Plots
Gemdat contains several built-in plots for visualizing trajectories, jumps, transitions, and radial distribution functions.
These are collected in the plots module. The intended usage is that you import gemdat.plots like this:
from gemdat import plots
plots.displacement_per_element(trajectory)
plots.jumps_vs_distance(trajectory, sites)
plots.radial_distribution(rdfs)
All plotting functions take a gemdat.Trajectory, gemdat.Jumps, gemdat.Transitions, gemdat.rdf.RDFData or a combination as input. In addition, for some plots you have a few parameters to tune the output.
All available plots are documented in the gemdat.plots API reference. Some highlights are listed below.
Trajectory and displacements plots
- gemdat.plots.displacement_per_atom
- gemdat.plots.displacement_per_element
- gemdat.plots.displacement_histogram
Simulation metrics plots
Jumps and transition plots
- gemdat.plots.jumps_vs_distance
- gemdat.plots.jumps_vs_time
- gemdat.plots.collective_jumps
- gemdat.plots.jumps_3d
- gemdat.plots.jumps_3d_animation