Syntax:
fix ID group-ID msd N file
Examples:
fix 1 all msd 100 diff.out
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 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 atomss in the bodies.
Restart, fix_modify, thermo 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 quantities calculated by this fix can be output by the thermo_style custom command. 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: none
Default: none