As professor Gul explained, the xyz format lack the crystal information, so you only will see "the molecule". For me, the image you send is ok: showing the atoms position with its bonds (but without the crystal periodicity). Take a look at the files using common text editor program.
[]'s, @mps On Wed, Oct 21, 2015 at 7:48 AM, Younas Khan <[email protected]> wrote: > Thank You sir for your kind reply. However, there are still some issues > which need to be clarified. For example when I take the conventional unit > cell, the xyz file consists of 8 co-ordinates. When I again visualize this > xyz file, it does not look like a conventional unit cell;it looks strange. > I have attached an image for clarity. > > On Wed, Oct 21, 2015 at 12:39 AM, Gul Rahman <[email protected]> wrote: > >> Younas, >> It is very simple >> 2 atoms cell is the primitive cell of bulk ZnS. >> 8 atoms cell is the conventional cell of bulk ZnS. >> 18 atoms will be the molecular/cluster (Zn14S4) structure of ZnS. xyz >> formate is for molecular, and you can also see the boundary conditions in >> all these structures. >> I will expect the same results from 2 and 8 atoms bulk ZnS, but will >> expect different results from Zn14S4 due to charge neutrality of ZnS. >> Gul >> >> Dr. Gul Rahman >> Assistant Professor, >> Department of Physics, >> Quaid-i-Azam University, >> Islamabad, Pakistan >> http://www.qau.edu.pk/profile.php?id=818020 >> >> >> >> On Tuesday, 20 October 2015, 22:45, Younas Khan < >> [email protected]> wrote: >> >> >> Hi all. My question is not siesta-specific, however its a good forum to >> discuss it. After designing a structure in a specific software (say >> materials studio) we can save it in various formats such as Pdb, .vasp or >> .xyz, however all these formats show different number of atoms for the same >> structure. For example, when we save a ZnS unit cell (zinc blend) structure >> in pdb it gives us co-ordinates of two atoms i.e Zn and S, in case of xyz I >> have 18 atoms (4 S and 14 Zn) and in case of .vasp I get 8 atoms (4 S and 4 >> Z). My question is: are these formats equally valid and will lead to same >> results??? What is the difference between them, if any. >> >> Thanks >> >> >> >> >> >
