Migration Paths

One of the primary features of this program is the ability to rapidly generate and view many, many migration barriers. Migration barriers are managed using the "Migration Paths" panel on the right side:

Migration paths panel

A description of these buttons is as follows:

Tool Description
From File Loads migration paths/energy barriers from a CSV file. Format is described here
Save To File Saves the existing migration paths to a CSV file
From Neighbors Launches the "From Neighbors" dialog (see below)
Clear Paths Deletes all migration paths
Clear Energy Barriers Deletes all energy barriers

Generating Paths

Once opened, the "From Neighbors" dialog allows you to generate migration paths between adjacent atoms:

Dialog for generating paths from neighbors

This dialog includes several options for deciding which atoms to connect with a path:

Option Description
Minimum Distance Minimum distance between atoms for a path to form
Maximum Distance Maximum distance between atoms for a path to form
Remove Obstructed Paths Any path with a third atom within this distance will be considered "obstructed," and consequently excluded
Filter To Selected Excludes paths leading to atoms outside the selection
Filter To Visible Excludes paths leading to invisible atoms
Filter By Element Requires that paths only connect atoms of the given element
Include Boundary Crossings Whether to include paths that cross the periodic boundary

Viewing Migration Paths

Once generated, the migration paths will be visible as white double-arrows in the viewport:

Example of migration paths

Viewing Energy Barriers

Once your energy barriers have been computed, you can load them back into the program to view the results. In the viewer, they are represented as arrows, and are colored according to the energy barrier using the viridis color map.

Example energy scale bar

In this state, the energy scale bar will also be enabled. This allows you to set the energy scale in the event that your data set contains outliers.

Additionally, energy barriers outside the scale's range can optionally be hidden from view. To toggle this, simply use option under Structure > Clip Energy Barriers:

Menu button for clipping energy barriers