In the simplest implementations we use different colors for sp1, sp2 or sp3 hybridized carbon atoms, upper right. Different types have different physical properties. (Image of nanodiamond formation inside amorphous carbon under pressure - A. Sorkin).
In more complex implementations we may chose diferent colors for
4 fold coordinated atoms that are neighbours of 3 fold coordinated ones,
or even different colored bonds connecting atoms of different coordinations.
The image on the lower right is a split interstitial defect. [