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### fix msd command

Syntax:

    fix ID group-ID msd N file keyword value ...

- ID, group-ID are documented in fix 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
- zero or more keyword/value pairs may be appended
- keyword = com

        com value = yes or no

Examples:

    fix 1 all msd 100 diff.out
    fix 1 all msd 1000 diff.out com yes

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 MSD is the square of the displacement of each atom, averaged over all the atoms in the group. The displacement of an atom is from its original position at the time the fix command was issued. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms.

The MSD values versus time are written to the specified file.

IMPORTANT NOTE: If an atom is part of a rigid body (see the fix rigid command), it's periodic image flags are altered, and the computed MSD will not reflect its true displacement. See the fix rigid 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 containing coordinates of the atoms in the bodies.

If the com option is set to yes then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated.

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

This fix writes the original coordinates of diffusing atoms to binary restart files, so that the mean-squared displacement will be accurate in a restarted simulation. See the read_restart 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 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. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions: none

Related commands:

fix coord/original

Default:

The option default is com = no.