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Re: [lammps-users] Fwd: reset_ids command
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Re: [lammps-users] Fwd: reset_ids command


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 27 Apr 2018 13:59:47 -0400



On Fri, Apr 27, 2018 at 1:46 PM, Hyungmook Kang <hmkang@...633...> wrote:
Thanks, Anders and Alex.

Dear someone who developed "reset_ids" command.

I found the command doesn't work for the case Tip4p water model which requires a rule of consecutive atom ID order for O and H. If you updated the command, it would be really helpful to many lammps users.

​it would be helpful to *you*. i don't think there are many LAMMPS users that need it, or else people would have asked for it already. don't assume that what you are doing is what many LAMMPS users are doing.
in fact, i would opine, that the cleaner and more flexible way to "tailor" systems for LAMMPS is through using external tools, e.g. VMD and the topotools plugin or moltemplate. doing this kinds of modeling operations are in strong conflict with the needs for an efficient parallel program.​ so in most cases, system and especially topology building and modifying options in LAMMPS should be seen as a last resort method, not the preferred solution.

beyond that, ​if you want somebody to improve the code or fix an issue, you have to first provide a simple and easy to reproduce test case. it is also highly advisable to upload those together with a sufficiently detailed description to the LAMMPS project issue tracker on github: ​https://github.com/lammps/lammps/issues

axel.

 

Thank you so much.
Mook. 



On Thu, Apr 26, 2018 at 11:02 PM, Anders Hafreager <andershaf@...24...> wrote:
No, before you had to write a script to remap (and keep track of all bonds) ids. 

Anders

On Fri, Apr 27, 2018 at 7:42 AM, Hyungmook Kang <hmkang@...633...> wrote:
Thank you so much, Axel. 

I checked my version is the latest stable version Mar 16 2018 and the command was newly added at Mar 20, 2018. 
I understand I can use it when I update my lammps to the version.

However, was there a similar way to renumber atoms before the version release?
How could renumber atoms with molecular atom style?

Thanks,
Mook

On Thu, Apr 26, 2018 at 9:11 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Thu, Apr 26, 2018 at 11:01 PM, Hyungmook Kang <hmkang@...633...> wrote:
Dear lammps users,

​[...]

I can't use compress keyword of delete atoms since I use molecular atom style.
So. I tried to use "reset_ids" command 

But I got an error on both linux and Mac envrionments.
ERROR: Unknown command: reset_ids (../input.cpp:246)

I checked my lammps is the lastly updated version.

​which version is that exactly?

have you looked at this page?

 

Could somebody let me know the way to solve this problem or another way to reset atom IDs?

​my updated executable does have the reset_ids command:

$ ~/compile/lammps/src/lmp_mpi
LAMMPS (20 Apr 2018)
  using 1 OpenMP thread(s) per MPI task
reset_ids
ERROR: Reset_ids command before simulation box is defined (../reset_ids.cpp:33)
Last command: reset_ids
​axel.​

 



Many Thanks
Mook


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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.


------------------------------------------------------------------------------
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@...655....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.