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

doc/html/_sources/compute_msd_chunk.txt

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+.. index:: compute msd/chunk
+
+compute msd/chunk command
+=========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID msd/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* msd/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 all msd/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the mean-squared displacement
+(MSD) for multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` doc page and ":ref:`Section_howto 23 <howto_23>` for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+
+Four quantites are calculated by this compute for each chunk.  The
+first 3 quantities are the squared dx,dy,dz displacements of the
+center-of-mass.  The 4th component is the total squared displacement,
+i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These
+calculations include all effects due to atoms passing thru periodic
+boundaries.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing chunks.
+
+The displacement of the center-of-mass of the chunk is from its
+original center-of-mass position, calculated on the timestep this
+compute command was first invoked.
+
+.. note::
+
+   The number of chunks *Nchunk* calculated by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant each
+   time this compute is invoked, so that the displacement for each chunk
+   from its original position can be computed consistently.  If *Nchunk*
+   does not remain constant, an error will be generated.  If needed, you
+   can enforce a constant *Nchunk* by using the *nchunk once* or *ids
+   once* options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+
+.. note::
+
+   This compute stores the original position (of the
+   center-of-mass) of each chunk.  When a displacement is calculated on a
+   later timestep, it is assumed that the same atoms are assigned to the
+   same chunk ID.  However LAMMPS has no simple way to insure this is the
+   case, though you can use the *ids once* option when specifying the
+   :doc:`compute chunk/atom <compute_chunk_atom>` command.  Note that if
+   this is not the case, the MSD calculation does not have a sensible
+   meaning.
+
+.. note::
+
+   The initial coordinates of the atoms in each chunk 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-chunk
+   quantities will also have the same ID, and thus be initialized
+   correctly with chunk reference positions from the restart file.
+
+The simplest way to output the results of the compute com/msd
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all com/msd cc1
+   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+4 for dx,dy,dz and the total displacement.  These values can be
+accessed by any command that uses global array values from a compute
+as input.  See :ref:`this section <howto_15>` for an
+overview of LAMMPS output options.
+
+The array values are "intensive".  The array values will be in
+distance^2 :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute msd <compute_msd>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm