https://github.com/pyscal/pyscal
Python library written in C++ for calculation of local atomic structural environment
https://github.com/pyscal/pyscal
bond-order-parameters lammps molecular-dynamics nucleation order-parameters solid-state-physics steinhardt steinhardt-bond-order-parameters
Last synced: 4 months ago
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Python library written in C++ for calculation of local atomic structural environment
- Host: GitHub
- URL: https://github.com/pyscal/pyscal
- Owner: pyscal
- License: bsd-3-clause
- Created: 2018-08-01T20:52:00.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-09-04T11:56:26.000Z (over 1 year ago)
- Last Synced: 2025-12-07T00:28:40.295Z (4 months ago)
- Topics: bond-order-parameters, lammps, molecular-dynamics, nucleation, order-parameters, solid-state-physics, steinhardt, steinhardt-bond-order-parameters
- Language: C++
- Homepage: https://pyscal.org
- Size: 13.1 MB
- Stars: 69
- Watchers: 3
- Forks: 16
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# pyscal - python Structural Environment Calculator
> [!TIP]
> Check out [pyscal3](https://github.com/pyscal/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](https://pyscal.org/).
**pyscal** is a python module for the calculation of local atomic structural environments including [Steinhardt's bond orientational order parameters](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.28.784) during post-processing of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using [pybind11](https://pybind11.readthedocs.io/en/stable/intro.html) which allows for fast calculations with possibilities for easy expansion in python.
Steinhardt's order parameters are widely used for [identification of crystal structures](https://aip.scitation.org/doi/full/10.1063/1.4774084). They are also used to identify if an atom is [solid or liquid](https://link.springer.com/chapter/10.1007/b99429).
## 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](https://joss.theoj.org/papers/10.21105/joss.01824) 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](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=315020929885190486&as_sdt=5).