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Re: [lammps-users] Read_restart changing box parameters
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Re: [lammps-users] Read_restart changing box parameters


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 26 Oct 2017 08:41:59 -0400

On Thu, Oct 26, 2017 at 8:20 AM, Carter Rhea <crhea@...7157...> wrote:
> Well My "Ugly Hack" was recommended on the following page:
> http://lammps.sandia.gov/doc/Section_errors.html
> Cannot change_box after reading restart file with per-atom infoThis is
> because the restart file info cannot be migrated with the atoms. You can get
> around this by performing a 0-timestep run which will assign the restart
> file info to actual atoms.

that is a workaround for not being able to use "change_box", this
avoids the error message when trying to user change_box.
that is not what i am referring to. please recall, that your original
email was claiming that read_restart does not read the box dimensions
correctly and changes them unexpectedly.
*that* is what i am concerned about, and it is your applying of
change_box, *that* is the ugly hack i am complaining about.

read_restart _MUST_ restore the correct box dimensions that were
present when the restart was written. any deviation from that is a
serious bug and must be corrected immediately in the source code.

the attached files are useless, since it uses a binary restart which
contains references to a custom pair style that is not part of the
official LAMMPS version. regardless of that, i would need an input to
*generate* a restart from scratch and then read it back, so that i
have conclusive proof of what were the box dimensions while writing
the restart and after reading it back.

axel.

>
>
>
>
> On Thu, Oct 26, 2017 at 8:09 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Thu, Oct 26, 2017 at 8:04 AM, Carter Rhea <crhea@...7157...> wrote:
>> > Dear Axel,
>> >  Thank you for the prompt reply. I agree that it seemed rather odd, but
>> > I
>> > noted the change in boundaries from the output of LAMMPS following the
>> > reading of the restart file. I have fixed it with the following simple
>>
>> that is no proof.
>>
>> > command:
>> >
>> > run         0
>> >
>> > change_box     all y final -0.5 0.5 boundary f f p
>> > change_box     all x final -5.0 5.0 boundary f f p
>>
>> this is not a fix but an ugly hack and it doesn't help us a single bit
>> in identifying and tracking down what may be a very serious bug in the
>> code.
>>
>> so please provide what i had asked for. you should want to know the
>> proper resolution of this, too, because if this is not reproducible,
>> it would mean, that there is something seriously wrong with your
>> simulation or you don't properly understand what you are doing or you
>> have a miscompiled executable. all of those are serious issues.
>>
>> axel.
>>
>>
>> >
>> > --
>> > Thank you,
>> >  Carter Rhea
>> > College of Charleston
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Check out the vibrant tech community on one of the world's most
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>> > _______________________________________________
>> > lammps-users mailing list
>> > lammps-users@lists.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.
>
>
>
>
> --
> Thank you,
>  Carter Rhea
> College of Charleston
>
> ------------------------------------------------------------------------------
> 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@lists.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.