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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,Commands_all.html)

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compute gyration/shape command :h3

[Syntax:]

compute ID group-ID gyration computeID :pre

ID, group-ID are documented in "compute"_compute.html command

gyration/shape = style name of this compute command

computeID = ID of "compute gyration"_compute_gyration.html command :ul

[Examples:]

compute 1 molecule gyration/shape pe :pre

[Description:]

Define a computation that calculates the eigenvalues of the gyration tensor of a

group of atoms and three shape parameters. The computation includes all effects 

due to atoms passing thru periodic boundaries.

The three computed shape parameters are the asphericity, b, the acylindricity, c, 

and the relative shape anisotropy, k:

:c,image(Eqs/compute_shape_parameters.jpg)

where lx ≤ ly ≤ lz are the three eigenvalues of the gyration tensor.

The asphericity  is always non-negative and zero only when the three principal 

moments are equal. This zero condition is met when the distribution of particles 

is spherically symmetric (hence the name asphericity) but also whenever the particle

 distribution is symmetric with respect to the three coordinate axes, e.g., 

when the particles are distributed uniformly on a cube, tetrahedron or other Platonic 

solid. The acylindricity is always non-negative and zero only when the two principal 

moments are equal. This zero condition is met when the distribution of particles is 

cylindrically symmetric (hence the name, acylindricity), but also whenever the particle 

distribution is symmetric with respect to the two coordinate axes, e.g., when the 

particles are distributed uniformly on a regular prism. the relative shape anisotropy 

is bounded between zero (if all points are spherically symmetric) and one 

(if all points lie on a line).

NOTE: The coordinates of an atom contribute to the gyration tensor 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

length 6, which can be accessed by indices 1-6. The first three values are the 

eigenvalues of the gyration tensor followed by the asphericity, the acylindricity

and the relative shape anisotropy.  The computed values can be used by any command 

that uses global  vector values from a compute as input.  See the "Howto

output"_Howto_output.html doc page for an overview of LAMMPS output

options.

The vector values calculated by this compute are

"intensive".  The first five vector values will be in

distance^2 "units"_units.html while the sixth one is dimensionless.

[Restrictions:] 

This compute is part of the USER-MISC package.  It is only enabled if

LAMMPS was built with that package.  See the "Build

package"_Build_package.html doc page for more info.

[Related commands:]

"compute gyration"_compute_gyration.html

[Default:] none

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:link(Theodorou)

[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).