Disordered Sites in CrystalMaker

CrystalMaker lets you specify disordered sites when you build, or edit your structure. Each site has an occupancy field, which accepts up to three element symbols and their fractional occupancies, e.g., "Si 0.5 Al 0.5". By entering site occupancies you can ensure that the correct formula and density are calculated for your structure. You will also need to correct occupancies to ensure that diffraction simulations proceed correctly.

Representing Disorder

There appears to be a common misconception that one can represent a disordered structure simply by randomly dispersing different site occupants through a structural model:

• CrystalMaker plots sites, not atoms. Whilst you can specify the site occupancy - and this is used in simulating diffraction data - what is actually plotted is simply a sphere, designating the position in space of the site.

• CrystalMaker does not 'magically' disperse disordered sites throughout the lattice. Neither can it come up with some kind of random distribution of atoms on the same site (e.g., an Al and Si mix). To do so might be nice for display purposes, but it would be wrong, for the following reasons (amongst others):

  1. Most structure are obtained through diffraction, which averages over space and time.

  2. There is an infinite number of distributions; to pick one would be arbitrary.

  3. Showing an 'ordered' distribution would violate the spacegroup symmetry.

  Positional disorder is spatially averaged, through the diffraction process, culminating in a structure's spacegroup symmetry. CrystalMaker does the only "honest" thing, and plots "grey" spheres. These indicate the position of a site, with your average occupancy: e.g., 50% Al and 50% Si - never 100% Al and 100% Si (that would lower symmetry, and imply ordering).