Crystals and Slabs¶

Periodicity¶

Many GUI modules support periodicity. Some menu commands (like the Edit → Crystal command in ADFinput) will only by available when you have a periodic system.

To set up periodicity you first need to switch to a method that supports periodicity. For example BAND, DFTB, Mopac, or UFF. Some of these, like UFF, are currently available without extra license.

On the Main panel of a method that supports periodicity, you will find a ‘Periodicity’ pull-down menu. Use it to use periodicity in 1 (Chain), 2 (Slab) or 3 (Bulk) dimensions. Once periodicity is enabled, menus like the Crystal menu will also be enabled.

The tool bar below the molecule editor also changes when you have a periodic system. The structures tool gets replaced by the crystal tool (represented by a snowflake), followed by the Slice tool. At the right side of the tool bar you find buttons to orient the camera, toggle perspective and toggle the display of periodic images.

To set up the lattice vectors, press the ”...’ details button next to periodicity, or go to the Lattice panel (in the Model section).

Building crystals¶

After setting the periodicity and lattice vectors, you can build your own crystal by adding atoms at the proper position. For many crystals this is a lot of work.

You can also build crystals using the** Edit → Crystal** command. The first list of options (Cubic, Hexagonal and so on) have sub-menus for some common crystals. If your crystal is not in there, you can use the “From Space Group...” command in the same menu. This brings up a dialog that will help you build any crystal.

The crystal tools are not only available from the Edit menu, you can also press the ‘Snowflake’ button in the molecule editor tool bar (next to the element button, if periodicity is enabled). It has the same options as the Edit → Crystal menu.

Build slabs¶

Building a slab is done most conveniently using the Slice tool: first build a crystal, next use the “Generate Slab...” command from the Crystal menu to make a slab. Next you will need to enter the Miller indices of the plane that will define your slab.

The Slice tool is available from the Edit → Crystal menu, or in the periodic toolbar (next to the snowflake).

Crystal menu¶

Map Atoms To Unit Cell¶

Edit → Crystal → Map Atoms To Unit Cell

Using the translational symmetry, the atoms are mapped to the unit cell. The unit cell used is normally centered around the origin.

Map Atoms To Cell¶

Edit → Crystal → Map Atoms To Cell

Using the translational symmetry, the atoms are mapped to the cell. The cell used has the origin as one of its corners, and has the lattice vectors (starting at the origin) as edges.

Set Cell Center¶

Edit → Crystal → Set Cell Center

The selected atoms define some point. This point will be mapped to the center of the cell. The cell used has the origin as one of its corners, and has the lattice vectors (starting at the origin) as edges. All atoms will be adjusted according to this translation.

Thus afterwards you may still have atoms outside the unit cell.

To set the Unit Cell Center, just use the Set Origin command as the unit cell is centered around the origin.

Remove Molecules Outside Cell¶

Edit → Crystal → Remove Molecules Outside Cell

Molecules that have one or more atoms outside the cell (0..1 in natural coordinates in all dimensions) will be deleted.