Update docs: bond_style
This commit is contained in:
Richard Berger
@ -1,29 +1,27 @@
|
|||||||
.. index:: bond\_style
|
.. index:: bond_style
|
||||||
|
|
||||||
bond\_style command
|
bond_style command
|
||||||
===================
|
==================
|
||||||
|
|
||||||
Syntax
|
Syntax
|
||||||
""""""
|
""""""
|
||||||
|
|
||||||
|
|
||||||
.. parsed-literal::
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
bond_style style args
|
bond_style style args
|
||||||
|
|
||||||
* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic*
|
* 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::
|
* *hybrid* args = list of one or more styles
|
||||||
|
|
||||||
args = none for any style except *hybrid*
|
|
||||||
*hybrid* args = list of one or more styles
|
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
|
|
||||||
.. parsed-literal::
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
bond_style fene
|
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
|
Here is an alphabetic list of bond 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:`bond\_coeff <bond_coeff>` command.
|
specified by the associated :doc:`bond_coeff <bond_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 bond\_style command, and coefficients
|
arguments specified in the bond\_style command, and coefficients
|
||||||
specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
|
specified by the associated :doc:`bond_coeff <bond_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.
|
||||||
@ -128,9 +126,6 @@ Related commands
|
|||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
bond\_style none
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
bond_style none
|
||||||
.. _lws: http://lammps.sandia.gov
|
|
||||||
.. _ld: Manual.html
|
|
||||||
.. _lc: Commands_all.html
|
|
||||||
|
|||||||
@ -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
|
|
||||||
Reference in New Issue
Block a user