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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3501 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-12-04 00:42:15 +00:00
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18
doc/compute_msd.html
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@ -29,8 +29,8 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all compute
fix 1 upper compute com yes
<PRE>compute 1 all msd
compute 1 upper msd com yes
</PRE>
<P><B>Description:</B>
</P>
@ -44,8 +44,8 @@ and averaged over atoms in the group. The 4th component is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.
</P>
<P>The slope of the mean-squared displacement versus time is proportional
to the diffusion coefficient of the diffusing atoms.
<P>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
@ -75,11 +75,11 @@ image</A> command.
</P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,
and the computed MSD will not reflect its true displacement. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the
atoms in the bodies.
and its contribution to the MSD may not reflect its true contribution.
See the <A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to
compute the MSD of rigid bodies as they cross periodic boundaries, you
will need to post-process a <A HREF = "dump.html">dump file</A> containing
coordinates of the atoms in the bodies.
</P>
<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,