moltemplate

That is correct. The graphene.lt file only contains the definition of
the 2-atom unit cell (named "Graphene/2AtomCellAlignX"). It does not
contain any commands to actually create a sheet of graphene. The
graphene's carbon atom (types) are defined, but not created.

To make some graphene, you would make copies of this unit cell using
the "new" command. (See below.)

    LT files can refer to each other. Typically, you would run
moltemplate on a file named "system.lt" (although it does not have to
be named "system.lt"). In the nanotube+water example, it is somewhat
complicated: The "system.lt" file refers to "graphene_walls.lt",
which refers to "graphene.lt". If you just want to create a simple
sheet of graphene, then you can bypass all that and create a new file
containing these lines:

import "graphene.lt"
sheet = new Graphene/2AtomCellAlignX
               [13].move(2.4595121467478, 0, 0)
               [14].move(1.2297560733739, 2.13, 0)
... and run moltemplate on that file.

(These numbers are the unit cell size. They come from the graphene.lt file.)