As part of the Nanointerface project, where we developed the initial scripts for cross-linking, there was always a question on how “good” the networks were. Whilst some of this was answered by trying to predict properties and match them to experimental data, there was also a more fundamental question around how “connected” were the networks.

This script attempts to answer that question by identifying groups of connected atoms and whether they are connected in a fragment (an isolated group of atoms), or a network (a group of atoms that are linked across periodic boundary conditions). The connected sets of atoms are all set to a unique element type and hence you can view each set of atoms. For each structure, the connectivity is broken down into whether an atom is connected in a network or fragment and how many atoms are connected. You can see an example of this in the image below.

Before examining the connectivity, all hydrogen atoms are stripped from the system to simplify the visualization. Thus the number of atoms reflects only the heavy atoms in the system.

Note that as all atoms are converted to a range of different elements, this is purely for visualization only and you shouldn’t attempt to run any calculations on this structure!

Please also note that this script is only configured to run in the Script Library. If you want to run from within the project, you will need to edit the script.

Cheers

Stephen