It's hard (for me at least) to tell what went wrong from that error
message. Perhaps you can try restarting the simulation using another
method:
1)
There is a "read_dump" command
see
http://lammps.sandia.gov/doc/read_dump.html
2)
Try creating a new data file using "read_restart", "write_data" and
then use "read_data" to load it:
http://lammps.sandia.gov/doc/write_data.html
(don't use restart2data)
3)
If you are really desperate, try the "dump2data.py" script (attached)
Syntax:
dump2data -last old_file.data < dump_file > new_file.data
This is a slow script and it is not fully tested. I have not tested
it with triclinic or 2D data, but I'm using it for my own simulations.
(I've had trouble with restart files in the past, so I was looking
for an alternative.)
There's probably a way to do this using pizza.py as well.
There are several ways to do this. I just wanted a one-line bash
command that would extract coordinates from a dump file and create a
data file.
-- documentation for dump2data.py --
With "dump2data.py" you can select which snapshot you want to read from using
-t 600000
(or use "-last" for the last frame)
You can center the coordinate data using
-center
(There is also a "-scale X" command, but it is not well tested.)
The atom style is "full" by default. You can change this using (for example),
-atomstyle "dipole"
(I have not yet tested hybrid styles, but I hope they work.
Surround them in quotes, such as "hybrid dipole ellipsoid")
You can output to XYZ format or raw coordinate data format using
"-xyz" or "-raw".
If you want to create multiple data files at regular time intervals use:
dump2data.py -interval 20000 old_file.data < dump_file
(I think) this will generate a series of files named
"old_file.data.1","old_file.data.2","old_file.data.3" ...
with the coordinates extracted from frames whose timestep is a
multiple of 20000.
Velocities:
If you need the velocities, then they must be present in your dump
file, and there must also be a "Velocities" section in the data file
(eg "old_file.data")
This is experimental software, so don't use this software unless you
have no other options. Try using "read_dump" or
"read_restart","write_data","read_data" instead.
Somebody will probably have replied to your post by the time I finish
typing this.
Good luck.
Andrew
dump2data.py (57.1 KB)