diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst new file mode 100644 index 0000000000..fa839aea35 --- /dev/null +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -0,0 +1,113 @@ +.. index:: compute gyration/shape/chunk + +compute gyration/shape/chunk command +==================================== + +Syntax +"""""" + + +.. parsed-literal:: + + compute ID group-ID gyration/shape/chunk compute-ID + +* ID, group-ID are documented in :doc:`compute ` command +* gyration/shape/chunk = style name of this compute command +* compute-ID = ID of :doc:`compute gyration/chunk ` command + +Examples +"""""""" + + +.. parsed-literal:: + + compute 1 molecule gyration/shape/chunk pe + +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: + +.. image:: Eqs/compute_shape_parameters.jpg + :align: center + +where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description +of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems +can be found in :ref:`(Theodorou) `. 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 :doc:`dump custom ` command for a discussion of "unwrapped" + coordinates. See the Atoms section of the :doc:`read\_data ` + 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 :doc:`set image ` 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 :doc:`Howto output ` 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 :doc:`units ` 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 :doc:`Build package ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`compute gyration/chunk ` +:doc:`compute gyration/shape ` + +**Default:** none + + +---------- + + +.. _Mattice2: + + + +**(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. + +.. _Theodorou2: + + + +**(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Commands_all.html diff --git a/doc/txt/compute_gyration_shape_chunk.txt b/doc/txt/compute_gyration_shape_chunk.txt deleted file mode 100644 index c74d571007..0000000000 --- a/doc/txt/compute_gyration_shape_chunk.txt +++ /dev/null @@ -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). -