pyscal - python Structural Environment Calculator¶
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. pyscal is inspired by BondOrderAnalysis code, but has since incorporated many additions and modifications. pyscal module includes the following functionality-
fast and efficient calculations using C++ and expansion using python.
links with Voro++ code, for calculation of Steinhardt parameters weighted using face area of Voronoi polyhedra.
classification of atoms as solid or liquid.
clustering of particles based on a user defined property.
methods for calculating radial distribution function, voronoi volume of particles, number of vertices and face area of voronoi polyhedra and coordination number.
Centrosymmetry parameter for identification of defects.
Adaptive common neighbor analysis for identification of crystal structures.