numpy ase matscipy networkx pandas matplotlib, seaborn, bokeh
at_cycles.py:
Script for visualising 2D networks from atomic environments of amorphous silica.
- Read in an Atoms configuration of a SiO2 network, already without the bridging oxygens between Si atoms (node=Si atom, edge=bridging O)
- Create a graph from it
- Identify all cycles in the network up to a given size
- Purge all cycles that are not minimal i.e., cycles that are composed of two or more smaller cycles.
- Identify neighbouring cycles
- Generate a dual network in which each node is a Si ring (or cycle), and each edge is a shared bridging oxygen.
- Print it with pretty colours ...
- Make basic ring statistics analysis
siosi_angles.py:
Script to analyse bond angle of in-plane Si-O-Si bridges in 2D silica