Methods and examples

• Methods
  • Methods to calculate neighbors of a particle
    • Fixed cutoff method
    • Adaptive cutoff methods
      • Solid angle based nearest neighbor algorithm (SANN)
      • Adaptive cutoff method
    • Voronoi tessellation
    • References
  • Steinhardt’s parameters
    • Averaged Steinhardt’s parameters
    • Voronoi weighted Steinhardt’s parameters
    • References
  • Classification of atoms as solid or liquid
    • References
  • Disorder parameter
    • References
  • Angular parameters
    • Angular criteria for identification of diamond structure
    • \(\chi\) parameters for structural identification
    • References
  • Voronoi tessellation to identify local structures
    • References
  • Centrosymmetry parameter
    • References
  • Entropy - Enthalpy parameters
    • Entropy fingerprint
    • References
• Examples
  • Getting started with pyscal
    • The System class
    • The Atom class
    • Combining System and Atom
    • Reading in an input file
  • Calculating coordination numbers
    • Read in a file
    • Calculating neighbors
      • Cutoff method
    • Adaptive cutoff methods
    • Voronoi method
    • Finally..
  • Calculating bond orientational order parameters
    • Perfect structures
      • Finding the cutoff distance
      • Steinhardt’s parameters - cutoff neighbor method
    • Structures with thermal vibrations
      • cutoff method
  • Analyzing a lammps trajectory
    • Adding a clustering condition
    • Using ASE
  • Disorder variable
  • Distinction of solid liquid atoms and clustering
    • Clustering algorithm
      • Clustering based on a custom property
  • Voronoi parameters
    • Voronoi volume
  • Angular parameter
    • Create structures
  • \(\chi\) parameters
  • Centrosymmetry parameter
  • Cowley short range order parameter
  • Entropy parameters
  • Calculating energy
    • Interatomic potentials
  • Entropy and enthalpy parameters
  • Visualizing System objects
  • pyscal Trajectory