Extending a unit cell to a supercell

[Vidushi Sharma]

Hello,

I am new to VESTA. I have an .xyz file which is the output from a Siesta simulation, and it contains a unit cell of a structure. I want to create a supercell from it, but when I try to do so using the usual procedure outlined in the manual and on the internet (i.e. Edit --> Edit Data -> Unit Cell -> Molecule -> Transform and enter 3, 3, 3 as the diagonal elements of the rotation matrix, and then select "Yes" (to change the unit cell volume) and "Search atoms in the new unit cell and add them as new sites") I get a huge blob as the output, which doesn't make sense.

All I want to do is translate the atoms in the original unit cell by a suitable amount above and below the plane they exist on, so as to create a supercell.

I am a bit confused by the options in the user manual. Should I be using the Custom structure, to enter the lattice constants of my structure FIRST, and THEN follow the above procedure? Doing that produces a whole bunch of redundant atoms and a structure much larger than I want.

I'd appreciate some help. Thank you!

[José Gadelha]

Hi Dear Sharma,

I think there are two possible solutions for you.

Firstly, for the next calculations add the following line in your Siesta input file (.fdf).

WriteCoorCerius .true

Then Siesta will write your system in a .xtl file. After that, open the .xtl file in a text editor to separate in two line the word "Cell" and the cell parameters, for example

"CELL 

a b c alpha beta gamma"

 After that open the .xtl file in VESTA and enjoy! :) 

Secondly, it is slightly more easy take the coordinates of the .xyz file and the lattice cell parameters of the system to create a .xsf file, that can be read in both xcrysden and VESTA.

Regards