From: Oloriegbe, S. <olo...@mi...> - 2012-11-01 16:59:53
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Thanks Bob, I didn't get your e-mail despite configuring jmol to allow me receive mails from the list. I was able to copy your response from the mail list website (see below). I eventually use; load "filename.cif" {555 555 0} supercell { 8 8 2 } and got a supercell with small box encompassing some of the atoms which appears to be fine with some other noisy residual atoms outside box. When I wrote out the XYZ file, all atoms appears in the output file. Is there any command that help print out atoms only in the small box of interest? Suleiman. {1 1 1} indicates you want a packed cell, which duplicates atoms on faces. try {555 555 0} instead and see if that helps. On Thu, Nov 1, 2012 at 8:51 AM, Oloriegbe, Suleiman <olorieg...@missouri.edu > wrote: > Could anyone on the list help me with getting rid of overlapping atoms > on edges, boundaries and corners after generating a superstructure from > jmol through a CIF file. The XYZ file would be use as input in Molecular > dynamics program LAMMPS. > > > > > > I use load "filename.CIF" {1 1 1} supercell {8 8 2}. There are 8 atoms per > unit cell, so I expect a total of > > 8* 8 * 8 * 2 = 1024 atoms, but I got 1171 atoms instead. > > > > I took the painstaking method of removing the overlapping atoms visually, > but such approach can be plague with errors, so any help doing it > automatically using a script would be appreciated. > > > > BTW. I read most of the Jmol documentation and non of the commands seems > to help. > > > > Suleiman. "It is better to light a candle than to curse the darkness." ...Eleanor Roosevelt ________________________________ From: Oloriegbe, Suleiman Sent: Thursday, November 01, 2012 8:51 AM To: jmo...@li... Subject: Generating Periodic Boundary Structure in Jmol for Molecular Dynamics Could anyone on the list help me with getting rid of overlapping atoms on edges, boundaries and corners after generating a superstructure from jmol through a CIF file. The XYZ file would be use as input in Molecular dynamics program LAMMPS. I use load "filename.CIF" {1 1 1} supercell {8 8 2}. There are 8 atoms per unit cell, so I expect a total of 8* 8 * 8 * 2 = 1024 atoms, but I got 1171 atoms instead. I took the painstaking method of removing the overlapping atoms visually, but such approach can be plague with errors, so any help doing it automatically using a script would be appreciated. BTW. I read most of the Jmol documentation and non of the commands seems to help. Suleiman. |