forked from lijiext/lammps
92 lines
3.2 KiB
Plaintext
92 lines
3.2 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/molecule command :h3
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[Syntax:]
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compute ID group-ID gyration/molecule keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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gyration/molecule = style name of this compute 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/molecule
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compute 2 molecule gyration/molecule tensor :pre
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[Description:]
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Define a computation that calculates the radius of gyration Rg of
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individual molecules. The calculation includes all effects due to
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atoms passing thru periodic boundaries.
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Rg is a measure of the size of a molecule, 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 molecule, Rcm is the center-of-mass
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position of the molecule, and the sum is over all atoms in the
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molecule and in the group.
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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 molecule.
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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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Rg for a particular molecule is only computed if one or more of its
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atoms are in the specified group. Normally all atoms in the molecule
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should be in the group, however this is not required. LAMMPS will
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warn you if this is not the case. Only atoms in the group contribute
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to the Rg calculation for the molecule.
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The ordering of per-molecule quantities produced by this compute is
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consistent with the ordering produced by other compute commands that
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generate per-molecule datums. Conceptually, them molecule IDs will be
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in ascending order for any molecule with one or more of its atoms in
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the specified group.
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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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[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 is the number of molecules. If the
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{tensor} keyword is specified, the global array has 6 columns. The
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vector or array can be accessed by any command that uses global values
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from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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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.
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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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