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lammps/doc/src/compute_gyration.txt
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compute_gyration.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 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 as
the square root of the Rg^2 value in 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^2 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. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
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^2 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 and
distance^2 "units"_units.html respectively.
[Restrictions:] none
[Related commands:]
"compute gyration/chunk"_compute_gyration_chunk.html
[Default:] none
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