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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 17:03:00 -0400

BTW: another explanation for your unexpected behavior could be an
incorrect implementation of the restart functions in your custom pair
style. that could result LAMMPS reading not enough or too many bytes
and then it may just read the wrong data into your box parameters.

axel.

On Thu, Oct 26, 2017 at 8:41 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
> 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
>>> > 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.
>>
>>
>>
>>
>> --
>> 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.



-- 
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.