Description
pyscal is a python module for the calculation of local atomic structural environments including Steinhardt’s bond orientational order parameters[1] 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 and easy extensions in python.
Practical Applications
Steinhardt’s order parameters are widely used for the identification of crystal structures [3]. They are also used to distinguish if an atom is in a solid or liquid environment [4]. pyscal is inspired by the BondOrderAnalysis code, but has since incorporated many additional features and modifications. The pyscal module includes the following functionalities:
- calculation of Steinhardt’s order parameters and their averaged version [2].
- links with the Voro++ code, for the calculation of Steinhardt parameters weighted using the face areas of Voronoi polyhedra [3].
- classification of atoms as solid or liquid [4].
- clustering of particles based on a user defined property.
- methods for calculating radial distribution functions, Voronoi volumes of particles, number of vertices and face area of Voronoi polyhedra, and coordination numbers.
Background information
See the application documentation for full details. A paper about pyscal is also available in Ref. [5].
The utilisation of Dask within the project came about as a result of the E-CAM High Throughput Computing ESDW held in Turin in 2018 and 2019.
The software module was developed by Sarath Menon, Grisell Díaz Leines and Jutta Rogal, and is under a GNU General Public License v3.0.
