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rLAMMPS lammps
compute_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>
compute msd command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID msd keyword values ...
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
msd = style name of this compute command
<LI>
zero or more keyword/value pairs may be appended
<LI>
keyword =
<I>
com
</I>
or
<I>
average
</I>
<PRE>
<I>
com
</I>
value =
<I>
yes
</I>
or
<I>
no
</I>
<I>
average
</I>
value =
<I>
yes
</I>
or
<I>
no
</I>
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 all msd
compute 1 upper msd com yes average yes
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the
<A
HREF =
"compute_msd_nongauss.html"
>
compute
msd/nongauss
</A>
command.
</P>
<P>
A vector of four quantites is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element 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 (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>
The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the
<I>
average
</I>
keyword is set to
<I>
yes
</I>
.
The value of the displacement will be
0.0 for atoms not in the specified compute group.
</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 calculated.
</P>
<P>
If the
<I>
average
</I>
option is set to
<I>
yes
</I>
then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.
</P>
<P>
IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the
<A
HREF =
"dump.html"
>
dump
custom
</A>
command for a discussion of "unwrapped" coordinates.
See the Atoms section of the
<A
HREF =
"read_data.html"
>
read_data
</A>
command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the
<A
HREF =
"set.html"
>
set image
</A>
command.
</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>
,
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with atom reference positions from the restart file.
When
<I>
average
</I>
is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.
</P>
<P><B>
Output info:
</B>
</P>
<P>
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 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 vector values will be in
distance^2
<A
HREF =
"units.html"
>
units
</A>
.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"compute_msd_nongauss.html"
>
compute msd/nongauss
</A>
,
<A
HREF =
"compute_displace_atom.html"
>
compute
displace_atom
</A>
,
<A
HREF =
"fix_store_state.html"
>
fix
store/state
</A>
,
<A
HREF =
"compute_msd_chunk.html"
>
compute
msd/chunk
</A>
</P>
<P><B>
Default:
</B>
</P>
<P>
The option default are com = no, average = no.
</P>
</HTML>
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