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Re: [lammps-users] Use "read_dump" multiple times
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Re: [lammps-users] Use "read_dump" multiple times


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 27 Apr 2018 13:50:10 -0400

On Fri, Apr 27, 2018 at 1:47 PM, Yidong Xia <yidongxia@...24...> wrote:
> I am not trying to read the same atoms, but dump files from different
> simulations as initial conditions to prepare a simulation of a larger
> system.

if they have the same atom id, they are the same atoms to LAMMPS. that
is how read_dump operates. it is explained in the documentation for
the command.

> read_dump       out_simulation_A.100.dump  100 x y z box no add yes
> read_dump       out_simulation_B.500.dump  500 x y z box no add yes
> read_dump       out_simulation_C.400.dump  500 x y z box no add yes
>
> Since this way
> does not go through as I initially considered, I can use LAMMPS data files
> for the same purpose.

read_data or replicate are the way to build larger systems.

axel.

>
> Again, thanks for your help!
>
> On Fri, Apr 27, 2018 at 11:42 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Fri, Apr 27, 2018 at 12:53 PM, Yidong Xia <yidongxia@...24...> wrote:
>> > Thanks for pointing out my problem. But how to overcome this in
>> > "read_dump"? Thanks.
>>
>> what you are asking for doesn't make sense. if you are reading the
>> same atoms, read dump should assign the data to the same atoms. that
>> is what it does and that is how it should work.
>> if you want to create new atoms from the same system, you can use,
>> e.g. replicate or read_data. no point in complicating read_dump as it
>> is already problematic to use it to import atoms.
>>
>> axel.
>>
>> >
>> > On Fri, Apr 27, 2018 at 10:48 AM, Axel Kohlmeyer <akohlmey@...24...>
>> > wrote:
>> >>
>> >> On Fri, Apr 27, 2018 at 12:37 PM, Yidong Xia <yidongxia@...24...>
>> >> wrote:
>> >> > Did anyone use "read_dump" multiple times to read a number of LAMMPS
>> >> > dump
>> >> > files where each file contain one snapshot?
>> >> >
>> >> > Recently I found that only the 1st "read_dump" added atoms into the
>> >> > system;
>> >> > the rest of "read_dump" did not add atoms even though I used "add
>> >> > yes"
>> >> > keyword. I've pasted one example here
>> >> >
>> >> >
>> >> > region          box block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
>> >> > create_box      3 box
>> >> >
>> >> > read_dump       out.100.dump  100 x y z box no add yes
>> >> > read_dump       out.500.dump  500 x y z box no add yes
>> >> > ...
>> >> >
>> >> > Another situation is, if I have "read_data" before "read_dump" at
>> >> > first,
>> >> > then none of the "read_dump" could actually add atoms in the system
>> >> >
>> >> > # the simulation box is already large enough to include all atoms in
>> >> > dump
>> >> > files
>> >> >
>> >> > read_data       LAMMPS_data1.dat
>> >> > read_data       LAMMPS_data2.dat add append
>> >> >
>> >> > read_dump       out.100.dump  100 x y z box no add yes
>> >> > read_dump       out.500.dump  500 x y z box no add yes
>> >> >
>> >> > I
>> >> > wonder if my setup is not right? Thanks for any feedback
>> >>
>> >> no, you simply didn't read the documentation careful enough.
>> >>
>> >> with the add yes keyword included indeed new atoms are added, but
>> >> *only* if their atom id is different from one that already exists.
>> >> otherwise it will simply overwrite the the read in parameters, which
>> >> is exactly what it should be doing.
>> >>
>> >> axel.
>> >>
>> >>
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > 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.
>> >
>> >
>>
>>
>>
>> --
>> 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.