forked from lijiext/lammps
96 lines
3.2 KiB
Plaintext
96 lines
3.2 KiB
Plaintext
.. index:: compute com/chunk
|
|
|
|
compute com/chunk command
|
|
=========================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
compute ID group-ID com/chunk chunkID
|
|
|
|
* ID, group-ID are documented in :doc:`compute <compute>` command
|
|
* com/chunk = style name of this compute command
|
|
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
compute 1 fluid com/chunk molchunk
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Define a computation that calculates the center-of-mass 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 center-of-mass
|
|
for each chunk, which includes all effects due to atoms passing thru
|
|
periodic boundaries.
|
|
|
|
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
|
|
center-of-mass 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 com/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 =
|
|
3 for the x,y,z center-of-mass coordinates 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
|
|
distance :doc:`units <units>`.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
none
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`compute com <compute_com>`
|
|
|
|
**Default:** none
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|