pyscal - python Structural Environment Calculator

pyscal is a python module for calculation of local structural environment. Read the complete documentation, check out the github repo or even try out some examples.

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 [2]. They are also used to identify if an atom is solid or liquid [3]. pyscal is inspired by BondOrderAnalysis code, but has since incorporated many additions and modifications. pyscal module includes the following functionality-

Highlights

  • fast and efficient calculations using C++ and expansion using python.
  • calculation of Steinhardt’s order parameters and their averaged version [4].
  • links with Voro++ code, for calculation of Steinhardt parameters weighted using face area 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 function, voronoi volume of particles, number of vertices and face area of voronoi polyhedra and coordination number.
  • calculation of angular parameters to identify diamond structure [5].

[1] Steinhardt, PJ, Nelson, DR, Ronchetti, M. Phys Rev B 28, 1983
[2] Lechner, W, Dellago, C, J Chem Phys, 2013
[3] Mickel, W, Kapfer, SC, Schroder-Turk, GE, Mecke, K, J Chem Phys 138, 2013
[4] Auer, S, Frenkel, D. Adv Polym Sci 173, 2005
[5] Uttormark, M. J., Thompson, M. O., Clancy, P. (1993). Physical Review B, 47

Doctoral student

Doctoral student at Ruhr Universit├Ąt Bochum and an aspiring scientific programmer with an interest in Python and C++.