[xcrysden] Saving the grid for an expanded system

[Juanjo Meléndez]

Dear Gavin

Thanks for your reply. I think that it will be easier to edit the xsf file. Thanks a lot!

Best

Juanjo

Juan J. Meléndez Martínez
Departamento de Física
Universidad de Extremadura
Avda. de Elvas, s/n 06006 Badajoz 
Teléfono: 924 28 96 55
Fax: 924 28 96 51
Email: melendez at unex.es <mailto:melendez at unex.es>
Web: materiales.unex.es/miembros/personal/jj-melendez/Index.html




> El 24 abr 2021, a las 18:44, Gavin Abo <gsabo at crimson.ua.edu> escribió:
> 
> 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)
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