pyscal
pyscal: A python module for structural analysis of atomic environments - Published in JOSS (2019)
Science Score: 59.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: scholar.google, springer.com, aps.org, joss.theoj.org -
✓Committers with academic emails
1 of 9 committers (11.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Scientific Fields
Repository
Python library written in C++ for calculation of local atomic structural environment
Basic Info
- Host: GitHub
- Owner: pyscal
- License: bsd-3-clause
- Language: C++
- Default Branch: master
- Homepage: https://pyscal.org
- Size: 13.1 MB
Statistics
- Stars: 64
- Watchers: 3
- Forks: 16
- Open Issues: 15
- Releases: 46
Topics
Metadata Files
README.md
pyscal - python Structural Environment Calculator
[!TIP] Check out pyscal3, a completely new pyscal which is faster and can handle a large number of atoms, with a much more user-friendly interface. This repository will continue receiving bug fixes, including any new raised issue. It will also be tested for new python versions. However, new features will only be added to
pyscal3.
Complete documentation with examples available here.
pyscal is a python module for the calculation of local atomic structural environments including Steinhardt's bond orientational order parameters during post-processing of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using pybind11 which allows for fast calculations with possibilities for easy expansion in python.
Steinhardt's order parameters are widely used for identification of crystal structures. They are also used to identify if an atom is solid or liquid.
Installation
pyscal can be installed directly using conda by the following statement-
conda install -c conda-forge pyscal
From repository
pyscal can be built from the repository by-
git clone https://github.com/pyscal/pyscal.git
cd pyscal
python setup.py install --user
Citing the work
If you use pyscal in your work, the citation of the following article will be greatly appreciated:
Sarath Menon, Grisell Díaz Leines and Jutta Rogal (2019). pyscal: A python module for structural analysis of atomic environments. Journal of Open Source Software, 4(43), 1824, https://doi.org/10.21105/joss.01824
Works using pyscal
For a complete list of publications which used pyscal, see here.
Owner
- Name: pyscal
- Login: pyscal
- Kind: organization
- Repositories: 2
- Profile: https://github.com/pyscal
GitHub Events
Total
- Watch event: 4
Last Year
- Watch event: 4
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| srmnitc | s****n@m****g | 895 |
| srmnitc | s****n@r****e | 62 |
| Jan Janssen | j****n | 5 |
| rogalj | 4****j | 4 |
| srmnitc | s****n@m****g | 2 |
| Saswat | s****n@g****m | 2 |
| Daniel S. Katz | d****z@i****g | 2 |
| stekajack | a****k@g****m | 1 |
| Pedro Antonio Santos Flórez | p****f@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 44
- Total pull requests: 63
- Average time to close issues: 2 months
- Average time to close pull requests: about 19 hours
- Total issue authors: 10
- Total pull request authors: 5
- Average comments per issue: 1.82
- Average comments per pull request: 0.57
- Merged pull requests: 57
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- srmnitc (25)
- jan-janssen (11)
- tanooj-s (1)
- lydiash (1)
- NoelJakse (1)
- TonyStarkMan (1)
- carle13 (1)
- dgehringer (1)
- narendra8995 (1)
- maurosgroi (1)
Pull Request Authors
- srmnitc (56)
- jan-janssen (4)
- dependabot[bot] (2)
- stekajack (1)
- saswatnayak1998 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- ase
- h5py
- ipywidgets
- matplotlib
- numpy
- plotly
- pybind11
- pytest
- pytest-cov
- ase
- h5py
- ipywidgets
- jupyterlab
- lammps
- matplotlib
- nodejs
- notebook
- numpy
- plotly
- python
- ase *
- furo *
- h5py *
- ipywidgets ==7.5
- m2r2 *
- nbsphinx *
- numpy *
- plotly ==4.11.0
- pybind11 *
- sphinx_rtd_theme *
- matplotlib *
- codecov *
- h5py *
- ipywidgets =7.5
- pip *
- plotly =4.11.0
- pytest *
- pytest-benchmark *
- pytest-cov *
- ase *
- ipywidgets *
- numpy *
- plotly *
- actions/cache v1 composite
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite