forked from lijiext/lammps
84 lines
2.5 KiB
Plaintext
84 lines
2.5 KiB
Plaintext
.. index:: compute gyration
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compute gyration command
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========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID gyration
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* gyration = style name of this compute command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 molecule gyration
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Description
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"""""""""""
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Define a computation that calculates the radius of gyration Rg of the
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group of atoms, including all effects due to atoms passing thru
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periodic boundaries.
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Rg is a measure of the size of the group of atoms, and is computed as
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the square root of the Rg^2 value in this formula
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.. image:: Eqs/compute_gyration.jpg
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:align: center
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where M is the total mass of the group, Rcm is the center-of-mass
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position of the group, and the sum is over all atoms in the group.
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A Rg^2 tensor, stored as a 6-element vector, is also calculated by
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this compute. The formula for the components of the tensor is the
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same as the above formula, except that (Ri - Rcm)^2 is replaced by
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(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
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components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
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that unlike the scalar Rg, each of the 6 values of the tensor is
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effectively a "squared" value, since the cross-terms may be negative
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and taking a sqrt() would be invalid.
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.. note::
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The coordinates of an atom contribute to Rg in "unwrapped" form,
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by using the image flags associated with each atom. See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
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See the Atoms section of the :doc:`read_data <read_data>` command for a
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discussion of image flags and how they are set for each atom. You can
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reset the image flags (e.g. to 0) before invoking this compute by
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using the :doc:`set image <set>` command.
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**Output info:**
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This compute calculates a global scalar (Rg) and a global vector of
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length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
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values can be used by any command that uses a global scalar value or
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vector values from a compute as input. See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
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options.
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The scalar and vector values calculated by this compute are
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"intensive". The scalar and vector values will be in distance and
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distance^2 :doc:`units <units>` respectively.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute gyration/chunk <compute_gyration_chunk>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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