[lammps-users] Forcing a neighbour list rebuild?

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1

Hi,
  I'm writing a dump routine that makes use of our own HDF5 based file
format. I noticed in the dump command docs that the periodic boundary
conditions are only enforced during neighbour list rebuilds and that
these don't necessarily happen on the same time step as the dump. One of
our users would really like to see them enforced before the atom
coordinates are written out.

Is there a way of forcing the rebuild during the dump? If so, what do I
need to add, and would this cause problems with the rest of the
calculation?

Thanks,
  Duncan

2

Hi,

  I'm writing a dump routine that makes use of our own HDF5 based file
format. I noticed in the dump command docs that the periodic boundary
conditions are only enforced during neighbour list rebuilds and that
these don't necessarily happen on the same time step as the dump. One of
our users would really like to see them enforced before the atom
coordinates are written out.

Is there a way of forcing the rebuild during the dump? If so, what do I

you can enforce neighbor list builds in every step using the
neigh_modify command, but you could also apply pbc by yourself
in your output module.

need to add, and would this cause problems with the rest of the
calculation?

the major problem would be that additional neighbor list builds
will cost additional time.

cheers,
   axel.

3

Don't change the atom coords in the dump output. That
will mess up other things in LAMMPS. Instead, just apply
the PBC yourself before you write the output, w/out changing
what is stored in the x array for the atom coords.

Steve