2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>fix msd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID msd N file
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>msd = style name of this fix command
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<LI>N = compute mean-squared displacement every this many timesteps
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<LI>file = filename to write mean-squared displacement info to
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all msd 100 diff.out
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</PRE>
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<P><B>Description:</B>
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</P>
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2007-08-29 22:13:51 +08:00
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<P>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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</P>
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<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
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rigid</A> 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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<A HREF = "fix_rigid.html">fix rigid</A> 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 <A HREF = "dump.html">dump file</A> containing coordinates of the
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atomss in the bodies.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-06-26 08:03:39 +08:00
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<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary
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restart files</A>, so that the mean-squared displacement
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will be accurate in a restarted simulation. See the
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<A HREF = "read_restart.html">read_restart</A> 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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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> 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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<A HREF = "thermo_style.html">thermo_style custom</A> command. No parameter of this
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fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
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command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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