More options in graph-building

[rkurchin]

Currently we have the cgcnn.py option plus the Voronoi option. It would make sense to add an option to cut off by distance (e.g. nearest, second-nearest, etc. neighbors). Things to figure out here:

• what's a reasonable "default" tolerance for counting neighbors as being in a set (e.g. all being nearest or second-nearest)? Once we set this we can ensure all their edge weights are the same which will be useful e.g. in DEQ stuff
• would it make sense to implement a cutoff about distances to an atom's periodic images of itself? e.g. a "stop-adding-edges" condition once an atom has hit its own image? In a lot of cases (i.e. really large unit cells) you probably wouldn't actually want to go anywhere near this far, but for smaller ones I doubt you'd often want to go much past this...