2009-12-04 07:58:51 +08:00
|
|
|
<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>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
2009-12-04 08:42:15 +08:00
|
|
|
<PRE>compute 1 all msd
|
|
|
|
|
compute 1 upper msd com yes
|
2009-12-04 07:58:51 +08:00
|
|
|
</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
|
2013-06-01 00:50:53 +08:00
|
|
|
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.
|
2009-12-04 07:58:51 +08:00
|
|
|
</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
|
2013-11-06 01:25:58 +08:00
|
|
|
and averaged over atoms in the group. The 4th element is the total
|
2009-12-04 07:58:51 +08:00
|
|
|
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
|
|
|
|
|
averaged over atoms in the group.
|
|
|
|
|
</P>
|
2009-12-04 08:42:15 +08:00
|
|
|
<P>The slope of the mean-squared displacement (MSD) versus time is
|
|
|
|
|
proportional to the diffusion coefficient of the diffusing atoms.
|
2009-12-04 07:58:51 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The displacement of an atom is from its original position at the time
|
2013-06-01 00:50:53 +08:00
|
|
|
the compute command was issued. The value of the displacement will be
|
|
|
|
|
0.0 for atoms not in the specified compute group.
|
2009-12-04 07:58:51 +08:00
|
|
|
</P>
|
2010-06-04 08:14:14 +08:00
|
|
|
<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
|
2013-06-01 00:50:53 +08:00
|
|
|
displacment of each atom is calcluated.
|
|
|
|
|
</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.
|
2009-12-04 07:58:51 +08:00
|
|
|
</P>
|
|
|
|
|
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
|
|
|
|
|
rigid</A> command), it's periodic image flags are altered,
|
2009-12-04 08:42:15 +08:00
|
|
|
and its contribution to the MSD may not reflect its true contribution.
|
|
|
|
|
See the <A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to
|
|
|
|
|
compute the MSD of rigid bodies as they cross periodic boundaries, you
|
|
|
|
|
will need to post-process a <A HREF = "dump.html">dump file</A> containing
|
|
|
|
|
coordinates of the atoms in the bodies.
|
2009-12-04 07:58:51 +08:00
|
|
|
</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 created fix will also have the same ID, and
|
|
|
|
|
thus be initialized correctly with atom coordinates from the restart
|
|
|
|
|
file.
|
|
|
|
|
</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
|
2011-08-26 01:01:01 +08:00
|
|
|
from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
|
|
|
|
|
section</A> for an overview of LAMMPS output
|
|
|
|
|
options.
|
2009-12-04 07:58:51 +08:00
|
|
|
</P>
|
2010-03-03 05:51:16 +08:00
|
|
|
<P>The vector values are "intensive". The vector values will be in
|
|
|
|
|
distance^2 <A HREF = "units.html">units</A>.
|
2010-01-24 07:20:05 +08:00
|
|
|
</P>
|
2009-12-04 07:58:51 +08:00
|
|
|
<P><B>Restrictions:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
2013-06-01 00:50:53 +08:00
|
|
|
<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
|
2010-06-04 08:37:28 +08:00
|
|
|
store/state</A>, <A HREF = "compute_msd_molecule.html">compute
|
2009-12-22 01:34:52 +08:00
|
|
|
msd/molecule</A>
|
2009-12-04 07:58:51 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The option default is com = no.
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
