Restart file and periodic domain

Hi, lammps users

I have some problem with visualisation of restart file in VMD (see
enclosed picture).
I save data in restart file, than convert it into data file using
restart2data and then use VMD, topo readlammpsdata <file> molecular.
The problem is particles are spread in flow direction because I have
periodic domain and it seems to me that lammps writes unmapped
coordinates. I tried to set restart_pbc_any=1 in my fix, it should
have led to remap (write_restart.cpp, lines 196-238) but it didn't.
I also tried to use pbc scripts in VMD: pbd set {14 14 14} -all; pbd
wrap; It composed cube but with strange bonds.

Best regards,
Kirill

Screen Shot 2012-05-15 at 9.21.44 AM.png

Hi, lammps users

I have some problem with visualisation of restart file in VMD (see
enclosed picture).
I save data in restart file, than convert it into data file using
restart2data and then use VMD, topo readlammpsdata <file> molecular.
The problem is particles are spread in flow direction because I have
periodic domain and it seems to me that lammps writes unmapped

the restart has wrapped coordinates and image counters,
so does the resulting data file.

coordinates. I tried to set restart_pbc_any=1 in my fix, it should
have led to remap (write_restart.cpp, lines 196-238) but it didn't.

the coordinates (are rewrapped), the unwrapping
is due to the image counters.

I also tried to use pbc scripts in VMD: pbd set {14 14 14} -all; pbd

nooo. topotools readlammpsdata should read the the
box dimensions from the data file. if not it is a bug,
that would require fixing. make sure you have the
latest version of the plugin, though.

wrap; It composed cube but with strange bonds.

that is because you didn't use pbc wrap correctly.
please read the pbctools plugin documentation
more carefully. by default pbc wrap disregards molecules
and wraps individual atoms. if you'd use:
pbc wrap -compound fragment it should keep
molecules intact. you may have to play a little
with the -center flag since VMD has the box
dimensions, but no knowledge of the origin
of the simulation cell.

axel.