Periodic Boundary Conditions (PBC)
2-1 Start a new file by selecting the option from the menu in the main window.
2-2 Make the benzene fragment the “current fragment” by double-clicking on the tool button and then clicking on the “benzene” button in the Ring Fragment palette.
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 toolbar button.
2-5 Turn on atom labels for the View window by selecting from the menu.
2-6 Show the Point Group dialog for the molecule by selecting from the menu of the main window. In the Point Group dialog, check the box and click on the button to symmetrize benzene to D6h. Then, select from the drop-down list.
2-7 Change the CC bond lengths to match the experimental values for graphite. Click on the 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 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 box, and then click the button.
2-8 Show the PBC dialog for the molecule by selecting from the menu of the main window.
2-9 In the Symmetry tab of the PBC dialog, select from the drop-down list.
2-10 In the Cell tab of the PBC dialog, push down the button, and make sure is selected to enable placement of the cell origin ( ) 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 instead of 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 instead of 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 from the drop-down list.
2-14 Delete the hydrogen atom by clicking on the 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 button.
2-16 At this point, we have defined a primitive unit cell for a PBC/2D model of graphite.
2-17 In the View tab of the PBC dialog, show three cells along both the “a” and “b” axes by selecting 3 from the corresponding spin boxes in the Cell Replication section. By default, the contents of replicate unit cells are shown in format.
2-18 In the View tab of the PBC dialog, select from the drop-down list to show the replicate contents in the same format as the reference unit cell contents.
2-19 In the Contents tab of the PBC dialog, select the item from popup menu to update the bonding between all atoms.
2-20 In the View tab of the PBC dialog, click on the 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” that 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.