| pyscal | |
| 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. |
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- Getting started : Explore basic features of pyscal and how to get started with pyscal.
- Finding neighbors : Various methods of finding the local neighborhood of an atom in pyscal, including cutoff and Voronoi methods.
- Bond orientational order parameters : Calculation of bond orientational parameters, averaged and Voronoi weighted versions, and distinction of structures.
- Disorder parameters : Disorder parameters based on Steinhardts parameters.
- Distinguishing solid and liquid atoms : Use Steinhardts parameters to distinguish between solid and liquid, and how to cluster solid atoms based on a property.
- Voronoi tessellation : Identifying Voronoi polyhedra and calculation of associated volume.
- Angular parameters : Angular parameters for identification of tetrahedral ordering.
- $\chi$ parameters : Angular parameters for structural identification.
- Centrosymmetry parameter : Parameters for identification of defects in crystals.
- Short range order : Calculating ordering in binary systems.
- Entropy parameter : Use a measure of entropy to distinguish solid and liquid.
- Calculation of energy : Use pyscal in combination with LAMMPS to calculate energy of atoms.
- Structural identification using entropy and enthalpy : Combine entropy and energy methods to identify crystal structures.
- Working with lammps trajectories : Reading in a lammps trajectory, calculating Steinhardt's parameter for slices and various cluster properties.