From 2a900f85aafc4462a8394ed4562ca68beb9893b3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:40:33 -0500 Subject: [PATCH] Update docs: bond_style --- doc/src/bond_style.rst | 27 ++++------ doc/txt/bond_style.txt | 115 ----------------------------------------- 2 files changed, 11 insertions(+), 131 deletions(-) delete mode 100644 doc/txt/bond_style.txt diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index f912411972..3c5c97b96b 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -1,29 +1,27 @@ -.. index:: bond\_style +.. index:: bond_style -bond\_style command -=================== +bond_style command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style style args * style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic* +* args = none for any style except *hybrid* -.. parsed-literal:: - - args = none for any style except *hybrid* - *hybrid* args = list of one or more styles + * *hybrid* args = list of one or more styles Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic bond_style fene @@ -74,11 +72,11 @@ between the 2 atoms in the bond. Here is an alphabetic list of bond styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the bond\_style command, and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. @@ -128,9 +126,6 @@ Related commands Default """"""" -bond\_style none +.. code-block:: LAMMPS - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html + bond_style none diff --git a/doc/txt/bond_style.txt b/doc/txt/bond_style.txt deleted file mode 100644 index aba6d3a778..0000000000 --- a/doc/txt/bond_style.txt +++ /dev/null @@ -1,115 +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 - -bond_style command :h3 - -[Syntax:] - -bond_style style args :pre - -style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \ - {harmonic} or {morse} or {nonlinear} or {quartic} :ul - args = none for any style except {hybrid} - {hybrid} args = list of one or more styles :pre - -[Examples:] - -bond_style harmonic -bond_style fene -bond_style hybrid harmonic fene :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute bond interactions between -pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the "pair_style"_pair_style.html -command. Bonds are defined between specified pairs of atoms and -remain in force for the duration of the simulation (unless the bond -breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a "read_data"_read_data.html or -"read_restart"_read_restart.html command from a data or restart file. -By contrast, pair potentials are typically defined between all pairs -of atoms within a cutoff distance and the set of active interactions -changes over time. - -Hybrid models where bonds are computed using different bond potentials -can be setup using the {hybrid} bond style. - -The coefficients associated with a bond style can be specified in a -data or restart file or via the "bond_coeff"_bond_coeff.html command. - -All bond potentials store their coefficient data in binary restart -files which means bond_style and "bond_coeff"_bond_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 bond_style -{hybrid} only stores the list of sub-styles in the restart file; bond -coefficients need to be re-specified. - -NOTE: When both a bond 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 2 bonded atoms. - -In the formulas listed for each bond style, {r} is the distance -between the 2 atoms in the bond. - -:line - -Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the bond_style command, and coefficients -specified by the associated "bond_coeff"_bond_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 bond"_Commands_bond.html -doc page are followed by one or more of (g,i,k,o,t) to indicate which -accelerated styles exist. - -"none"_bond_none.html - turn off bonded interactions -"zero"_bond_zero.html - topology but no interactions -"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul - -"class2"_bond_class2.html - COMPASS (class 2) bond -"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond -"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"gromos"_bond_gromos.html - GROMOS force field bond -"harmonic"_bond_harmonic.html - harmonic bond -"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond -"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff -"mm3"_bond_mm3.html - MM3 anharmonic bond -"morse"_bond_morse.html - Morse bond -"nonlinear"_bond_nonlinear.html - nonlinear bond -"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling -"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles -"quartic"_bond_quartic.html - breakable quartic bond -"table"_bond_table.html - tabulated by bond length :ul - -:line - -[Restrictions:] - -Bond styles can only be set for atom styles that allow bonds to be -defined. - -Most bond 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:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] - -bond_style none