git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14879 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/_sources/compute_dipole_chunk.txt

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+.. index:: compute dipole/chunk
+
+compute dipole/chunk command
+============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID dipole/chunk chunkID charge-correction
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* dipole/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional)
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 fluid dipole/chunk molchunk 
+   compute dw water dipole/chunk 1 geometry
+
+Description
+"""""""""""
+
+Define a computation that calculates the dipole vector and total dipole
+for multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+to a single chunk (or no chunk).  The ID for this command is specified
+as chunkID.  For example, a single chunk could be the atoms in a
+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
+defined and examples of how they can be used to measure properties of
+a system.
+
+This compute calculates the x,y,z coordinates of the dipole vector
+and the total dipole moment for each chunk, which includes all effects
+due to atoms passing thru periodic boundaries. For chunks with a net
+charge the resulting dipole is made position independent by subtracting
+the position vector of the center of mass or geometric center times the
+net charge from the computed dipole vector.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation.  You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+
+.. note::
+
+   The coordinates of an atom contribute to the chunk's
+   dipole in "unwrapped" form, by using the image flags
+   associated with each atom.  See the :doc:`dump custom <dump>` command
+   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   the :doc:`read_data <read_data>` command for a discussion of image flags
+   and how they are set for each atom.  You can reset the image flags
+   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+
+The simplest way to output the results of the compute com/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+.. parsed-literal::
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all dipole/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+
+**Output info:**
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+4 for the x,y,z dipole vector components and the total dipole of each
+chunk. These values can be accessed by any command that uses global
+array values from a compute as input.  See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
+options.
+
+The array values are "intensive".  The array values will be in
+dipole units, i.e. charge units times distance :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute com/chunk <compute_com_chunk>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm

doc/_sources/write_coeff.txt

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+.. index:: write_coeff
+
+write_coeff command
+===================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   write_coeff file
+
+.. parsed-literal::
+
+   file = name of data file to write out
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   write_coeff polymer.coeff
+
+Description
+"""""""""""
+
+Write a text format file with the currently defined force field
+coefficients in a way, that it can be read by LAMMPS with the 
+:doc:`include <include>` command. In combination with the nocoeff
+option of :doc:`write_data <write_data>` this can be used to move
+the Coeffs sections from a data file into a separate file.
+
+.. note::
+
+   The write_coeff command is not yet fully implemented in two
+   respects.  First, some pair styles do not yet write their coefficient
+   information into the coeff file.  This means you will need to specify
+   that information in your input script that reads the data file, via
+   the :doc:`pair_coeff <pair_coeff>` command.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+none
+
+Related commands
+""""""""""""""""
+
+:doc:`read_data <read_data>`, :doc:`write_restart <write_restart>`,
+:doc:`write_data <write_data>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm