Periodic Boundary Conditions (PBC)

Tutorial 4 - Build a Face-Centered Cubic Unit Cell for Diamond Crystal Using Space Group Symmetry, PBC/3D

4-2  Show the PBC dialog for the molecule by selecting "PBC" from the "Edit" menu of the main window.

4-3  In the "Symmetry" tab of the PBC dialog, select "Three" from the "Lattice Dimensions" combobox.

4-4  In the "Symmetry" tab of the PBC dialog, check the "Enable Space Group Symmetry" checkbox and then select the "227 (F d -3 m:1)" item from the "Constrain to Space Group" combobox.

4-5  In the "Contents" tab of the PBC dialog, add a carbon atom at fractional coordinates (0, 0, 0) by first selecting "C" from the "Symbol" column and then selecting the "Add" button.

4-6  In the "Cell" tab of the PBC dialog, select "Fix Contents' Fractional Coordinates" from the "Cell Changes" combobox 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 "Cell Changes" option being used.

4-7  In the "Contents" tab of the PBC dialog, select "Rebond All" from the "Bonds" popup menu and then select "Dull" instead of "Low Layer" for the "Replicate Format".

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 "Show All Boundary Atoms" 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 using the corresponding spin boxes in the "Cell Replication" section.  Also, select the "Low Layer" item from the "Replicate Format" combobox.

4-11 In the "Symmetry" tab of the PBC dialog, uncheck the "Enable Space Group Symmetry" checkbox.

4-12  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 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.