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
			6.23"_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. (dxdx + dydy + 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: If you want the quantities calculated by this compute to be
			continuous when running from a "restart file"_read_restart.html, then
			you should use the same ID for this compute, as in the original run.
			This is so that the fix this compute creates to store per-chunk
			quantities will also have the same ID, and thus be initialized
			correctly with chunk reference positions from the restart file.

			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

lammps/doc/src/compute_msd_chunk.txt0bcd90195d55master

compute_msd_chunk.txtView Options

lammps/doc/src/compute_msd_chunk.txt
0bcd90195d55master

compute_msd_chunk.txt
View Options