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 05:44:11 +08:00
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due to atoms passing thru periodic boundaries. Four quantites per
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atom are computed: the x,y,z displacements and the total displacement.
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See below for details.
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2009-11-30 23:48:33 +08:00
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</P>
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2009-12-04 05:44:11 +08:00
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<P>To store the original coordinates at the time this compute is issued,
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the compute creates its own fix of style "coord/original", as if this
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command had been issued:
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</P>
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<PRE>fix compute-ID_coord_original group-ID coord/original
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</PRE>
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<P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for
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details. Note that the ID of the new fix is the compute-ID +
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underscore + "coord_original", and the group for the new fix is
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the same as the compute group.
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</P>
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<P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
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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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<P>The displacements can be output directly via the <A HREF = "dump.html">dump
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custom</A> command.
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2008-01-04 08:56:10 +08:00
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</P>
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<P>The value of the displacement will be 0.0 for atoms not in the
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2009-12-04 05:44:11 +08:00
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specified compute group.
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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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<P>This compute calculates a vector of length 4 for each atom, which can
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be accessed by indices 1-4 by any command that uses per-atom computes
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as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview
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of LAMMPS output options. The first 3 components of the vector are
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the x,y,z displacements. The 4th component is the total displacement,
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i.e. sqrt(dx*dx + dy*dy + dz*dz).
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</P>
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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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<P><A HREF = "dump.html">dump custom</A>, <A HREF = "fix_msd.html">fix msd</A>
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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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