Thanks Camps. So it means it is equivalent to use either the 8 atoms co-ordinates (the conventional cell) or the primitive cell (2 atoms) co-ordinates i.e. both should give similar results.
On Wed, Oct 21, 2015 at 2:59 PM, I. Camps <[email protected]> wrote: > 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 >>> >>> >>> >>> >>> >> >
