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? 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? Than you very much for your reply again. 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, 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
