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Update docs: angle_style

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Richard Berger
2019-11-15 11:22:25 -05:00
parent fb64068fbc
commit cdd56cd08f
2 changed files with 14 additions and 131 deletions
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33
doc/src/angle_style.rst
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@ -1,13 +1,13 @@
.. index:: angle\_style .. index:: angle_style
angle\_style command angle_style command
==================== ===================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
angle_style style angle_style style
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
angle_style harmonic angle_style harmonic
angle_style charmm angle_style charmm
@ -29,19 +29,19 @@ Description
Set the formula(s) LAMMPS uses to compute angle interactions between Set the formula(s) LAMMPS uses to compute angle interactions between
triplets of atoms, which remain in force for the duration of the triplets of atoms, which remain in force for the duration of the
simulation. The list of angle triplets is read in by a simulation. The list of angle triplets is read in by a
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
from a data or restart file. from a data or restart file.
Hybrid models where angles are computed using different angle Hybrid models where angles are computed using different angle
potentials can be setup using the *hybrid* angle style. potentials can be setup using the *hybrid* angle style.
The coefficients associated with a angle style can be specified in a The coefficients associated with a angle style can be specified in a
data or restart file or via the :doc:`angle\_coeff <angle_coeff>` command. data or restart file or via the :doc:`angle_coeff <angle_coeff>` command.
All angle potentials store their coefficient data in binary restart All angle potentials store their coefficient data in binary restart
files which means angle\_style and :doc:`angle\_coeff <angle_coeff>` files which means angle_style and :doc:`angle_coeff <angle_coeff>`
commands do not need to be re-specified in an input script that commands do not need to be re-specified in an input script that
restarts a simulation. See the :doc:`read\_restart <read_restart>` restarts a simulation. See the :doc:`read_restart <read_restart>`
command for details on how to do this. The one exception is that 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 angle\_style *hybrid* only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified. file; angle coefficients need to be re-specified.
@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified.
.. note:: .. note::
When both an angle and pair style is defined, the When both an angle and pair style is defined, the
:doc:`special\_bonds <special_bonds>` command often needs to be used to :doc:`special_bonds <special_bonds>` command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms. 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 Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients the style to display the formula it computes and coefficients
specified by the associated :doc:`angle\_coeff <angle_coeff>` command. specified by the associated :doc:`angle_coeff <angle_coeff>` command.
Click on the style to display the formula it computes, any additional Click on the style to display the formula it computes, any additional
arguments specified in the angle\_style command, and coefficients arguments specified in the angle\_style command, and coefficients
specified by the associated :doc:`angle\_coeff <angle_coeff>` command. specified by the associated :doc:`angle_coeff <angle_coeff>` command.
There are also additional accelerated pair styles included in the There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. 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 Related commands
"""""""""""""""" """"""""""""""""
:doc:`angle\_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
angle_style none angle_style none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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doc/txt/angle_style.txt
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@ -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