Sorry that I didn’t explain it clearly. The boundary condition I used was periodic, and I used dump custom option to dump unwrapped coordinate, so some atoms may pass the boundaries and are outside the simulation box. When I used read_dump command to restart a simulation, I thought LAMMPS would eventually rewrap the unwrapped coordinates during the simulation, since LAMMPS always stores atom coordinates as values which are inside the simulation box. So I expected that the coordinates in XYZ files would be values inside the box.
I guess the problem is I don’t understand how lammps treats these coordinates when it first reads it from a file. Does it just leave them unchanged even they are outside the box and do the simulation as though they are inside the box?
Thanks for your reply.
Sorry that I didn't explain it clearly. The boundary condition I used was
periodic, and I used dump custom option to dump unwrapped coordinate, so
some atoms may pass the boundaries and are outside the simulation box. When
I used read_dump command to restart a simulation, I thought LAMMPS would
eventually rewrap the unwrapped coordinates during the simulation, since
LAMMPS always stores atom coordinates as values which are inside the
simulation box. So I expected that the coordinates in XYZ files would be
values inside the box.
I guess the problem is I don't understand how lammps treats these
coordinates when it first reads it from a file. Does it just leave them
unchanged even they are outside the box and do the simulation as though
they are inside the box?
LAMMPS stores coordinates as wrapped coordinates plus image flags. that is
how it can reconstruct unwrapped coordinates, if you request them. the
behavior how LAMMPS handles wrapped/unwrapped coordinates with read_dump,
is documented in the manual.
axel.