No warning given by from_ase when atoms are isolated
Subject of the issue
A warning should be given to the user when isolated atoms emerge when converting an atomistic model into a graph using a compact adjacency rule.
Current situation
Due to the usage of compact adjacency rules, an atom that is further than the cutoff distance from all other atoms would have no edges and a zero degree. A warning should be given in this case, since this is usually caused by an incorrect length scale/cutoff setting.
Expected behavior
At the end of the from_ase
method, we can check for existence of zero-degree atoms and raise a warning of proper type.
Edited by Yu-Hang "Maxin" Tang