forked from lijiext/lammps
112 lines
4.1 KiB
Plaintext
112 lines
4.1 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute gyration/chunk command :h3
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[Syntax:]
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compute ID group-ID gyration/chunk chunkID keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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gyration/chunk = style name of this compute command :l
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chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
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zero or more keyword/value pairs may be appended :l
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keyword = {tensor} :l
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{tensor} value = none :pre
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:ule
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[Examples:]
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compute 1 molecule gyration/chunk molchunk
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compute 2 molecule gyration/chunk molchunk tensor :pre
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[Description:]
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Define a computation that calculates the radius of gyration Rg for
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multiple chunks of atoms.
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In LAMMPS, chunks are collections of atoms defined by a "compute
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chunk/atom"_compute_chunk_atom.html command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the "compute
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chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
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23"_Section_howto.html#howto_23 for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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This compute calculates the radius of gyration Rg for each chunk,
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which includes all effects due to atoms passing thru periodic
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boundaries.
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Rg is a measure of the size of a chunk, and is computed by this
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formula
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:c,image(Eqs/compute_gyration.jpg)
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where M is the total mass of the chunk, Rcm is the center-of-mass
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position of the chunk, and the sum is over all atoms in the
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chunk.
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Note that only atoms in the specified group contribute to the
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calculation. The "compute chunk/atom"_compute_chunk_atom.html command
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defines its own group; atoms will have a chunk ID = 0 if they are not
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
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"all" group for this command if you simply want to include atoms with
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non-zero chunk IDs.
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If the {tensor} keyword is specified, then the scalar Rg value is not
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calculated, but an Rg tensor is instead calculated for each chunk.
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The formula for the components of the tensor is the same as the above
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formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
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Rcmy) for the xy component, etc. The 6 components of the tensor are
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ordered xx, yy, zz, xy, xz, yz.
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IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
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"unwrapped" form, by using the image flags associated with each atom.
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See the "dump custom"_dump.html command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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"read_data"_read_data.html command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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(e.g. to 0) before invoking this compute by using the "set
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image"_set.html command.
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The simplest way to output the results of the compute gyration/chunk
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calculation to a file is to use the "fix ave/time"_fix_ave_time.html
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command, for example:
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compute cc1 all chunk/atom molecule
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compute myChunk all gyration/chunk cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
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[Output info:]
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This compute calculates a global vector if the {tensor} keyword is not
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specified and a global array if it is. The length of the vector or
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number of rows in the array = the number of chunks {Nchunk} as
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calculated by the specified "compute
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chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword
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is specified, the global array has 6 columns. The vector or array can
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be accessed by any command that uses global values from a compute as
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input. See "this section"_Section_howto.html#howto_15 for an overview
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of LAMMPS output options.
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All the vector or array values calculated by this compute are
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"intensive". The vector or array values will be in distance
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"units"_units.html, since they are the square root of values
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represented by the formula above.
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[Restrictions:] none
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[Related commands:] none
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"compute gyration"_compute_gyration.html
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[Default:] none
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