[xcrysden] Saving the grid for an expanded system

[Gavin Abo]

If I recall correctly, while viewing a unit cell in xcrysden, there is 
option that can be selected that can repeat the unit cell in different 
directions so that it looks like a supercell.  It only worked view only 
and could not edit and save the structure. What you describe is similar 
to that, so the behavior you describe sounds normal for xcrysden but 
others in the mailing list may correct me if I'm wrong about that.

If you want xcryden to show the supercell instead of unit cell, you most 
likely have to go back to your DFT program and change it there from a 
unit cell to a supercell.  For example, if you were using WEIN2k, you 
would have to change case.struct file.

As described at

http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html

WIEN2k has a "supercell" or "structeditor" program that can take the 
unit cell and duplicate it in multiple directions to have a supercell.

If you feel it is not necessary for you to have the supercell in the DFT 
calculation, either rerun the charge density calculation on the unit 
cell to get the view as you described or you could look into modifying 
the case.xsf file by hand.  The XSF format is described at:

http://www.xcrysden.org/doc/XSF.html

On 4/23/2021 9:02 AM, Juan Jose Melendez Martinez wrote:
> Dear all
>
> I have generated a supercell by expanding a single unit cell along each crystal axis; xcrysden behaves very nicely for this. I can also expand a 3D grid defined for the unit cell to the whole supercell, and then I can see the charge distribution within the latter, for instance. Once I got the grid (say the charge density) in the whole supercell, I saved it via the "Save Grid" command. And then I found a couple of issues:
>
> 1) The xsf file saved from the previous procedure contains the atoms in the supercell. However, when I load the file, I get the unit cell, not the supercell that I expected.
>
> 2) I realized that the grid was saved for the unit cell only, not for the whole supercell. I can expand the grid again, but I cannot use it to compute charge differences, for instance.
>
> Did any of you experience something like this before? Any help, please?
>
> Thanks very much in advance.
>
> Juanjo
>
> Juan J. Meléndez
> Department of Physics
> University of Extremadura
> Badajoz (Spain)