mirror of https://github.com/lammps/lammps.git
69 lines
2.2 KiB
Plaintext
69 lines
2.2 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix msd command :h3
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[Syntax:]
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fix ID group-ID msd N file :pre
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ID, group-ID are documented in "fix"_fix.html command
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msd = style name of this fix command
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N = compute mean-squared displacement every this many timesteps
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file = filename to write mean-squared displacement info to :ul
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[Examples:]
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fix 1 all msd 100 diff.out :pre
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[Description:]
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Compute the mean-squared displacement (MSD) of the group of atoms
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every N steps, including all effects due to atoms passing thru
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periodic boundaries. The slope of the mean-squared displacement
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versus time is proportional to the diffusion coefficient of the
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diffusing atoms. The "origin" of the displacement for each atom is
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its position at the time the fix command was issued. Write the
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results to the specified file.
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IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
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rigid"_fix_rigid.html command), it's periodic image flags are altered,
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and the computed MSD will not reflect its true displacement. See the
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"fix rigid"_fix_rigid.html command for details. Thus, to compute the
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MSD of rigid bodies as they cross periodic boundaries, you will need
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to post-process a "dump file"_dump.html containing coordinates of the
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atomss in the bodies.
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[Restart, fix_modify, thermo output, run start/stop, minimize info:]
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This fix writes the original coordinates of diffusing atoms to "binary
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restart files"_restart.html, so that the mean-squared displacement
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will be accurate in a restarted simulation. See the
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"read_restart"_read_restart.html command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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None of the "fix_modify"_fix_modify.html options are relevant to this
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fix. No quantities calculated by this fix can be output by the
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"thermo_style custom"_thermo_style.html command. No parameter of this
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fix can be used with the {start/stop} keywords of the "run"_run.html
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command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:] none
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[Related commands:] none
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[Default:] none
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