Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/fix_store_coord.html
348d238aff25lammm-master-deprecated

Last Change
Raw File

fix_store_coord.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>fix store/coord command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID store/coord keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>store/coord = style name of this fix 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>fix 1 all store/coord
fix 1 upper store/coord com yes
</PRE>
<P><B>Description:</B>
</P>
<P>Store the original coordinates of atoms in the group at the time the
fix command is issued. This is used for computing a displacement of
the atoms at later times, via the <A HREF = "compute_displace_atom.html">compute
displace/atom</A> command. Or the original
coordinates can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A> that use per-atom quantities such as
the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>IMPORTANT NOTE: The original 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
fix by using the <A HREF = "set.html">set image</A> command.
</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,
and its original coordinates may not be what you expect. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details.
</P>
<P>If the <I>com</I> keyword is set to <I>yes</I> then the position
of each atom relative to the center-of-mass of the group of
atoms is stored, instead of the absolute position. This option
is used by the <A HREF = "compute_msd.html">compute msd</A> command.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
restart files</A>, so that the values can be restored when a
simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix produces a per-atom array which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The number of columns
for each atom is 3, and the columns store the original unwrapped
x,y,z coords of each atom. The per-atom values be accessed on any
timestep.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
displace/atom</A>, <A HREF = "fix_store_force.html">fix
store/force</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
</P>
</HTML>
c4science · Help