forked from lijiext/lammps
90 lines
3.2 KiB
HTML
90 lines
3.2 KiB
HTML
<HTML>
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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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<HR>
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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 keyword value ...
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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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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>com</I>
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<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
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</PRE>
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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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fix 1 all msd 1000 diff.out com yes
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</PRE>
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<P><B>Description:</B>
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</P>
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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 MSD is the square of the displacement of
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each atom, averaged over all the atoms in the group. The displacement
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of an atom is from its original position at the time the fix command
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was issued. The slope of the mean-squared displacement versus time is
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proportional to the diffusion coefficient of the diffusing atoms.
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</P>
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<P>The MSD values versus time are written 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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atoms in the bodies.
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</P>
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<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift
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in the center-of-mass of the group of atoms is subtracted out before
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the displacment of each atom is calcluated.
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</P>
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<P><B>Restart, fix_modify, 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 global scalar or vector or per-atom quantities are stored by
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this fix for access by various <A HREF = "Section_howto.html#4_15">output
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commands</A>. No parameter of this fix can be
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used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_coord_original.html">fix coord/original</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option default is com = no.
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</P>
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</HTML>
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