lammps/doc/fix_msd.txt

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fix msd command :h3

[Syntax:]

fix ID group-ID msd N file :pre

ID, group-ID are documented in "fix"_fix.html command
msd = style name of this fix command
N = compute mean-squared displacement every this many timesteps
file = filename to write mean-squared displacement info to :ul

[Examples:]

fix 1 all msd 100 diff.out :pre

[Description:]

Compute the mean-squared displacement (MSD) of the group of atoms
every N steps, including all effects due to atoms passing thru
periodic boundaries.  The slope of the mean-squared displacement
versus time is proportional to the diffusion coefficient of the
diffusing atoms.  The "origin" of the displacement for each atom is
its position at the time the fix command was issued.  Write the
results to the specified file.

IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and the computed MSD will not reflect its true displacement.  See the
"fix rigid"_fix_rigid.html command for details.  Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a "dump file"_dump.html containing coordinates of the
atomss in the bodies.

[Restart, fix_modify, output, run start/stop, minimize info:]

This fix writes the original coordinates of diffusing atoms to "binary
restart files"_restart.html, so that the mean-squared displacement
will be accurate in a restarted simulation.  See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.

None of the "fix_modify"_fix_modify.html options are relevant to this
fix.  No global scalar or vector or per-atom quantities are stored by
this fix for access by various "output
commands"_Section_howto.html#4_15.  No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.

[Restrictions:] none

[Related commands:] none

[Default:] none