git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/src/compute_property_chunk.txt

@@ -0,0 +1,118 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute property/chunk command :h3
+
+[Syntax:]
+
+compute ID group-ID property/chunk chunkID input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+property/chunk = style name of this compute command :l
+input = one or more attributes :l
+  attributes = count, id, coord1, coord2, coord3
+    count = # of atoms in chunk 
+    id = original chunk IDs before compression by "compute chunk/atom"_compute_chunk_atom.html
+    coord123 = coordinates for spatial bins calculated by "compute chunk/atom"_compute_chunk_atom.html :pre
+:ule
+
+[Examples:]
+
+compute 1 all property/chunk count
+compute 1 all property/chunk ID coord1 :pre
+
+[Description:]
+
+Define a computation that stores the specified attributes of chunks of
+atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a "compute
+chunk/atom"_compute_chunk_atom.html 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 "compute
+chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
+23"_Section_howto.html#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 and stores the specified attributes of chunks
+as global data so they can be accessed by other "output
+commands"_Section_howto.html#howto_15 and used in conjunction with
+other commands that generate per-chunk data, such as "compute
+com/chunk"_compute_com_chunk.html or "compute
+msd/chunk"_compute_msd_chunk.html.
+
+Note that only atoms in the specified group contribute to the
+calculation of the {count} attribute.  The "compute
+chunk/atom"_compute_chunk_atom.html 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.
+
+The {count} attribute is the number of atoms in the chunk.
+
+The {id} attribute stores the original chunk ID for each chunk.  It
+can only be used if the {compress} keyword was set to {yes} for the
+"compute chunk/atom"_compute_chunk_atom.html command referenced by
+chunkID.  This means that the original chunk IDs (e.g. molecule IDs)
+will have been compressed to remove chunk IDs with no atoms assigned
+to them.  Thus a compresed chunk ID of 3 may correspond to an original
+chunk ID (molecule ID in this case) of 415.  The {id} attribute will
+then be 415 for the 3rd chunk.
+
+The {coordN} attributes can only be used if a {binning} style was used
+in the "compute chunk/atom"_compute_chunk_atom.html command referenced
+by chunkID.  For {bin/1d}, {bin/2d}, and {bin/3d} styles the attribute
+is the center point of the bin in the corresponding dimension.  Style
+{bin/1d} only defines a {coord1} attribute.  Style {bin/2d} adds a
+{coord2} attribute.  Style {bin/3d} adds a {coord3} attribute.
+
+Note that if the value of the {units} keyword used in the "compute
+chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the
+{coordN} attributes will be in distance "units"_units.html.  If the
+value of the {units} keyword is {reduced}, the {coordN} attributes
+will be in unitless reduced units (0-1).
+
+The simplest way to output the results of the compute property/chunk
+calculation to a file is to use the "fix ave/time"_fix_ave_time.html
+command, for example:
+
+compute cc1 all chunk/atom molecule
+compute myChunk1 all property/chunk cc1
+compute myChunk2 all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector :pre
+
+[Output info:]
+
+This compute calculates a global vector or global array depending on
+the number of input values.  The length of the vector or number of
+rows in the array is the number of chunks.
+
+This compute calculates a global vector or global array where the
+number of rows = the number of chunks {Nchunk} as calculated by the
+specified "compute chunk/atom"_compute_chunk_atom.html command.  If a
+single input is specified, a global vector is produced.  If two or
+more inputs are specified, a global array is produced where the number
+of columns = the number of inputs.  The vector or array can be
+accessed by any command that uses global values from a compute as
+input.  See "this section"_Section_howto.html#howto_15 for an overview
+of LAMMPS output options.
+
+The vector or array values are "intensive".  The values will be
+unitless or in the units discussed above.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix ave/chunk"_fix_ave_chunk.html
+
+[Default:] none