Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F73556563
fix_store_coord.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
Mon, Jul 22, 16:27
Size
3 KB
Mime Type
text/html
Expires
Wed, Jul 24, 16:27 (2 d)
Engine
blob
Format
Raw Data
Handle
19223244
Attached To
rLAMMPS lammps
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 coord/original command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID coord/original keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>coord/original = 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 coord/original
fix 1 upper coord/original 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>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
</P>
</HTML>
Event Timeline
Log In to Comment