Diamond Version 5 User Manual: Polyhedra

Polyhedra Overview

Previous article: Plane and line objects
Next article: Creating Coordination Polyhedra

Coordination polyhedra serve for the characterization of an atom's neighbourhood. They are built by connecting the centers of coordinated atoms by lines. More complex structure units can be described by a framework of connected polyhedra. Two polyhedra can be connected by a common corner, a common edge or a common plane.

Diamond supports the creation and display of convex coordination polyhedra and treats them as individual objects within the ball-and-stick model (or other models) rather than as an independent model.

In this part of the manual, you will find articles

- about features and limitations,

- how to create coordination polyhedra,

- how to select the atom types for central and ligand atoms,

- about the difference between generic and fixed spheres,

- using atomic environments,

- taking the neighbouring atoms as is,

- how to define polyhedra with polygons that are not triangular,

- how to define a polyhedron without central atom,

- about designs for coordination polyhedra,

- how to use hatching on the polyhedron faces,

- how to display polyhedra with front faces open,

- about global settings for all polyhedra,

- how to select existing polyhedra,

- how to change the designs of existing polyhedra,

- how to delete polyhedra.

Besides the coordination polyhedra Diamond also supports Voronoi polyhedra.

Features and Limitations

Diamond can construct polyhedra with up to 128 ligand atoms. Each polygon (polyhedron face) can have up to eight corners (and must have at least three corners, of course), but it must be convex. There is in principle no limit for the maximum distance between central point and ligand atom.

Polyhedron faces can be partially opened as well as being transparent, with or without edges and with or without hatching.

Example: Polyhedron framework of Sodalite with rectangular and hexagonal polygons and with partially open faces. The Diamond Tutorial will show you how to build up such a framework.

Reference:

Name
Sodium tecto-alumoberyllotetrasilicate chloride (8/2/2)
Formula
Na8 (Al Be Si4 O12)2 Cl2
Author(s)
Hassan I, Grundy H D
Title
The crystal structure and thermal expansion of tugtupite, Na8(Al2Be2Si8O24)Cl2
Journal
CAMIA 29 (1991), pp. 385 - 390
Mineral name
Tugtupite - from Ilimaussaq, South Greenland
Comment
TEM 1178

Example 2: Two representations of a fullerene molecule (C60) as polyhedron with no central atom and hexagonal and pentagonal faces. The left version in flat representation with some faces open and the other hatched, the right version using transparent faces (transparency factor: 0.5).

Previous article: Plane and line objects
Next article: Creating Coordination Polyhedra