Homec4science
Diffusion lammps (runner) Browse

lammps/doc/compute_gyration.txt
2eeae0aade06runner

Last Change
Raw File

compute_gyration.txt
View Options

"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 command :h3
[Syntax:]
compute ID group-ID gyration :pre
ID, group-ID are documented in "compute"_compute.html command
gyration = style name of this compute command :ul
[Examples:]
compute 1 molecule gyration :pre
[Description:]
Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.
Rg is a measure of the size of the group of atoms, and is computed by
this formula
:c,image(Eqs/compute_gyration.jpg)
where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.
A Rg tensor, stored as a 6-element vector, is also calculated by this
compute. 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 vector are ordered xx, yy, zz, xy, xz, yz.
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 scalar (Rg) and a global vector of
length 6 (Rg tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance
"units"_units.html.
[Restrictions:] none
[Related commands:]
"compute gyration/molecule"_compute_gyration_molecule.html
[Default:] none
c4science · Help