forked from lijiext/lammps
74 lines
2.4 KiB
Plaintext
74 lines
2.4 KiB
Plaintext
"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.
|
|
|
|
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^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
|