diff --git a/doc/src/compute_gyration_shape.txt b/doc/src/compute_gyration_shape.txt new file mode 100644 index 0000000000..b9b62cfaa7 --- /dev/null +++ b/doc/src/compute_gyration_shape.txt @@ -0,0 +1,86 @@ +"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 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 + +:line + +:link(Theodorou) +[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). +