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.. index:: compute dipole/chunk
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compute dipole/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 dipole/chunk chunkID charge-correction
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* dipole/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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* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional)
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Examples
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""""""""
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.. parsed-literal::
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compute 1 fluid dipole/chunk molchunk
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compute dw water dipole/chunk 1 geometry
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Description
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"""""""""""
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Define a computation that calculates the dipole vector and total dipole
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for 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 x,y,z coordinates of the dipole vector
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and the total dipole moment for each chunk, which includes all effects
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due to atoms passing thru periodic boundaries. For chunks with a net
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charge the resulting dipole is made position independent by subtracting
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the position vector of the center of mass or geometric center times the
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net charge from the computed dipole vector.
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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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dipole 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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.. parsed-literal::
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compute cc1 all chunk/atom molecule
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compute myChunk all dipole/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 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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4 for the x,y,z dipole vector components and the total dipole of each
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chunk. These values can be accessed by any command that uses global
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array 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 array values are "intensive". The array values will be in
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dipole units, i.e. charge units times 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/chunk <compute_com_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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.. index:: write_coeff
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write_coeff command
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===================
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Syntax
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""""""
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.. parsed-literal::
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write_coeff file
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.. parsed-literal::
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file = name of data file to write out
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Examples
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""""""""
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.. parsed-literal::
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write_coeff polymer.coeff
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Description
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"""""""""""
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Write a text format file with the currently defined force field
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coefficients in a way, that it can be read by LAMMPS with the
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:doc:`include <include>` command. In combination with the nocoeff
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option of :doc:`write_data <write_data>` this can be used to move
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the Coeffs sections from a data file into a separate file.
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.. note::
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The write_coeff command is not yet fully implemented in two
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respects. First, some pair styles do not yet write their coefficient
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information into the coeff file. This means you will need to specify
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that information in your input script that reads the data file, via
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the :doc:`pair_coeff <pair_coeff>` command.
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----------
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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:`read_data <read_data>`, :doc:`write_restart <write_restart>`,
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:doc:`write_data <write_data>`
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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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