It seems I am missing something. My original data file has no overlapping atoms however the dump file is showing overlapping and Thomas mentioned that this is because of the periodic boundary conditions, so what am I missing in this situation plz?
Kristof, thank you very much, this was really helpful for me as I am new to LAMMPS and this was new info to me.
Thomas, thank you for that it is really narrowing my search to how to solve this problem but may I ask please some clarification for what you mean by it starts with atoms 1+2 and goes on with 3+4. I am sorry for asking so much but I am just trying to get the point and where to search for a solution.
On Fri, Jul 14, 2017 at 7:31 AM, Meral Sharkas <eng_meral.sh10@...16...> wrote: > Thank you Axel for your reply, so does that mean I used replicate command in > a wrong way as I get answers with another data files?
no. you cannot use the replicate command in the wrong way.
> > Sent from Yahoo Mail on Android > > On Fri, Jul 14, 2017 at 2:03 PM, Axel Kohlmeyer > <akohlmey@...24...> wrote: > On Fri, Jul 14, 2017 at 6:47 AM, Meral Sharkas via lammps-users > <lammps-users@...396... sourceforge.net> wrote: >> Dear Lammps users, >> >> Please I have a question. >> I used a CIF file for generating a unit cell by VESTA and then used >> "replicate" command to create my supercell, however when I ran my system >> for >> I always get (-nan ) as an output for all my parameters and when I >> replicated the unit cell by packmol I started to get results. >> >> Is there any reason for that? > > LAMMPS strictly follows the GI-GO principle (garbage in, garbage out). > so your input must be wrong, when you get NaNs. it is not a LAMMPS > problem, but how you generate that input. > > axel. > > >> >> Please find the attached cif,data and log files. >> >> Thanks in advance > >> >> >> >> >> ------------------------------ ------------------------------ ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> ______________________________ _________________ >> lammps-users mailing list >> lammps-users@...429...96... sourceforge.net >> https://lists.sourceforge.net/ lists/listinfo/lammps-users >> > > > > -- > Dr. Axel Kohlmeyer akohlmey@...24...
http://goo.gl/1wk0 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy.
-- Dr. Axel Kohlmeyer akohlmey@...24...http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.