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lammps/doc/compute_msd_chunk.txt
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compute_msd_chunk.txt
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"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 msd/chunk command :h3
[Syntax:]
compute ID group-ID msd/chunk chunkID :pre
ID, group-ID are documented in "compute"_compute.html command
msd/chunk = style name of this compute command
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul
[Examples:]
compute 1 all msd/chunk molchunk :pre
[Description:]
Define a computation that calculates the mean-squared displacement
(MSD) for multiple 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.
Four quantites are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
calculations include all effects due to atoms passing thru periodic
boundaries.
Note that only atoms in the specified group contribute to the
calculation. 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 slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing chunks.
The displacement of the center-of-mass of the chunk is from its
original center-of-mass position, calculated on the timestep this
compute command was first invoked.
NOTE: The number of chunks {Nchunk} calculated by the "compute
chunk/atom"_compute_chunk_atom.html command must remain constant each
time this compute is invoked, so that the displacement for each chunk
from its original position can be computed consistently. If {Nchunk}
does not remain constant, an error will be generated. If needed, you
can enforce a constant {Nchunk} by using the {nchunk once} or {ids
once} options when specifying the "compute
chunk/atom"_compute_chunk_atom.html command.
NOTE: This compute stores the original position (of the
center-of-mass) of each chunk. When a displacement is calculated on a
later timestep, it is assumed that the same atoms are assigned to the
same chunk ID. However LAMMPS has no simple way to insure this is the
case, though you can use the {ids once} option when specifying the
"compute chunk/atom"_compute_chunk_atom.html command. Note that if
this is not the case, the MSD calculation does not have a sensible
meaning.
NOTE: The initial coordinates of the atoms in each chunk are stored in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
"read_data"_read_data.html 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 "set
image"_set.html command.
NOTE: Unlike the "compute msd"_compute_msd.html command, this compute
does not store the initial center-of-mass coorindates of its molecules
in a restart file. Thus you cannot continue the MSD per chunk
calculation of this compute when running from a "restart
file"_read_restart.html.
The simplest way to output the results of the compute com/msd
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 myChunk all com/msd cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
[Output info:]
This compute calculates a 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. The number of columns =
4 for dx,dy,dz and the total displacement. These values can be
accessed by any command that uses global array values from a compute
as input. See "this section"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The array values are "intensive". The array values will be in
distance^2 "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute msd"_compute_msd.html
[Default:] none
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