2008-01-04 08:56:10 +08:00
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<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>
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<HR>
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<H3>compute displace/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2009-12-04 05:44:11 +08:00
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<PRE>compute ID group-ID displace/atom
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2008-01-04 08:56:10 +08:00
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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2009-12-04 05:44:11 +08:00
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<LI>displace/atom = style name of this compute command
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2008-01-04 08:56:10 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2009-12-04 05:44:11 +08:00
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<PRE>compute 1 all displace/atom
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2008-01-04 08:56:10 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the current displacement of each
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atom in the group from its original coordinates, including all effects
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2009-12-04 07:58:11 +08:00
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due to atoms passing thru periodic boundaries.
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</P>
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2009-12-04 08:04:34 +08:00
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<P>A vector of four quantites per atom is calculated by this compute.
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The first 3 elements of the vector are the dx,dy,dz displacements.
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2009-12-04 07:58:11 +08:00
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The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
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dz*dz).
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2009-11-30 23:48:33 +08:00
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</P>
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2009-12-04 08:04:34 +08:00
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<P>The displacement of an atom is from its original position at the time
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the compute command was issued. To store the original coordinates,
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2010-06-04 08:37:28 +08:00
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the compute creates its own fix of style "store/state", as if this
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command had been issued:
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2009-12-04 05:44:11 +08:00
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</P>
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2010-06-04 08:37:28 +08:00
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<PRE>fix compute-ID_store_state group-ID store/state xu yu zu
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2009-12-04 05:44:11 +08:00
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</PRE>
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2010-06-04 08:37:28 +08:00
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<P>See the <A HREF = "fix_store_state.html">fix store/state</A> command for details.
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Note that the ID of the new fix is the compute-ID + underscore +
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"store/state", and the group for the new fix is the same as the
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compute group.
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2009-12-04 05:44:11 +08:00
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</P>
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2009-12-04 07:58:11 +08:00
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<P>The value of the displacement will be 0.0 for atoms not in the
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specified compute group.
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</P>
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2010-06-04 08:37:28 +08:00
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<P>IMPORTANT NOTE: Fix store/state stores the initial coordinates in
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2009-12-04 05:44:11 +08:00
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"unwrapped" form, by using the image flags associated with each atom.
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See the <A HREF = "dump.html">dump custom</A> command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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2009-11-30 23:48:33 +08:00
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<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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2009-12-04 05:44:11 +08:00
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(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
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2009-11-30 23:48:33 +08:00
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image</A> command.
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</P>
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2009-12-04 07:58:11 +08:00
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<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
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rigid</A> command), it's periodic image flags are altered,
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2009-12-04 08:42:15 +08:00
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and the computed displacement may not reflect its true displacement.
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2009-12-04 08:04:34 +08:00
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See the <A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to
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compute the displacement of rigid bodies as they cross periodic
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boundaries, you will need to post-process a <A HREF = "dump.html">dump file</A>
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containing coordinates of the atoms in the bodies.
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2008-01-04 08:56:10 +08:00
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</P>
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2009-12-04 05:51:22 +08:00
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<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
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to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
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then you should use the same ID for this compute, as in the original
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run. This is so that the created fix will also have the same ID, and
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thus be initialized correctly with atom coordinates from the restart
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file.
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</P>
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2008-01-04 08:56:10 +08:00
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<P><B>Output info:</B>
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</P>
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2009-12-05 05:04:00 +08:00
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<P>This compute calculates a per-atom array with 4 columns, which can be
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accessed by indices 1-4 by any command that uses per-atom values from
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a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
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overview of LAMMPS output options.
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2008-01-04 08:56:10 +08:00
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</P>
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2010-01-24 07:20:05 +08:00
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<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
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</P>
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2008-01-04 08:56:10 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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2010-06-04 08:37:28 +08:00
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<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_state.html">fix
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store/state</A>
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2008-01-04 08:56:10 +08:00
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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