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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 14 Jul 2017 12:59:31 -0400

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.
>
>
> ------------------------------ ------------------------------
> ------------------
> 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@...396... 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.