Examples

Important

All examples require that the file common.py be placed in the working directory.

The original Jupyter notebooks, common.py, and the trajectory files can be found in the docs/examples directory in the source tree.

• Getting started with lionanalysis
  • Introduction
  • Example trajectory: RuH.xyz
  • Simple lionanalysis run to print number of Ru and H atoms as a function of time
  • Load and plot data with pandas, matplotlib, seaborn
  • Defining groups and finding out atomic environments
  • Visualize atoms in different groups
• Number density of particles for an axis
• Radial and angular distribution functions, hydrogen bond definition
  • Radial distribution functions
  • Angular distribution function
  • Hydrogen bond statistics and defining groups based on angle criteria
  • Plot coordination number vs. frame number
• Lifetime time correlation functions and hydroxide ions
  • Hydroxide ion definition, show hydroxides in different color
  • Lifetime from continuous and intermittent time correlation functions
  • Lifetime from SSP: Stable States Picture
• Mean squared displacement and proton transfer free energy landscape
  • Sodium diffusion coefficient
  • Hydroxide ion diffusion coefficient
  • Na-O radial distribution function
  • Proton transfer free energy landscape
  • Advanced PTFEL for local environments
• Block averages (standard deviation, standard error)