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fix_msd.html
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Sun, Feb 2, 19:02
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Tue, Feb 4, 19:02 (2 d)
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rLAMMPS lammps
fix_msd.html
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<HTML>
<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>
</CENTER>
<HR>
<H3>
fix msd command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
fix ID group-ID msd N file
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"fix.html"
>
fix
</A>
command
<LI>
msd = style name of this fix command
<LI>
N = compute mean-squared displacement every this many timesteps
<LI>
file = filename to write mean-squared displacement info to
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
fix 1 all msd 100 diff.out
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Compute the mean-squared displacement 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.
</P>
<P><B>
Restart, fix_modify, thermo output, run start/stop, minimize info:
</B>
</P>
<P>
This fix writes the original coordinates of diffusing atoms to
<A
HREF =
"restart.html"
>
binary
restart files
</A>
, so that the mean-squared displacement
will be accurate in a restarted simulation. See the
<A
HREF =
"read_restart.html"
>
read_restart
</A>
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.
</P>
<P>
None of the
<A
HREF =
"fix_modify.html"
>
fix_modify
</A>
options are relevant to this
fix. No quantities calculated by this fix can be output by the
<A
HREF =
"thermo_style.html"
>
thermo_style custom
</A>
command. No parameter of this
fix can be used with the
<I>
start/stop
</I>
keywords of the
<A
HREF =
"run.html"
>
run
</A>
command. This fix is not invoked during
<A
HREF =
"minimize.html"
>
energy
minimization
</A>
.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
none
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
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