forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10673 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
550e3eae7a
commit
e8110de88d
|
|
@ -0,0 +1,90 @@
|
||||||
|
<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>
|
||||||
|
|
@ -0,0 +1,80 @@
|
||||||
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||||
|
|
||||||
|
:link(lws,http://lammps.sandia.gov)
|
||||||
|
:link(ld,Manual.html)
|
||||||
|
:link(lc,Section_commands.html#comm)
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
compute msd/nongauss command :h3
|
||||||
|
|
||||||
|
[Syntax:]
|
||||||
|
|
||||||
|
compute ID group-ID msd/nongauss keyword values ... :pre
|
||||||
|
|
||||||
|
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||||
|
msd/nongauss = style name of this compute command :l
|
||||||
|
zero or more keyword/value pairs may be appended :l
|
||||||
|
keyword = {com} :l
|
||||||
|
{com} value = {yes} or {no} :pre
|
||||||
|
:ule
|
||||||
|
|
||||||
|
[Examples:]
|
||||||
|
|
||||||
|
compute 1 all msd/nongauss
|
||||||
|
compute 1 upper msd/nongauss com yes :pre
|
||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
:c,image(Eqs/compute_msd_nongauss.jpg)
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
If the {com} option is set to {yes} 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.
|
||||||
|
|
||||||
|
See the "compute msd"_compute_msd.html doc page for further IMPORTANT
|
||||||
|
NOTES, which also apply to this compute.
|
||||||
|
|
||||||
|
[Output info:]
|
||||||
|
|
||||||
|
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 "this
|
||||||
|
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||||
|
options.
|
||||||
|
|
||||||
|
The vector values are "intensive". The first vector value will be in
|
||||||
|
distance^2 "units"_units.html, the second is in distance^4 units, and
|
||||||
|
the 3rd is dimensionless.
|
||||||
|
|
||||||
|
[Restrictions:]
|
||||||
|
|
||||||
|
This compute is part of the MISC package. It is only enabled if LAMMPS
|
||||||
|
was built with that package. See the "Making
|
||||||
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"compute msd"_compute_msd.html
|
||||||
|
|
||||||
|
[Default:]
|
||||||
|
|
||||||
|
The option default is com = no.
|
||||||
Loading…
Reference in New Issue