.. 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
""""""""

.. code-block:: LAMMPS

   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 through
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

.. math::

 {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2

where :math:`M` is the total mass of the group, :math:`r_{cm}` is the
center-of-mass position of the group, and the sum is over all atoms in
the group.

A :math:`{R_g}^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 :math:`(r_i - r_{cm})^2` is replaced
by :math:`(r_{i,x} - r_{cm,x}) \cdot (r_{i,y} - r_{cm,y})` for the xy component,
and so on.  The 6 components of the vector are ordered xx, yy, zz, xy, xz, yz.
Note that unlike the scalar :math:`R_g`, 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 :math:`R_g` 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 (:math:`R_g`) and a global vector of
length 6 (:math:`{R_g}^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 the :doc:`Howto output <Howto_output>` doc page 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>`,
:doc:`compute gyration/shape <compute_gyration_shape>`

Default
"""""""

none
