The GUI is composed of several panels. The top is the title panel. The bottom is the status bar. Between the top and bottom panels are the left, center and right panels. The center panel (black) is used to display the graphene lattice. The left panel contains controls for specifying the type, dimension, and periodic boundary conditions of the lattice. The buttons in the left panel are self-explaining. They are used to create the lattice, show the neighboring atoms of a selected atom, delete or set coordinates of a selected atom, and save the data files of the graphene lattice. The right panel contains 4 buttons for viewing the lattice. They are, from the top down, "zoom in", "zoom out", "fit" and "pan".

Some functions of the tool are described below:

• In the left panel, select "Zigzag" or "Armchair"
• Type in the cell rows and columns of the lattice to be created. The figure shown in the left panel illustrates the meaning of a "row" and or a "column" of atom cells.
• Select a type of periodic boundary condition. By default, the lattice is non-periodic (radio button "None"). The user can specify lattice periodicity in vertical or horizontal directions, or both. Note that, to satisfy the periodic arrangement of the atoms, sometimes a row or column of atoms need to be added to the lattice. A message will be shown if this happens.
• Click "Create Lattice" button. A graphene lattice will be created and shown in the center panel. Note that the default bond length is set to be 1.39 angstrom.

• Press down the "Show Neighbors" button.
• Select an atom in the lattice by click on the atom. The selected atom will become green, and its nearest and second nearest neighbors will be shown in red.

• Press down the "Delete Atom" button.
• Select an atom in the lattice by click on the atom. The selected atom and the bonds attached to it will be deleted. One can create vacancy defects (initial configuration, not relaxed) by using this function.

• Click the "Set Atom Coordinates" button.
• Select an atom in the lattice by click on the atom. The current coordinates of the selected atom will be shown in a dialog box. New coordinates can be typed in for the selected atom. The coordinates of the lattice will be shifted according to the new position of the selected atom.

• Click the "Save Files" button.
• A directory selection dialog box will show. Select the directory where the files will be saved. Click "OK". Three files will be save to the directory: "atoms.dat", "atom_neighbors.dat" and "bonds.dat". "atoms.dat" stores the atom number, x- and y-coordinates of the atoms in each of its columns. In "atom_neighbors.dat", each row stores the atom number (1st number) of an atom and the atom numbers of its nearest and second nearest neighbors. If the atom number of a neighbor is "-1", it means the particular neighbor atom is absent.