2009-12-04 07:58:51 +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 msd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID msd keyword values ...
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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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<LI>msd = style name of this compute command
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>com</I>
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<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
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</PRE>
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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 08:42:15 +08:00
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<PRE>compute 1 all msd
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compute 1 upper msd com yes
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2009-12-04 07:58:51 +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 mean-squared displacement
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(MSD) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries.
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</P>
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<P>A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th component is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.
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</P>
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2009-12-04 08:42:15 +08:00
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<P>The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing atoms.
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2009-12-04 07:58:51 +08:00
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</P>
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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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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>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift
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in the center-of-mass of the group of atoms is subtracted out before
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the displacment of each atom is calcluated. The <I>com</I> option
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is also passed to the created fix coord/original.
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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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<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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(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
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image</A> command.
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</P>
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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 its contribution to the MSD may not reflect its true contribution.
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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 MSD of rigid bodies as they cross periodic boundaries, you
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will need to post-process a <A HREF = "dump.html">dump file</A> containing
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coordinates of the atoms in the bodies.
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2009-12-04 07:58:51 +08:00
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</P>
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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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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 by any command that uses global vector values
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from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
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for an overview of LAMMPS output options.
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</P>
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<P>The vector values are "intensive", meaning they are independent of the
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number of atoms in the simulation.
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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 = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_coord_original.html">fix
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coord/original</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option default is com = no.
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</P>
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</HTML>
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