Loading doc/src/compute_gyration_shape_chunk.txt→doc/src/compute_gyration_shape_chunk.rst +113 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c .. index:: compute gyration/shape/chunk :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Commands_all.html) compute gyration/shape/chunk command ==================================== :line Syntax """""" compute gyration/shape/chunk command :h3 [Syntax:] .. parsed-literal:: compute ID group-ID gyration/shape/chunk compute-ID :pre compute ID group-ID gyration/shape/chunk compute-ID 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 * ID, group-ID are documented in :doc:`compute <compute>` command * gyration/shape/chunk = style name of this compute command * compute-ID = ID of :doc:`compute gyration/chunk <compute_gyration_chunk>` command [Examples:] Examples """""""" compute 1 molecule gyration/shape/chunk pe :pre [Description:] .. 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 Loading @@ -29,11 +33,12 @@ 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) .. 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 "(Mattice)"_#Mattice2 while an application to polymer systems can be found in "(Theodorou)"_#Theodorou2. The asphericity is always non-negative and zero of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems can be found in :ref:`(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., Loading @@ -48,46 +53,61 @@ is bounded between zero (if all points are spherically symmetric) and one The tensor keyword must be specified in the compute gyration/chunk command. NOTE: The coordinates of an atom contribute to the gyration tensor in .. 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 See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates. See the Atoms section of the :doc:`read\_data <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 "set image"_set.html command. compute by using the :doc:`set image <set>` command. [Output info:] **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 that uses global array values from a compute as input. See the :doc:`Howto output <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 "units"_units.html while the sixth one is dimensionless. distance\^2 :doc:`units <units>` while the sixth one is dimensionless. Restrictions """""""""""" [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. LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. Related commands """""""""""""""" :doc:`compute gyration/chunk <compute_gyration_chunk>` :doc:`compute gyration/shape <compute_gyration_shape>` **Default:** none ---------- .. _Mattice2: [Related commands:] **(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. "compute gyration/chunk"_compute_gyration_chunk.html "compute gyration/shape"_compute_gyration_shape.html .. _Theodorou2: [Default:] none :line :link(Mattice2) [(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). :link(Theodorou2) [(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Commands_all.html Loading
doc/src/compute_gyration_shape_chunk.txt→doc/src/compute_gyration_shape_chunk.rst +113 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c .. index:: compute gyration/shape/chunk :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Commands_all.html) compute gyration/shape/chunk command ==================================== :line Syntax """""" compute gyration/shape/chunk command :h3 [Syntax:] .. parsed-literal:: compute ID group-ID gyration/shape/chunk compute-ID :pre compute ID group-ID gyration/shape/chunk compute-ID 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 * ID, group-ID are documented in :doc:`compute <compute>` command * gyration/shape/chunk = style name of this compute command * compute-ID = ID of :doc:`compute gyration/chunk <compute_gyration_chunk>` command [Examples:] Examples """""""" compute 1 molecule gyration/shape/chunk pe :pre [Description:] .. 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 Loading @@ -29,11 +33,12 @@ 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) .. 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 "(Mattice)"_#Mattice2 while an application to polymer systems can be found in "(Theodorou)"_#Theodorou2. The asphericity is always non-negative and zero of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems can be found in :ref:`(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., Loading @@ -48,46 +53,61 @@ is bounded between zero (if all points are spherically symmetric) and one The tensor keyword must be specified in the compute gyration/chunk command. NOTE: The coordinates of an atom contribute to the gyration tensor in .. 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 See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates. See the Atoms section of the :doc:`read\_data <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 "set image"_set.html command. compute by using the :doc:`set image <set>` command. [Output info:] **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 that uses global array values from a compute as input. See the :doc:`Howto output <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 "units"_units.html while the sixth one is dimensionless. distance\^2 :doc:`units <units>` while the sixth one is dimensionless. Restrictions """""""""""" [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. LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. Related commands """""""""""""""" :doc:`compute gyration/chunk <compute_gyration_chunk>` :doc:`compute gyration/shape <compute_gyration_shape>` **Default:** none ---------- .. _Mattice2: [Related commands:] **(Mattice)** Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. "compute gyration/chunk"_compute_gyration_chunk.html "compute gyration/shape"_compute_gyration_shape.html .. _Theodorou2: [Default:] none :line :link(Mattice2) [(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). :link(Theodorou2) [(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Commands_all.html
