Getting started

This page shows you how to get started using Gemdat in your own Python scripts or in a Jupyter notebook.

Loading simulation data

The first step is to load your simulation data. These are represented in gemdat by a trajectory. A trajectory is essentially a list of coordinates for all species over time. To load a trajectory:

from gemdat import Trajectory

trajectory = Trajectory.from_vasprun('./path/to/vasprun.xml')

If not all timesteps are relevant, the trajectory can be sliced to only include relevant timesteps:

trajectory = trajectory[100:] # Exclude the first 100 timesteps

For now, select the trajectory for the diffusing species, Lithium, by its symbol:

diff_trajectory = trajectory.filter('Li')

Plotting trajectory properties

You can do this by importing the plots submodule. In the example below, we are plotting the vibration of the diffusing element by passing its trajectory.

from gemdat import plots

plots.plot_vibrational_amplitudes(diff_trajectory)

See the plots page for more information about which plots for trajectories are available.

Analyzing jumps and transitions

To find out how Lithium jumps from site to site, we must know what the sites are. Gemdat contains a small internal database with available structures.

Alternatively, you can load the sites from 1. a cif file, 2. a density or volume or 3. construct your own Structure.

from gemdat import load_known_material

structure = load_known_material('argyrodite', supercell=(2, 1, 1))

The gemdat.Transitions and gemdat.Jumps classes are responsible for calculating the transitions between sites and jumps properties. We pass the structure with the jump sites to the trajectory containing both the host and diffusing species, and specify what the diffusing element is.

from gemdat import Jumps

transitions = trajectory.transitions_between_sites(
    sites=sites,
    floating_specie='Li',
)

jumps = Jumps(transitions=transitions)

See the documentation for gemdat.Transitions and gemdat.Jumps to find out which properties are available.

Plotting jumps and transition properties

Gemdat contains several functions for plotting jumps and transitions. These take the gemdat.Jumps object we just constructed as input.

For example, to visualize all jumps in 3d:

plots.plot_jumps_3d(sites)

Radial distribution functions

This function calculates the radial distribution function (RDF) from the floating_specie,

from gemdat.rdf import radial_distribution

rdf_data = radial_distribution(transitions=transitions, floating_specie='Li')

This returns a dictionary with all possible transitions between the jump sites. You can use the plotting module to visualize the RDFs:

for rdfs in rdf_data.values():
   plots.radial_distribution(rdfs)