be run using python -m unittest discover

The code has been tested with Python versions 3.5 and above.

Documentation

An overview of the capabilities of bsym along with example code is provided in the codumentation.

I want to generate a set of symmetry-inequivalent crystal structures

bsym can enumerate symmetry-inequivalent crystal structures generated by partial substitutions, starting from a parent structure described by a pymatgen Structure object.
Example code is in the documentation. Also refer to the bsym.interface.pymatgen.unique_structure_substitutions documentation.

Citing `bsym`

This code can be cited as:

Morgan, Benjamin J. (2017). bsym - a Basic Symmetry Module. The Journal of Open Source Software. http://doi.org/10.21105/joss.00370

BibTeX

@article{Morgan_JOSS2017b, doi = {10.21105/joss.00370}, url = {https://doi.org/10.21105/joss.00370}, year = {2017}, month = {aug}, publisher = {The Open Journal}, volume = {2}, number = {16}, author = {Benjamin J. Morgan}, title = {bsym: A basic symmetry module}, journal = {The Journal of Open Source Software} }

Owner

Name: Benjamin Morgan
Login: bjmorgan
Kind: user
Location: Bath, UK
Company: University of Bath

Repositories: 73
Profile: https://github.com/bjmorgan

Computational Chemistry at the University of Bath, UK.

JOSS Publication

bsym: A basic symmetry module

Published

August 18, 2017

DOI

10.21105/joss.00370

Volume 2, Issue 16, Page 370

Authors

Benjamin J. Morgan

Department of Chemistry, University of Bath, Bath, BA2 7AY, United Kingdom.

Editor

Lorena A Barba

Citation (CITATION.cff)

cff-version: 1.0.3
message: If you use this software, please cite both the software repository and the JOSS paper.
author: 
  - family-names: Morgan
    given-names: Benjamin J.
    orcid: https://orcid.org/0000-0002-3056-8233
title: bsym
version: 1.1.0
doi: 10.5281/zenodo.596912
repository-code: https://github.com/bjmorgan/bsym
license: MIT
references:
  - type: article
    authors:
      - family-names: Morgan
        given-names: Benjamin J.
    title: "bsym: A basic symmetry module"
    year: 2017
    journal: Journal of Open Source Software
    volume: 2
    issue: "16"
    doi: 10.21105/joss.00370

CodeMeta (codemeta.json)

{
  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": "http://orcid.org/0000-0002-3056-8233",
      "@type": "Person",
      "email": "b.j.morgan@bath.ac.uk",
      "name": "Benjamin Morgan",
      "affiliation": "Department of Chemistry, University of Bath, Bath, BA2 7AY, United Kingdom."
    }
  ],
  "identifier": "",
  "codeRepository": "https://github.com/bjmorgan/bsym",
  "datePublished": "2017-07-22",
  "dateModified": "2017-07-22",
  "dateCreated": "2017-07-22",
  "description": "bsym - A basic symmetry module",
  "keywords": "symmetry, configurations, disorder",
  "license": "MIT",
  "title": "bsym",
  "version": "1.0.b1"
}

GitHub Events

Total

Watch event: 2
Delete event: 2
Push event: 5
Pull request event: 2
Create event: 2

Last Year

Watch event: 2
Delete event: 2
Push event: 5
Pull request event: 2
Create event: 2

Committers

Last synced: 5 months ago

All Time

Total Commits: 377
Total Committers: 2
Avg Commits per committer: 188.5
Development Distribution Score (DDS): 0.032

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Benjamin Morgan	b**2@g**m	365
Pezhman Zarabadi-Poor	p**p@g**m	12

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 3
Total pull requests: 2
Average time to close issues: about 7 hours
Average time to close pull requests: about 4 hours
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 2.0
Average comments per pull request: 0.5
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 13 minutes
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

aronwalsh (3)

Pull Request Authors

bjmorgan (2)
pzarabadip (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 87 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 11
Total maintainers: 1

pypi.org: bsym

A Basic Symmetry Module

Homepage: https://github.com/bjmorgan/bsym
Documentation: https://bsym.readthedocs.io/
License: MIT
Latest release: 1.2.0
published almost 5 years ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 87 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 13.3%

Stargazers count: 15.2%

Average: 16.4%

Dependent repos count: 21.6%

Downloads: 22.0%

Maintainers (1)

bmorgan

Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi

Sphinx >=1.6.3
numpy *
pymatgen *
tqdm *

requirements.txt pypi

numpy *
pymatgen >=v2017.10.16
tqdm *

tests/notebook_tests/requirements.txt pypi

jupyter * test
version_information * test

.github/workflows/build.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
paambaati/codeclimate-action v2.7.5 composite

setup.py pypi

bsym

Science Score: 98.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

Installation

Tests

Documentation

I want to generate a set of symmetry-inequivalent crystal structures

Citing bsym

BibTeX

Owner

JOSS Publication

bsym: A basic symmetry module

Authors

Editor

Tags

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: bsym

Rankings

Maintainers (1)

Dependencies

Citing `bsym`