compute_gyration_chunk.txt
3b8ecd5c0634lammps-icms

compute_gyration_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 gyration/chunk command :h3

			[Syntax:]

			compute ID group-ID gyration/chunk chunkID keyword value ... :pre

			ID, group-ID are documented in "compute"_compute.html command :ulb,l
			gyration/chunk = style name of this compute command :l
			chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
			zero or more keyword/value pairs may be appended :l
			keyword = {tensor} :l
			{tensor} value = none :pre
			:ule

			[Examples:]

			compute 1 molecule gyration/chunk molchunk
			compute 2 molecule gyration/chunk molchunk tensor :pre

			[Description:]

			Define a computation that calculates the radius of gyration Rg 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.

			This compute calculates the radius of gyration Rg for each chunk,
			which includes all effects due to atoms passing thru periodic
			boundaries.

			Rg is a measure of the size of a chunk, and is computed by this
			formula

			:c,image(Eqs/compute_gyration.jpg)

			where M is the total mass of the chunk, Rcm is the center-of-mass
			position of the chunk, and the sum is over all atoms in the
			chunk.

			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.

			If the {tensor} keyword is specified, then the scalar Rg value is not
			calculated, but an Rg tensor is instead calculated for each chunk.
			The formula for the components of the tensor is the same as the above
			formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
			Rcmy) for the xy component, etc. The 6 components of the tensor are
			ordered xx, yy, zz, xy, xz, yz.

			NOTE: The coordinates of an atom contribute to Rg 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.

			The simplest way to output the results of the compute gyration/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 myChunk all gyration/chunk cc1
			fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre

			[Output info:]

			This compute calculates a global vector if the {tensor} keyword is not
			specified and a global array if it is. The length of the vector or
			number of rows in the array = the number of chunks {Nchunk} as
			calculated by the specified "compute
			chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword
			is specified, the global array has 6 columns. 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.

			All the vector or array values calculated by this compute are
			"intensive". The vector or array values will be in distance
			"units"_units.html, since they are the square root of values
			represented by the formula above.

			[Restrictions:] none

			[Related commands:] none

			"compute gyration"_compute_gyration.html

			[Default:] none

lammps/doc/src/compute_gyration_chunk.txt3b8ecd5c0634lammps-icms

compute_gyration_chunk.txtView Options

lammps/doc/src/compute_gyration_chunk.txt
3b8ecd5c0634lammps-icms

compute_gyration_chunk.txt
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