132 lines
4.4 KiB
ReStructuredText
132 lines
4.4 KiB
ReStructuredText
.. 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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.. code-block:: LAMMPS
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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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.. code-block:: LAMMPS
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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 :math:`R_g` for
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multiple chunks of atoms.
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In LAMMPS, chunks are collections of atoms defined by a
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: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.
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See the :doc:`compute chunk/atom <compute_chunk_atom>` and
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:doc:`Howto chunk <Howto_chunk>`
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doc pages for details of how chunks can be defined and examples of how
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they can be used to measure properties of a system.
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This compute calculates the radius of gyration :math:`R_g` for each chunk,
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which includes all effects due to atoms passing through periodic
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boundaries.
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:math:`R_g` is a measure of the size of a chunk, and is computed by the
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formula
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.. math::
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R_g^2 = \frac{1}{M} \sum_i m_i (r_i - r_{\text{cm}})^2
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where :math:`M` is the total mass of the chunk, :math:`r_{\text{cm}}` is
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the center-of-mass 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 :math:`R_g` value is not
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calculated, but an :math:`R_g` 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 :math:`(r_i - r_{\text{cm}})^2` is replaced by
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:math:`(r_{i,x} - r_{\text{cm},x}) \cdot (r_{i,y} - r_{\text{cm},y})` for the
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:math:`xy` component, and so on. The six components of the tensor are
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ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
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.. note::
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The coordinates of an atom contribute to :math:`R_g` in "unwrapped" form,
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by using the image flags associated with each atom. See the :doc:`dump custom <dump>`
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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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.. code-block:: LAMMPS
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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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"""""""""""
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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>`
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command. If the *tensor* keyword is specified, the global array has six
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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 the :doc:`Howto output <Howto_output>` page for an
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overview 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
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""""""""""""""""
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none
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:doc:`compute gyration <compute_gyration>`
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Default
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"""""""
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none
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