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

doc/html/_sources/compute_gyration.txt

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+.. index:: compute gyration
+
+compute gyration command
+========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID gyration
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gyration = style name of this compute command
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 molecule gyration
+
+Description
+"""""""""""
+
+Define a computation that calculates the radius of gyration Rg of the
+group of atoms, including all effects due to atoms passing thru
+periodic boundaries.
+
+Rg is a measure of the size of the group of atoms, and is computed as
+the square root of the Rg^2 value in this formula
+
+.. image:: Eqs/compute_gyration.jpg
+   :align: center
+
+where M is the total mass of the group, Rcm is the center-of-mass
+position of the group, and the sum is over all atoms in the group.
+
+A Rg^2 tensor, stored as a 6-element vector, is also calculated by
+this compute.  The formula for the components of the tensor is the
+same as the above formula, except that (Ri - Rcm)^2 is replaced by
+(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc.  The 6
+components of the vector are ordered xx, yy, zz, xy, xz, yz.  Note
+that unlike the scalar Rg, each of the 6 values of the tensor is
+effectively a "squared" value, since the cross-terms may be negative
+and taking a sqrt() would be invalid.
+
+.. note::
+
+   The coordinates of an atom contribute to Rg 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.
+
+**Output info:**
+
+This compute calculates a global scalar (Rg) and a global vector of
+length 6 (Rg^2 tensor), which can be accessed by indices 1-6.  These
+values can be used by any command that uses a global scalar value or
+vector values from a compute as input.  See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
+options.
+
+The scalar and vector values calculated by this compute are
+"intensive".  The scalar and vector values will be in distance and
+distance^2 :doc:`units <units>` respectively.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute gyration/chunk <compute_gyration_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm