Hi all,
I am using LAMMPS for my work.I have one small clarification.
During the simulation run, I have dumped the atom coodinates to be in unscaled format for analysis.
Right now, I am trying to calculate MSD for my trajectory. To do that should i have to dump the
coordinates in unwrapped format or can i use the same unscaled coorindates for the MSD calculation.
Sincerely
Naresh
Hi all,
I am using LAMMPS for my work.I have one small clarification.
During the simulation run, I have dumped the atom coodinates to be in unscaled format for analysis.
Right now, I am trying to calculate MSD for my trajectory. To do that should i have to dump the
coordinates in unwrapped format or can i use the same unscaled coorindates for the MSD calculation.
if you use the msd compute in lammps, you don't need to dump anything,
but can compute the msd while doing the simulation.
other than that, it depends on whether your analysis code
can handle wrapped coordinates (mine can). you should
also take note that it is often more accurate to use the
first time derivative of the MSD than the value itself, if you
want to compute self-diffusion.
axel.
To add to Axel's answer, you can also dump the atom's image flags
in your dump file, which makes it easy for a post-analysis program
to unwrap the atom coords.
Steve