ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Move compute_gyration_shape_chunk.txt into txt/ folder

Browse Source
This commit is contained in:
Richard Berger
2019-11-11 15:32:09 -05:00
parent 93b03aa82c
commit 22a033f5d4
1 changed files with 0 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

93
doc/src/compute_gyration_shape_chunk.txt
View File

@ -1,93 +0,0 @@
"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)
:line
compute gyration/shape/chunk command :h3
[Syntax:]
compute ID group-ID gyration/shape/chunk compute-ID :pre
ID, group-ID are documented in "compute"_compute.html command
gyration/shape/chunk = style name of this compute command
compute-ID = ID of "compute gyration/chunk"_compute_gyration_chunk.html command :ul
[Examples:]
compute 1 molecule gyration/shape/chunk pe :pre
[Description:]
Define a computation that calculates the eigenvalues of the gyration tensor and
three shape parameters of multiple chunks of atoms. The computation includes
all effects due to atoms passing through 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. A general description
of these parameters is provided in "(Mattice)"_#Mattice2 while an application to polymer systems
can be found in "(Theodorou)"_#Theodorou2. 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).
The tensor keyword must be specified in the compute gyration/chunk command.
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 array with six columns,
which can be accessed by indices 1-6. The first three columns 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 array values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array calculated by this compute is
"intensive". The first five columns 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/chunk"_compute_gyration_chunk.html
"compute gyration/shape"_compute_gyration_shape.html
[Default:] none
:line
:link(Mattice2)
[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
:link(Theodorou2)
[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).