Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F92773072
compute_msd_nongauss.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Nov 23, 14:45
Size
2 KB
Mime Type
text/html
Expires
Mon, Nov 25, 14:45 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
22509690
Attached To
rLAMMPS lammps
compute_msd_nongauss.html
View Options
<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>
Event Timeline
Log In to Comment