"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/molecule command :h3

[Syntax:]

compute ID group-ID gyration/molecule :pre

ID, group-ID are documented in "compute"_compute.html command
gyration/molecule = style name of this compute command :ul

[Examples:]

compute 1 molecule gyration/molecule :pre

[Description:]

Define a computation that calculates the radius of gyration Rg of
individual molecules.  The calculation includes all effects due to
atoms passing thru periodic boundaries.

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

:c,image(Eqs/compute_gyration.jpg)

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

Rg for a particular molecule is only computed if one or more of its
atoms are in the specified group.  Normally all atoms in the molecule
should be in the group, however this is not required.  LAMMPS will
warn you if this is not the case.  Only atoms in the group contribute
to the Rg calculation for the molecule.

Let Nmolecules be the number of molecules for which Rg is calculated.
If not all molecules have atoms in the group, then the molecule with
the lowest ID is the first of the Nmolecules.  The next lowest ID is
the second, etc, up to Nmolecules.

IMPORTANT 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.

[Output info:]

This compute calculates a global vector of Rg values where the length
of the vector = Nmolecules.  These values can be used by any command
that uses global vector values from a compute as input.  See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.

The vector values calculated by this compute are "intensive".  The
vector values will be in distance "units"_units.html.

[Restrictions:] none

[Related commands:] none

"compute gyration"_compute_gyration.html

[Default:] none
