Thanks a lot dear Andrei for your help Best Regards Mahshid --- On Sun, 4/11/10, [email protected] <[email protected]> wrote:
From: [email protected] <[email protected]> Subject: Re: [SIESTA-L] Deforming the shape of supercell To: [email protected] Date: Sunday, April 11, 2010, 7:42 PM > Dear Andrei, > Thank you for your prompt reply. I did not underestand your solution: > "if you want a nanoparticle, make it compact (connected) PRIOR TO > putting it into a large supercell site". I mean how I can compact the > nanoparticle? Dear Mahshid, sorry if it was not clear. Think about a molecular crystal: you define a molecule, AND THEN you describe how the moleulces are situated in the crystal. In order to describe a nanoparticle: put the atoms together such as they must belong in a single particle, AND THEN you define the translation vectors which place the particles one relative to the other. The point is: in bulk, some atoms may have their coordinates elsewhere, but brought into the right place by translations (as in your example of the 2*1*2 supercell). For an isolated nanoparticle in vacuum, it is not much practical. > And in your hint (And a hint: unless you have a special reason > to keep your unit cell not orthorhombic (or even cubic), don't) you mean > that it is better to use a cubic supercell instead the hegzagonal? If the exact positioning of nanoparticles is irrelevant (they must be just kept far away to prevent the overlap of basis functions, right?) - I would say, yes. At least I had an impression it worked better, in older versions of Siesta. Some Siesta developpers may wish to comment... Best regards Andrei > > > --- On Sun, 4/11/10, [email protected] > <[email protected]> wrote: > > > From: [email protected] <[email protected]> > Subject: Re: [SIESTA-L] Deforming the shape of supercell > To: [email protected] > Date: Sunday, April 11, 2010, 2:11 PM > > > Dear Mahshid, > > your "small" supercell contains two parallel (Zn-O)*4 chains > with a considerable distance between them, so that there are > no bonds between the chains. You can see it in XCrySDen > if you click on a small icon in the low panel, > the second on the right from the "Dihedral" button, > which icon shows "translational asymmetric unit", > i.e., how your coordinates are REALLY defined. On the contrary, > clicking on the first button on the right from "Dihedral", > which is also default on invokig XCrySDen, is the "nicely-cut unit cell" > regime. > Now, with your translation vectors as you defined for the 2*1*2 supercell > this is not a problem, because the translation vectors bring two chains > close one to another, as they should be, and all the bonds > are correctly recovered. > You can see how it happens if you choose in the XCrySDen menu > Display -> Crystal Cells > and > Modify -> Number of units drawn -> say, 2 2 1 > > Then, as you increase translation vectors, > you still have two parallel chains > with a considerable distance between them, according to the coordinates > you provided, > however now moved apart by your huge translation vectors. > You can see what happens, again repeating > Display -> Crystal Cells > and > Modify -> Number of units drawn -> say, 2 2 1 > for your supercell. > > A solution: > if you want a nanoparticle, make it compact (connected) PRIOR TO > putting it into a large supercell site. > A comment: you don't need so large translation vectors. > In order to prevent interaction between nanoparticles, you only need > the vectors to be long enough to prevent the overlap of basis functions > "across the cell boundary". Otherwise you spend your computer > resources in vain. > And a hint: unless you have a special reason > to keep your unit cell not orthorhombic (or even cubic), don't. > > Best regards > > Andrei > > > >> Thanks for replying dear Andrei >> My calculation started with bulk zno( four atoms per unit cell ) .I used >> lattice parameters and atoms position of experimental data and >> bandstructure,DOS is ok. >> Then i made supercell 2*1*2 of the unit cell using wien2k and save it as >> zno.xsf . its shape using xcrysden was okey. >> Then for constructing vacuum i increased lattice parameter in x,y,z >> direction (see the enclosed zno.xsf , super_zno.xsf file). is this >> procdure is wright for adding vacuum? >> But surprisingly if you look at the super_zno.xsf you will see that >> there >> is a a gap between Zn atoms!!! with no any bonds. What dose this mean >> and >> what has happen? >> Even I have not done any relaxation and calculations? >> >> Best Regards >> Mahshid > > > >
