Hello All,
I am using write_data to get the positions of atoms in my CNT after equilibrium. CNT is broken in three pieces when I look at the data after equilibrium. It seems it moves outside the periodic box and that is the reason I cannot see the correct shape of the tube. Could you please guide me how to get the correct data so that CNT maintains its shape . (which command to use and how to use it?)
Thanks a lot
If everything is done correctly, the CNT does maintain its shape. I suspect you are just ignoring the image flags. If atoms move outside the box, their image flags get incremented or decremented.
If you use write_dump to write out the coordinates, you can use xu, yu, zu instead of x,y,z and you will get the unwrapped coordinates. If you load the data file into VMD or OVITO, it should apply them, too.
If you don’t want the CNT to leave the box, you may need to make some adjustments to your simulation, e.g. apply fix spring tether to the CNT to pull it back, or just exclude a few random atoms from time integration, so they cannot move and thus the CNT cannot move either.
Bottom line, this is more a visualization/data processing problem than a LAMMPS problem.
Thank you so much. this information helps a lot.