Periodic Boundary Conditions (PBC)

Tutorial 2 - Build a Graphite Sheet From Benzene, PBC/2D

2-1 Create a new molecule and corresponding view window by clicking on the "New" toolbar button.

2-2 Make the benzene fragment the "Current Fragment" by double-clicking on the "Ring Fragment" tool button and then clicking on the "benzene" button in the "Select Ring Fragment" dialog.

2-3 Click anywhere in the empty view window to create a benzene molecule.

2-4 Center the molecule in the view window by clicking on the "Center" toolbar button.

2-5 Turn on atom labels for the view window by checking "Labels" from the "View" menu of the main window.

2-6 Show the "Point Group" dialog for the molecule by selecting "Point Group" from the "Edit" menu of the main window. In the "Point Group" dialog, check the "Enable Point Group Symmetry" box and click on the "Symmetrize" button to symmetrize benzene to D6h. Then, select the "D6h" item from the "Constraint to Subgroup" combobox.

2-7 Change the CC bond lengths to match the experimental values for graphite. Click on the "Modify Bond" toolbar button and then click on atoms 1 and 2 in the the view window. In the corresponding "Semichem Smartslide" dialog, change the bond length value from 1.39499 to 1.42 in the input field and then click on the OK button. Note that all of the CC bond lengths have increased to 1.42 to preserve the D6h symmetry. In the Point Group dialog, uncheck the "Enable Point Group Symmetry" box and then click the "OK" button.

2-8 Show the PBC dialog for the molecule by selecting "PBC" from the "Edit" menu of the main window.

2-9 In the "Symmetry" tab of the PBC dialog, select "Two" from the "Lattice Dimensions" combobox.

2-10 In the "Cell" tab of the PBC dialog, push down the "Place" button and make sure the "Vertex" option is selected to enable placement of the cell origin ("O (0,0)") vertex at any atom selected in the view window using the mouse. In the view window, click on atom 6.

2-11 In the "Cell" tab of the PBC dialog, select "a (1,0)" instead of "O (0,0)" to enable placement of the "a" cell vertex at any atom selected in the view window using the mouse. In the view window, click on atom 2.

2-12 In the "Cell" tab of the PBC dialog, select "b (0,1)" instead of "a (1,0)" to enable placement of the "b" cell vertex at any atom selected in the view window using the mouse. In the view window, click on atom 4.

2-13 In the "Cell" tab of the PBC dialog, select the "Delete All Atoms Outside Cell" item from the "Trim Contents" popup menu.

2-14 Delete the hydrogen atom by clicking on the "Delete Atom" toolbar button and then clicking on the hydrogen atom in the view window.

2-15 In the "Cell" tab of the PBC dialog, click on the "Center Contents" button.

2-16 At this point we have defined a primitive unit cell for a PBC/2D model of graphite.

2-15 In the "View" tab of the PBC dialog, show three cells along both the "a" and "b" axes using the corresponding spin boxes in the "Cell Replication" section. By default, the contents of replicate unit cells are shown in "Low Layer" format.

2-16 In the "View" tab of the PBC dialog, select the "Normal" item from the "Replicate Contents Format" combobox to show the replicate contents in the same format as the reference unit cell contents.

2-17 In the "Contents" tab of the PBC dialog, select the "Rebond All" item from "Bonds" popup menu to update the bonding between all atoms.

2-18 In the "View" tab of the PBC dialog, click on the "Combine" button in the "Cell Replication" section. This will cause the reference unit cell and the replicate unit cells shown on screen to be combined into a larger "supercell" which is nine times the primitive unit cell. Note the atom number changes. Note also that the number of cells being viewed is automatically reduced to one to avoid potential confusion.