Diamond Version 5 User Manual: Polyhedra

Polyhedra With No Central Atom

In this article:
- Getting the dummy atom
- Cubes and other 3D objects without central atom inside

Previous article: Creating Coordination Polyhedra
Next article: Polyhedron construction from atoms and bonds

Getting the dummy atom

In Diamond, you can define no coordination polyhedron without a central atom. If there is no atom in the structural parameters that can be used as central atom, you can define a dummy atom for the center. The dummy atom will be added to the atoms in the parameter list but has no chemical meaning. The dummy atom will also be added to the list of atom groups, and thus also to the list of bond groups, where you can change the basic behaviour for all atoms derived from that dummy atom (atoms' style, bonding sphere, etc.)

The easiest way to create a dummy atom is to select all atoms that will build the polyhedron, that means the atoms in the coordination sphere, and then create an atom in the center of those selected atoms. The article "Inserting (dummy) atoms and bonds" describes in principal how to create a dummy atom in the center of selected atoms. Since the dummy atom is automatically created at the new position and is appended to the list of atom groups, you can create a polyhedron using one of the methods described in "Creating Coordination Polyhedra".

The picture shows a fulleren molecule (C60) as polyhedron with a dummy atom in its center:

Cubes and other 3D objects without central atom inside

In the following sample we use a simple cubic structure with only one atom on (0,0,0) in Pm-3m. We take the eight A atoms on the corners of the unit cell for a polyhedron building. This polyhedron is a cube with a dummy atom as center at (1/2,1/2,1/2).

Therefore we load a ready-to-use structure picture of α-Po from the structure type database. (For more details about this database, read the article "Database with inorganic structure types".)

Use the File -> New command, which opens the New Document dialog where you choose the option Load a structure from the structure type database. After OK this creates an empty document window and opens the Insert Structure From Type dialog. Click on the Browse button, which opens the Structure Type dialog. In the list of structure types choose "alpha-Po, primitive cubic (sc)" and press OK, which brings you back to the Insert Structure From Type dialog. In this dialog, ensure that the Load structure picture(s) radio button is checked. So you have access to the pictures delivered with the selected structure type (α-Po).

Thanks to the Load structure pictures option, you will see two thumbnails of structure pictures in your document window: "Unit cell" and "Super cell with coordination polyhedron".

Click on "Unit cell" to open this structure picture, where the Po atom in (0,0,0) along with the seven symmetry-equivalent Po atoms in the residual seven corners of the unit cell have been created. Select these eight Po atoms and then run the command Build -> Polyhedra -> Construct Polyhedron. Since only atoms but no bonds are selected, only the first two options are available in the Mode of operation group. A dummy atom is proposed as central atom. Using OK creates a polyhedron with six square faces. (More details about the Construct Polyhedron dialog in the next article.)

The default polyhedron design shows opaque (not translucent) white faces. For the screenshot below we have changed the transparency factor to 0.5. For details about polyhedron design, see the article "Polyhedron design and hatching".

So far with a simple example showing a cubic polyhedron. More complicated polyhedra can be constructed from appropriate structures as well.

Previous article: Creating Coordination Polyhedra
Next article: Polyhedron construction from atoms and bonds

Reference:
COD-1509138: William H. Beamer, Charles R. Maxwell; "Physical Properties of Polonium. II. X-Ray Studies and Crystal Structure"; Journal of Chemical Physics, 17, 1293-1298 (1949).