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Update docs: bond_style
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Richard Berger
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.. index:: bond\_style
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.. index:: bond_style
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bond\_style command
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===================
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bond_style command
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==================
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Syntax
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""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style style args
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* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic*
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* args = none for any style except *hybrid*
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.. parsed-literal::
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args = none for any style except *hybrid*
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*hybrid* args = list of one or more styles
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* *hybrid* args = list of one or more styles
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Examples
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""""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style harmonic
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bond_style fene
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@ -74,11 +72,11 @@ between the 2 atoms in the bond.
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Here is an alphabetic list of bond styles defined in LAMMPS. Click on
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the style to display the formula it computes and coefficients
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specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
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specified by the associated :doc:`bond_coeff <bond_coeff>` command.
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Click on the style to display the formula it computes, any additional
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arguments specified in the bond\_style command, and coefficients
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specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
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specified by the associated :doc:`bond_coeff <bond_coeff>` command.
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There are also additional accelerated pair styles included in the
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LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
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@ -128,9 +126,6 @@ Related commands
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Default
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"""""""
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bond\_style none
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.. code-block:: LAMMPS
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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bond_style none
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@ -1,115 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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bond_style command :h3
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[Syntax:]
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bond_style style args :pre
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style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
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{harmonic} or {morse} or {nonlinear} or {quartic} :ul
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args = none for any style except {hybrid}
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{hybrid} args = list of one or more styles :pre
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[Examples:]
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bond_style harmonic
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bond_style fene
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bond_style hybrid harmonic fene :pre
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[Description:]
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Set the formula(s) LAMMPS uses to compute bond interactions between
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pairs of atoms. In LAMMPS, a bond differs from a pairwise
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interaction, which are set via the "pair_style"_pair_style.html
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command. Bonds are defined between specified pairs of atoms and
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remain in force for the duration of the simulation (unless the bond
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breaks which is possible in some bond potentials). The list of bonded
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atoms is read in by a "read_data"_read_data.html or
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"read_restart"_read_restart.html command from a data or restart file.
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By contrast, pair potentials are typically defined between all pairs
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of atoms within a cutoff distance and the set of active interactions
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changes over time.
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Hybrid models where bonds are computed using different bond potentials
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can be setup using the {hybrid} bond style.
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The coefficients associated with a bond style can be specified in a
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data or restart file or via the "bond_coeff"_bond_coeff.html command.
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All bond potentials store their coefficient data in binary restart
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files which means bond_style and "bond_coeff"_bond_coeff.html commands
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do not need to be re-specified in an input script that restarts a
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simulation. See the "read_restart"_read_restart.html command for
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details on how to do this. The one exception is that bond_style
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{hybrid} only stores the list of sub-styles in the restart file; bond
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coefficients need to be re-specified.
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NOTE: When both a bond and pair style is defined, the
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"special_bonds"_special_bonds.html command often needs to be used to
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turn off (or weight) the pairwise interaction that would otherwise
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exist between 2 bonded atoms.
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In the formulas listed for each bond style, {r} is the distance
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between the 2 atoms in the bond.
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:line
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Here is an alphabetic list of bond styles defined in LAMMPS. Click on
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the style to display the formula it computes and coefficients
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specified by the associated "bond_coeff"_bond_coeff.html command.
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Click on the style to display the formula it computes, any additional
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arguments specified in the bond_style command, and coefficients
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specified by the associated "bond_coeff"_bond_coeff.html command.
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There are also additional accelerated pair styles included in the
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LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
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The individual style names on the "Commands bond"_Commands_bond.html
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doc page are followed by one or more of (g,i,k,o,t) to indicate which
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accelerated styles exist.
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"none"_bond_none.html - turn off bonded interactions
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"zero"_bond_zero.html - topology but no interactions
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"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
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"class2"_bond_class2.html - COMPASS (class 2) bond
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"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
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"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
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"gromos"_bond_gromos.html - GROMOS force field bond
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"harmonic"_bond_harmonic.html - harmonic bond
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"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
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"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
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"mm3"_bond_mm3.html - MM3 anharmonic bond
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"morse"_bond_morse.html - Morse bond
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"nonlinear"_bond_nonlinear.html - nonlinear bond
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"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
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"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
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"quartic"_bond_quartic.html - breakable quartic bond
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"table"_bond_table.html - tabulated by bond length :ul
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:line
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[Restrictions:]
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Bond styles can only be set for atom styles that allow bonds to be
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defined.
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Most bond styles are part of the MOLECULE package. They are only
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enabled if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info. The doc pages for
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individual bond potentials tell if it is part of a package.
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[Related commands:]
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"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
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[Default:]
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bond_style none
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