Distinction of solid liquid atoms and clustering#

In this example, we will take one snapshot from a molecular dynamics simulation which has a solid cluster in liquid. The task is to identify solid atoms and cluster them. More details about the method can be found here.

The first step is, of course, importing all the necessary module.

from pyscal3 import System
import numpy as np

Now we will set up a System with this input file, and calculate neighbors. Here we will use a cutoff method to find neighbors. More details about finding neighbors can be found here.

sys = System('cluster.dump')

Lets start by visualising the structure