(sorry! I just sent by accident an unfinished message by touching the wrong button I complete it here)
Dear Zahra Talebi You can directly load an visualize any fdf using "deneb", it is a new software for windows and linux that you can freely download from the webpage of atelgraphics, they have also some demonstration videos in their youtube channel (search for "atelgraphics" in youtube). It works fine for me so far (i am using the windows version). I use it to visualize any fdf even to edit them. You can also visualize the "movie" contained in the .ANI files resulting from a SIESTA Molecular dynamics (I think there was some recent question in this list about that.) -- Water dissociation over a surface of platinum is the first video demo that you can find on http://www.youtube.com/watch?v=E10MVIpi2Kg&feature=g-all -- Gold dimer into a C60 is the other video (that shows the loading of an MD animation) you can find it on http://www.youtube.com/watch?NR=1&v=xzmlwYQcWMA&feature=endscreen I hope it helps Regards Jose A === Jose A. Torres, PhD Atelgraphics SL Faraday 7, primera planta ICLAD building, Campus Cantoblanco ________________________________ De: Khan Muhammad <me...@kaist.ac.kr> Para: Zahra Talebi <talebi_z2...@yahoo.com>; siesta home <siesta-l@uam.es> Enviado: Viernes 30 de noviembre de 2012 6:25 Asunto: RE: Re: [SIESTA-L] seeing structure There is a python script "geom2geom" provided with Inelastica package, that can be used to convert the structure from fdf to xyz format before running your calculation. Which can be seen by using any type of visualization tool e.g. xcrysden, vesta, xmakemol, jmol etc. The compiled script is also attached with this email. However, you may need to compile the python package for it. usage: geom2geom name1.fdf name2.xyz -x 2 -y 3 -z 3 With Best Regards Muhammad Ejaz Khan PhD candidate Graduate School of Nanoscience and Technology, KAIST -----------------------Original Message----------------------- >From: Zahra Talebi <talebi_z2...@yahoo.com> >To: Sanjiv Jha <san...@nmsu.edu> >Sent date: 2012-11-29 13:25:56 GMT +0900 (Asia/Seoul) >Subject: Re: [SIESTA-L] seeing structure > > >hi >thanks for your quick answer, >I want to see the structure before running siesta. do you have solution for >that. > > >From: Sanjiv Jha <san...@nmsu.edu> >To: Zahra Talebi <talebi_z2...@yahoo.com> >Sent: Thursday, November 29, 2012 7:48 AM >Subject: RE: [SIESTA-L] seeing structure > > > >When you run the .fdf file, you will get .xyz file. This can be visualised by >Jmol. > > > >Best regards, >Sanjiv K Jha >Graduate Student >Department Of Physics, NMSU >Office: GN 361 > >From: siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] on behalf of Zahra >Talebi [talebi_z2...@yahoo.com] >Sent: Wednesday, November 28, 2012 9:16 PM >To: siesta home >Subject: [SIESTA-L] seeing structure > > >hi every body >I wanted to know is there a way to see the structure of what we write in fdf >by xcrysden just after writing the fdf, or better to say by knowing the place >of our atoms in our structure and knowing the primitive vectores or supercell >vectores? > >
