Boundary3D/Aline is not maintained anymore, due to (my) difficultites in updating it consistently with the latest versions of Linux and especially the graphical software needed for the visualization through the graphical user interface (GUI).
It could realize many interesting interactive numerical experiments, such as the construction of crystal samples, possibly with crystal defects of various types, and simulate their time evolution.
Thanks to the possibility of visualizing in different colors, it could reveal many features otherwise hidden. For example, in this video the GUI makes a "scanning" in the (average potential) energy, finding that the atoms composing a Lennard-Jones cube can be divided into 4 groups.
You can see clearly these groups, visualized once at time, by using a narrow moving mean potential energy window:
atoms in the bulk (in blue) - note that the GUI resolves actually the "actual bulk" from atoms near the surfaces and near the edges with different average potential energies
atoms on the surfaces (in green)
atoms along the edges (in yellow)
atoms at the corners (in red)