From cdd56cd08f137de0fdc3bcfa8b60ffd44c51064c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:22:25 -0500 Subject: [PATCH] Update docs: angle_style --- doc/src/angle_style.rst | 33 +++++------- doc/txt/angle_style.txt | 112 ---------------------------------------- 2 files changed, 14 insertions(+), 131 deletions(-) delete mode 100644 doc/txt/angle_style.txt diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 6d7c70565b..3e22113d85 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style +.. index:: angle_style -angle\_style command -==================== +angle_style command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style harmonic angle_style charmm @@ -29,19 +29,19 @@ Description Set the formula(s) LAMMPS uses to compute angle interactions between triplets of atoms, which remain in force for the duration of the simulation. The list of angle triplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Hybrid models where angles are computed using different angle potentials can be setup using the *hybrid* angle style. The coefficients associated with a angle style can be specified in a -data or restart file or via the :doc:`angle\_coeff ` command. +data or restart file or via the :doc:`angle_coeff ` command. All angle potentials store their coefficient data in binary restart -files which means angle\_style and :doc:`angle\_coeff ` +files which means angle_style and :doc:`angle_coeff ` commands do not need to be re-specified in an input script that -restarts a simulation. See the :doc:`read\_restart ` +restarts a simulation. See the :doc:`read_restart ` command for details on how to do this. The one exception is that angle\_style *hybrid* only stores the list of sub-styles in the restart file; angle coefficients need to be re-specified. @@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified. .. note:: When both an angle and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 3 bonded atoms. @@ -62,11 +62,11 @@ between the 3 atoms in the angle. Here is an alphabetic list of angle styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`angle\_coeff ` command. +specified by the associated :doc:`angle_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the angle\_style command, and coefficients -specified by the associated :doc:`angle\_coeff ` command. +specified by the associated :doc:`angle_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. @@ -115,17 +115,12 @@ individual bond potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_style.txt b/doc/txt/angle_style.txt deleted file mode 100644 index 2f2da678d8..0000000000 --- a/doc/txt/angle_style.txt +++ /dev/null @@ -1,112 +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 - -angle_style command :h3 - -[Syntax:] - -angle_style style :pre - -style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \ - {cosine/squared} or {harmonic} :ul - -[Examples:] - -angle_style harmonic -angle_style charmm -angle_style hybrid harmonic cosine :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute angle interactions between -triplets of atoms, which remain in force for the duration of the -simulation. The list of angle triplets is read in by a -"read_data"_read_data.html or "read_restart"_read_restart.html command -from a data or restart file. - -Hybrid models where angles are computed using different angle -potentials can be setup using the {hybrid} angle style. - -The coefficients associated with a angle style can be specified in a -data or restart file or via the "angle_coeff"_angle_coeff.html command. - -All angle potentials store their coefficient data in binary restart -files which means angle_style and "angle_coeff"_angle_coeff.html -commands do not need to be re-specified in an input script that -restarts a simulation. See the "read_restart"_read_restart.html -command for details on how to do this. The one exception is that -angle_style {hybrid} only stores the list of sub-styles in the restart -file; angle coefficients need to be re-specified. - -NOTE: When both an angle and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 3 bonded atoms. - -In the formulas listed for each angle style, {theta} is the angle -between the 3 atoms in the angle. - -:line - -Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the angle_style command, and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -angle"_Commands_bond.html#angle doc page are followed by one or more -of (g,i,k,o,t) to indicate which accelerated styles exist. - -"none"_angle_none.html - turn off angle interactions -"zero"_angle_zero.html - topology but no interactions -"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul - -"charmm"_angle_charmm.html - CHARMM angle -"class2"_angle_class2.html - COMPASS (class 2) angle -"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order -"cosine"_angle_cosine.html - angle with cosine term -"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms -"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines -"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift -"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant -"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term -"cross"_angle_cross.html - cross term coupling angle and bond lengths -"dipole"_angle_dipole.html - angle that controls orientation of a point dipole -"fourier"_angle_fourier.html - angle with multiple cosine terms -"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term -"harmonic"_angle_harmonic.html - harmonic angle -"mm3"_angle_mm3.html - anharmonic angle -"quartic"_angle_quartic.html - angle with cubic and quartic terms -"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms -"table"_angle_table.html - tabulated by angle :ul - -:line - -[Restrictions:] - -Angle styles can only be set for atom_styles that allow angles to be -defined. - -Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual bond potentials tell if it is part of a package. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] - -angle_style none :pre