Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/_sources/compute_gyration.txt
9cf43f2a0b7fefficient_neuronet

Last Change
Raw File

compute_gyration.txt
View Options

.. 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
c4science · Help