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Re: [lammps-users] Replication command
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Re: [lammps-users] Replication command


From: Thomas Asche <thomas.asche@...6513...>
Date: Fri, 14 Jul 2017 19:34:13 +0200

No, it is just the same atom - translated by one box length - defined again.

Your conversion is wrong here, because those atoms should be in the box only once. Guess it happens for all atoms with one of the x,y,z components being zero in your file.

That messes up your cell composition by the way. Please check how many atoms you would expect in your cell.


Am 14.07.2017 um 18:59 schrieb Axel Kohlmeyer:
On Fri, Jul 14, 2017 at 12:40 PM, Meral Sharkas
<eng_meral.sh10@...16...> wrote:
Dear Kristof,

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?
how about having too small a box, so that atoms overlap due to PBC?

axel.

Thank you all for your great help..

Sent from Yahoo Mail on Android

On Fri, Jul 14, 2017 at 5:43 PM, Kristof Bal
<kristof.bal@...24...> wrote:


2017-07-14 16:30 MT+02:00 Meral Sharkas <eng_meral.sh10@...16...>:

Hi Thomas,

Apologies, I got you now, atoms 1,2 and 3,4 overlapped

I guess I should use delete atoms command to avoid that..


Or just, you know, make a data file without overlapping atoms...

Kristof



Sent from Yahoo Mail on Android

On Fri, Jul 14, 2017 at 5:20 PM, Meral Sharkas
<eng_meral.sh10@...16...> wrote:
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.

I am appreciating your help....

Regards


On Friday, July 14, 2017 3:58 PM, Kristof Bal <kristof.bal@...24...> wrote:




2017-07-14 14:08 GMT+02:00 Meral Sharkas via lammps-users
<lammps-users@...396... sourceforge.net>:

Is there any way to detect where is my fault? I am pretty sure it is in the
data file but how can I detect it?


NaN energies are usually obtained when certain atoms overlap. You should
check your data file for this.

Of course, you wil get these NaN values with or without replication.

Kristof



Sent from Yahoo Mail on Android

On Fri, Jul 14, 2017 at 2:40 PM, Axel Kohlmeyer
<akohlmey@...24...> wrote:
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.

axel.

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



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--
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.


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--
Thomas S. Asche, M. Sc.
AK Festkörper- und Materialchemie

Leibniz Universität Hannover
Institut für Anorganische Chemie
Callinstr. 9, 30167 Hannover
Raum: 004

Tel.:   +49 (511) 762 3058
Fax:    +49 (511) 762 3006
E-Mail: thomas.asche@...6513...