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Re: [lammps-users] How to convert simulation box type
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Re: [lammps-users] How to convert simulation box type


From: "Khourshaei Shar, Ali" <akhoursh@...6666...>
Date: Tue, 31 Oct 2017 04:56:01 +0000

Dear Sara and Andrew,


I really appreciate your responses. About the ambiguity of my question, Actually I have a structure with monoclinic lattice structure ( So my .cif file is monoclinic ). For the sake of simulation, I need to have a cubic simulation box. But if I use that .cif file obviously it is not cubic. By the way, my apology to send the question several time. I wasn't familiar of how this community works.

Sincerely,

Ali


From: jewett.aij@...24... <jewett.aij@...24...> on behalf of Andrew Jewett <jewett@...6853.....>
Sent: Tuesday, October 31, 2017 12:33:39 AM
To: Sara Adibi
Cc: Khourshaei Shar, Ali; lammps-users@lists.sourceforge.net
Subject: Re: [lammps-users] How to convert simulation box type
 
On Mon, Oct 30, 2017 at 8:03 PM, Sara Adibi <sara.adibi@...24...> wrote:
> Hi,
>
> I am not sure about what you want to do but you may want to have a look at
> the following link:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lammps.sandia.gov_doc_change-5Fbox.html&d=DwIBaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=yHk4n55JH-8POYrYXkO3rTxHW3XBn5rpl8AWJtuSyq4&m=w_g2mj3P8oIOtTHDS_3d06ohYlqMLs78GeWcPZHRoEU&s=xu9mszhkxNdRTmAlTnzlDc7YNk4JW9_zlfXI3za90L8&e=
>
> Thanks,
> Sara

Good link!  One minor warning: the "change_box" command will
instantaneously change the boundary conditions of your simulation.
This might cause atoms to overlap.  If that happens, your the forces
between particles will be huge and your simulation will probably
crash, especially if you don't minimize the system first.  For
details, see:
https://urldefense.proofpoint.com/v2/url?u=http-3A__lammps.sandia.gov_doc_minimize.html&d=DwIBaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=yHk4n55JH-8POYrYXkO3rTxHW3XBn5rpl8AWJtuSyq4&m=w_g2mj3P8oIOtTHDS_3d06ohYlqMLs78GeWcPZHRoEU&s=CwoZPCPIFS5R8caRugYjs5Qp_AMAbc8rMtLDo-ucuqQ&e=

To avoid this problem, you can deform the box shape gradually from a
triclinic to a rectangular shape.  For more details check out:
https://urldefense.proofpoint.com/v2/url?u=http-3A__lammps.sandia.gov_doc_fix-5Fdeform.html&d=DwIBaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=yHk4n55JH-8POYrYXkO3rTxHW3XBn5rpl8AWJtuSyq4&m=w_g2mj3P8oIOtTHDS_3d06ohYlqMLs78GeWcPZHRoEU&s=km7axLjuXsfERzIQXNlgv3ATbs0kfPAZhae0Q6_STe4&e=

I'm not sure if this answered your question.

If instead you are just generally curious how to build a system with
rectangular boundary conditions, then feel free to read my answer to
the other message that you posted a few days ago.

cheers

andrew

(probably not a good idea to post multiple copies of the same question
to the list)


> On Fri, Oct 27, 2017 at 3:40 PM, Khourshaei Shar, Ali
> <akhoursh@...6666...> wrote:
>>
>> Dear LAMMPS users,
>>
>> Hi,
>>
>>
>> Currently I'm working on a simulation and My initial simulation box is
>> triclinic. However, I have to make a cubic one for some mechanical
>> simulation. So, any help on how to make a cubic simulation box fast and easy
>> ?!
>>
>> Thanks in advance,
>>
>> Ali
>>
>>
>>
>>
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