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rLAMMPS lammps
compute_property_chunk.html
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<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
compute property/chunk command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID property/chunk chunkID input1 input2 ...
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
property/chunk = style name of this compute command
<LI>
input = one or more attributes
<PRE>
attributes = count, id, coord1, coord2, coord3
count = # of atoms in chunk
id = original chunk IDs before compression by
<A
HREF =
"compute_chunk_atom.html"
>
compute chunk/atom
</A>
coord123 = coordinates for spatial bins calculated by
<A
HREF =
"compute_chunk_atom.html"
>
compute chunk/atom
</A>
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 all property/chunk count
compute 1 all property/chunk ID coord1
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a computation that stores the specified attributes of chunks of
atoms.
</P>
<P>
In LAMMPS, chunks are collections of atoms defined by a
<A
HREF =
"compute_chunk_atom.html"
>
compute
chunk/atom
</A>
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
<A
HREF =
"compute_chunk_atom.html"
>
compute
chunk/atom
</A>
doc page and "
<A
HREF =
"Section_howto.html#howto_23"
>
Section_howto
23
</A>
for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
</P>
<P>
This compute calculates and stores the specified attributes of chunks
as global data so they can be accessed by other
<A
HREF =
"Section_howto.html#howto_15"
>
output
commands
</A>
and used in conjunction with
other commands that generate per-chunk data, such as
<A
HREF =
"compute_com_chunk.html"
>
compute
com/chunk
</A>
or
<A
HREF =
"compute_msd_chunk.html"
>
compute
msd/chunk
</A>
.
</P>
<P>
Note that only atoms in the specified group contribute to the
calculation of the
<I>
count
</I>
attribute. The
<A
HREF =
"compute_chunk_atom.html"
>
compute
chunk/atom
</A>
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.
</P>
<P>
The
<I>
count
</I>
attribute is the number of atoms in the chunk.
</P>
<P>
The
<I>
id
</I>
attribute stores the original chunk ID for each chunk. It
can only be used if the
<I>
compress
</I>
keyword was set to
<I>
yes
</I>
for the
<A
HREF =
"compute_chunk_atom.html"
>
compute chunk/atom
</A>
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
<I>
id
</I>
attribute will
then be 415 for the 3rd chunk.
</P>
<P>
The
<I>
coordN
</I>
attributes can only be used if a
<I>
binning
</I>
style was used
in the
<A
HREF =
"compute_chunk_atom.html"
>
compute chunk/atom
</A>
command referenced
by chunkID. For
<I>
bin/1d
</I>
,
<I>
bin/2d
</I>
, and
<I>
bin/3d
</I>
styles the attribute
is the center point of the bin in the corresponding dimension. Style
<I>
bin/1d
</I>
only defines a
<I>
coord1
</I>
attribute. Style
<I>
bin/2d
</I>
adds a
<I>
coord2
</I>
attribute. Style
<I>
bin/3d
</I>
adds a
<I>
coord3
</I>
attribute.
</P>
<P>
Note that if the value of the
<I>
units
</I>
keyword used in the
<A
HREF =
"compute_chunk_atom.html"
>
compute
chunk/atom command
</A>
is
<I>
box
</I>
or
<I>
lattice
</I>
, the
<I>
coordN
</I>
attributes will be in distance
<A
HREF =
"units.html"
>
units
</A>
. If the
value of the
<I>
units
</I>
keyword is
<I>
reduced
</I>
, the
<I>
coordN
</I>
attributes
will be in unitless reduced units (0-1).
</P>
<P>
The simplest way to output the results of the compute property/chunk
calculation to a file is to use the
<A
HREF =
"fix_ave_time.html"
>
fix ave/time
</A>
command, for example:
</P>
<PRE>
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>
<P><B>
Output info:
</B>
</P>
<P>
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.
</P>
<P>
This compute calculates a global vector or global array where the
number of rows = the number of chunks
<I>
Nchunk
</I>
as calculated by the
specified
<A
HREF =
"compute_chunk_atom.html"
>
compute chunk/atom
</A>
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
<A
HREF =
"Section_howto.html#howto_15"
>
this section
</A>
for an overview
of LAMMPS output options.
</P>
<P>
The vector or array values are "intensive". The values will be
unitless or in the units discussed above.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"fix_ave_chunk.html"
>
fix ave/chunk
</A>
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
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