visualizing vacancy movement.

[amitwsu]

I have a large structure with 100s of atoms and few vacancies. It becomes hard to visualize the movement of vacancy embedded deep into the structure. So the question is

Is there a way to only display vacancy (may be as a ball) and not show all other atoms in the simulation box?

Also, if I toggle an atom to ghost atom then is that the same as removing the atom from the crystal and creating a vacancy?

Thanks
Amit

[Jess Wellendorff]

A ghost atom consists of all the basis functions for the atom, but has no nucleus and contributes no electrons to the system. Not sure how to highlight a defect since it is by definition not an atom.

[Anders Blom]

One possibility is to compute the LocalStructure. Most of your atoms are probably still in FCC or BCC arrangements, while those around the vacancy are not. You can use this to color the atoms around the vacancy in the Viewer differently, and even hide those with crystalline local structure, and in this way you can "see" the vacancy.

Using a ghost atom is possible, but not if  you are doing any optimization or molecular dynamics, as the ghost atom tends to move and sit on top of other atoms, i.e. it's not constrained to the vacancy site.

[Ulrik G. Vej-Hansen]

The procedure Anders describes is shown in this tutorial: http://docs.quantumwise.com/tutorials/akmc-empirical-sige.html