forked from lijiext/lammps
123 lines
4.2 KiB
Plaintext
123 lines
4.2 KiB
Plaintext
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.. index:: compute gyration/chunk
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compute gyration/chunk 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/chunk chunkID keyword value ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* gyration/chunk = style name of this compute command
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* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
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* zero or more keyword/value pairs may be appended
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* keyword = *tensor*
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.. parsed-literal::
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*tensor* value = none
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Examples
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""""""""
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.. parsed-literal::
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compute 1 molecule gyration/chunk molchunk
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compute 2 molecule gyration/chunk molchunk tensor
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Description
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"""""""""""
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Define a computation that calculates the radius of gyration Rg for
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multiple chunks of atoms.
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In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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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
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defined and examples of how they can be used to measure properties of
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a system.
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This compute calculates the radius of gyration Rg for each chunk,
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which includes all effects due to atoms passing thru periodic
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boundaries.
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Rg is a measure of the size of a chunk, and is computed by this
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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 chunk, Rcm is the center-of-mass
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position of the chunk, and the sum is over all atoms in the
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chunk.
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Note that only atoms in the specified group contribute to the
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calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
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defines its own group; atoms will have a chunk ID = 0 if they are not
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
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"all" group for this command if you simply want to include atoms with
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non-zero chunk IDs.
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If the *tensor* keyword is specified, then the scalar Rg value is not
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calculated, but an Rg tensor is instead calculated for each chunk.
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The formula for the components of the tensor is the same as the above
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formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
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Rcmy) for the xy component, etc. The 6 components of the tensor are
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ordered xx, yy, zz, xy, xz, yz.
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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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The simplest way to output the results of the compute gyration/chunk
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calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
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command, for example:
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.. parsed-literal::
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compute cc1 all chunk/atom molecule
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compute myChunk all gyration/chunk cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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**Output info:**
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This compute calculates a global vector if the *tensor* keyword is not
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specified and a global array if it is. The length of the vector or
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number of rows in the array = the number of chunks *Nchunk* as
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calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. If the *tensor* keyword
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is specified, the global array has 6 columns. The vector or array can
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be accessed by any command that uses global values from a compute as
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input. See :ref:`this section <howto_15>` for an overview
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of LAMMPS output options.
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All the vector or array values calculated by this compute are
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"intensive". The vector or array values will be in distance
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:doc:`units <units>`, since they are the square root of values
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represented by the formula above.
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Restrictions
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""""""""""""
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none
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**Related commands:** none
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:doc:`compute gyration <compute_gyration>`
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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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