Hi, All,
I have been searching the correct command with LAMMPS to calculate MSD using multiple reference states, to no avail.
It seems that I can output the atom position files at different time steps with “fix store/state”.
Presumably, I can write my own code to calculate the MSD based the position files using multiple reference states.
But are there any tools already available that can do the post-processing to get MSD?
Any advice would be greatly appreciated.
Best Regards,
Decai Yu
Hi, All,
I have been searching the correct command with LAMMPS to calculate MSD using
multiple reference states, to no avail.
what do you mean by "multiple reference states". what about the MSD
compute that is included in LAMMPS?
It seems that I can output the atom position files at different time steps
with "fix store/state".
why not use a "dump"?
Presumably, I can write my own code to calculate the MSD based the position
files using multiple reference states.
But are there any tools already available that can do the post-processing to
get MSD?
why use external tools, when LAMMPS has integrated ones?
have you looked at the contents of examples/DIFFUSE?
axel.
Axel,
Thanks.
This is what I saw from the README of Example/DIFFUSE:
“In both cases a single time origin is
used. This allows the diffusion coefficient to be estimated
on-the-fly using variables in the LAMMPS input scripts. For better
statistics you typically want to use multiple time origins,
post-processing the data from dump files.”
I meant multiple time origins by “multiple reference states”
I don’t know how to do the post-processing from dump files.
This has come up many times on the mail list
for compute msd and compute vacf. We have
resisted implementing a multi-time0 version b/c
in parallel, carrying around 100s or 1000s
of starting points for each atom is potentially
very inefficient. People have talked about
more efficient methods, but no one has implemented
one for LAMMPS yet.
Steve