pyscal - python Structural Environment Calculator

Warning

📢 This repository is no longer maintained

This repository contains pyscal v2. It is no longer actively developed and will not receive bug fixes or new features.

The current version of pyscal is v4, developed at pyscal/pyscal3.

• Install: pip install pyscal3 or conda install -c conda-forge pyscal3
• Then: import pyscal or import pyscal3 (both work)
• Documentation: https://pyscal.org

New users should start with v4. This repository is kept online so that existing references and citations continue to resolve.

---

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.