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rLAMMPS lammps
compute_msd_nongauss.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>
compute msd/nongauss command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID msd/nongauss keyword values ...
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
msd/nongauss = style name of this compute command
<LI>
zero or more keyword/value pairs may be appended
<LI>
keyword =
<I>
com
</I>
<PRE>
<I>
com
</I>
value =
<I>
yes
</I>
or
<I>
no
</I>
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 all msd/nongauss
compute 1 upper msd/nongauss com yes
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.
</P>
<P>
A vector of three quantites is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.
</P>
<CENTER><IMG
SRC =
"Eqs/compute_msd_nongauss.jpg"
>
</CENTER>
<P>
The NGP is a commonly used quantity in studies of dynamical
heterogeneity. Its minimum theoretical value (-0.4) occurs when all
atoms have the same displacement magnitude. NGP=0 for Brownian
diffusion, while NGP > 0 when some mobile atoms move faster than
others.
</P>
<P>
If the
<I>
com
</I>
option is set to
<I>
yes
</I>
then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated.
</P>
<P>
See the
<A
HREF =
"compute_msd.html"
>
compute msd
</A>
doc page for further IMPORTANT
NOTES, which also apply to this compute.
</P>
<P><B>
Output info:
</B>
</P>
<P>
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See
<A
HREF =
"Section_howto.html#howto_15"
>
this
section
</A>
for an overview of LAMMPS output
options.
</P>
<P>
The vector values are "intensive". The first vector value will be in
distance^2
<A
HREF =
"units.html"
>
units
</A>
, the second is in distance^4 units, and
the 3rd is dimensionless.
</P>
<P><B>
Restrictions:
</B>
</P>
<P>
This compute is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the
<A
HREF =
"Section_start.html#start_3"
>
Making
LAMMPS
</A>
section for more info.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"compute_msd.html"
>
compute msd
</A>
</P>
<P><B>
Default:
</B>
</P>
<P>
The option default is com = no.
</P>
</HTML>
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