Periodic Boundary Conditions (PBC)
4-1 Start a new file by selecting the option from the menu in the main window.
4-2 Show the PBC dialog for the molecule by selecting from the menu of the main window.
4-3 In the Symmetry tab of the PBC dialog, select from the drop-down list.
4-4 In the Symmetry tab of the PBC dialog, check the checkbox, and then select from the drop-down list.
4-5 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.
4-6 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.
4-7 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.
4-8 At this point, we have defined a Face-Centered Cubic unit cell for a PBC/3D model of a diamond crystal.
4-9 In the View tab of the PBC dialog, check the checkbox to show all atoms in or on the boundary of the cell.
4-10 In the View tab of the PBC dialog, show two cells along each of the “a”, “b”, and “c” axes by selecting from the corresponding spin boxes in the Cell Replication section. Also, select the item from the drop-down list.
4-11 In the Symmetry tab of the PBC dialog, uncheck the checkbox.
4-12 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 8 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.