95 lines
3.1 KiB
ReStructuredText
95 lines
3.1 KiB
ReStructuredText
.. index:: compute com/chunk
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compute com/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 com/chunk chunkID
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* com/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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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 fluid com/chunk molchunk
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Description
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"""""""""""
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Define a computation that calculates the center-of-mass for multiple
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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>` and :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 x,y,z coordinates of the center-of-mass
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for each chunk, which includes all effects due to atoms passing through
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periodic boundaries.
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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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.. note::
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The coordinates of an atom contribute to the chunk's
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center-of-mass in "unwrapped" form, by using the image flags
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associated with each atom. See the :doc:`dump custom <dump>` command
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for a discussion of "unwrapped" coordinates. See the Atoms section of
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the :doc:`read_data <read_data>` command for a discussion of image flags
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and how they are set for each atom. You can reset the image flags
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(e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
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The simplest way to output the results of the compute com/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 com/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 array where the number of rows = the
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number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
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3 for the x,y,z center-of-mass coordinates of each chunk. These
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values can be accessed by any command that uses global array values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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The array values are "intensive". The array values will be in
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distance :doc:`units <units>`.
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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 com <compute_com>`
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Default
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"""""""
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none
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