git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/compute_msd.txt

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+.. index:: compute msd
+
+compute msd command
+===================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID msd keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* msd = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *com* or *average*
+.. parsed-literal::
+
+     *com* value = *yes* or *no*
+     *average* value = *yes* or *no*
+
+
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 all msd
+   compute 1 upper msd com yes average yes
+
+Description
+"""""""""""
+
+Define a computation that calculates the mean-squared displacement
+(MSD) of the group of atoms, including all effects due to atoms
+passing thru periodic boundaries.  For computation of the non-Gaussian
+parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <compute_msd_nongauss>` command.
+
+A vector of four quantites is calculated by this compute.  The first 3
+elements of the vector are the squared dx,dy,dz displacements, summed
+and averaged over atoms in the group.  The 4th element is the total
+squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
+averaged over atoms in the group.
+
+The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing atoms.
+
+The displacement of an atom is from its reference position. This is
+normally the original position at the time
+the compute command was issued, unless the *average* keyword is set to *yes*\ .  
+The value of the displacement will be
+0.0 for atoms not in the specified compute group.
+
+If the *com* option is set to *yes* then the effect of any drift in
+the center-of-mass of the group of atoms is subtracted out before the
+displacment of each atom is calculated.
+
+If the *average* option is set to *yes* then the reference position of
+an atom is based on the average position of that atom, corrected for
+center-of-mass motion if requested.  The average position is a running
+average over all previous calls to the compute, including the current
+call. So on the first call it is current position, on the second call
+it is the arithmetic average of the current position and the position
+on the first call, and so on.  Note that when using this option, the
+precise value of the mean square displacement will depend on the
+number of times the compute is called. So, for example, changing the
+frequency of thermo output may change the computed displacement. Also,
+the precise values will be changed if a single simulation is broken up
+into two parts, using either multiple run commands or a restart
+file. It only makes sense to use this option if the atoms are not
+diffusing, so that their average positions relative to the center of
+mass of the system are stationary. The most common case is crystalline
+solids undergoing thermal motion.
+
+.. note::
+
+   Initial coordinates are stored in "unwrapped" form, by using the
+   image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   See the Atoms section of the :doc:`read_data <read_data>` 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 compute by
+   using the :doc:`set image <set>` command.
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-atom
+   quantities will also have the same ID, and thus be initialized
+   correctly with atom reference positions from the restart file.  When
+   *average* is set to yes, then the atom reference positions are
+   restored correctly, but not the number of samples used obtain them. As
+   a result, the reference positions from the restart file are combined
+   with subsequent positions as if they were from a single sample,
+   instead of many, which will change the values of msd somewhat.
+
+**Output info:**
+
+This compute calculates a global vector of length 4, which can be
+accessed by indices 1-4 by any command that uses global vector values
+from a compute as input.  See :ref:`this section <howto_15>` for an overview of LAMMPS output
+options.
+
+The vector values are "intensive".  The vector values will be in
+distance^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd/nongauss <compute_msd_nongauss>`, :doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`, :doc:`compute msd/chunk <compute_msd_chunk>`
+
+Default
+"""""""
+
+The option default are com = no, average = no.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm