Periodic Boundary Conditions (PBC)
6-1 Start a new file by selecting the option from the menu in the main window.
6-2 Show the PBC dialog for the molecule by selecting from the menu of the main window.
6-3 In the Symmetry tab of the PBC dialog, select from the drop-down list.
6-4 In the Symmetry tab of the PBC dialog, check the checkbox, and then select from the drop-down list.
6-5 In the Contents tab of the PBC dialog, add a carbon atom at fractional coordinates (0, 0, 0) by first selecting from the column (be sure to tab out of the field) and then selecting the button.
6-6 In the Cell tab of the PBC dialog, select from the drop-down list, and then change the “a” cell length from 4 to the experimental value of 3.56 in the corresponding input field. Note that all of the cell lengths change to 3.56, and also the space group symmetry is preserved because of the option being used.
6-7 In the Contents tab of the PBC dialog, select from the popup menu. Then, go to the the View tab and select instead of from the drop-down list.
6-8 At this point, we have defined a Face-Centered Cubic unit cell for a PBC/3D model of a diamond crystal.
6-9 Then, do the following steps: (a) uncheck the box in the Symmetry tab; (b) select from the drop-down list of the Cell tab.
6-10 In the Cell tab of the PBC dialog, push down the button, and select instead of to enable placement of the head of the “a” lattice vector at any atom selected in the View window using the mouse. In the View window, click on atom 7.
6-11 In the Cell tab of the PBC dialog, push down the button, and select instead of to enable placement of the head of the “b” lattice vector at any atom selected in the View window using the mouse. In the View window, click on atom 3.
6-12 In the Cell tab of the PBC dialog, push down the button, and select instead of to enable placement of the head of the “c” lattice vector at any atom selected in the View window using the mouse. In the View window, click on atom 5.
6-13 In the Cell tab of the PBC dialog, select from the popup menu.
6-14 In the Contents tab of the PBC dialog, select from the popup menu.
6-15 In the View tab of the PBC dialog, select from the drop-down list.
6-16 We now have a primitive unit cell for diamond crystal that gives the same crystal structure as that from the face-centered cubic unit cell we started with.
6-17 In the View tab of the PBC dialog, check the checkbox.