回复: How to specify which form of coordinates in theXYZ file written by "dump xyz"

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.​