forked from lijiext/lammps
118 lines
4.3 KiB
Plaintext
118 lines
4.3 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
dihedral_style command :h3
|
|
|
|
[Syntax:]
|
|
|
|
dihedral_style style :pre
|
|
|
|
style = {none} or {hybrid} or {charmm} or {class2} or {harmonic} or {helix} or \
|
|
{multi/harmonic} or {opls} :ul
|
|
|
|
[Examples:]
|
|
|
|
dihedral_style harmonic
|
|
dihedral_style multi/harmonic
|
|
dihedral_style hybrid harmonic charmm :pre
|
|
|
|
[Description:]
|
|
|
|
Set the formula(s) LAMMPS uses to compute dihedral interactions
|
|
between quadruplets of atoms, which remain in force for the duration
|
|
of the simulation. The list of dihedral quadruplets 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 dihedrals are computed using different dihedral
|
|
potentials can be setup using the {hybrid} dihedral style.
|
|
|
|
The coefficients associated with a dihedral style can be specified in
|
|
a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html
|
|
command.
|
|
|
|
All dihedral potentials store their coefficient data in binary restart
|
|
files which means dihedral_style and
|
|
"dihedral_coeff"_dihedral_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 dihedral_style {hybrid} only stores
|
|
the list of sub-styles in the restart file; dihedral coefficients need
|
|
to be re-specified.
|
|
|
|
IMPORTANT NOTE: When both a dihedral 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 4 bonded atoms.
|
|
|
|
In the formulas listed for each dihedral style, {phi} is the torsional
|
|
angle defined by the quadruplet of atoms. This angle has a sign
|
|
convention as shown in this diagram:
|
|
|
|
:c,image(Eqs/dihedral_sign.jpg)
|
|
|
|
where the I,J,K,L ordering of the 4 atoms that define the dihedral
|
|
is from left to right.
|
|
|
|
This sign convention effects several of the dihedral styles listed
|
|
below (e.g. charmm, helix) in the sense that the energy formula
|
|
depends on the sign of phi, which may be reflected in the value of the
|
|
coefficients you specify.
|
|
|
|
IMPORTANT NOTE: When comparing the formulas and coefficients for
|
|
various LAMMPS dihedral styles with dihedral equations defined by
|
|
other force fields, note that some force field implementations
|
|
divide/multiply the energy prefactor {K} by the multiple number of
|
|
torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
|
|
not do this, i.e. the listed dihedral equation applies to each
|
|
individual dihedral. Thus you need to define {K} appropriately via
|
|
the "dihedral_coeff"_dihedral_coeff.html command to account for this
|
|
difference if necessary.
|
|
|
|
:line
|
|
|
|
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
|
|
the style to display the formula it computes and coefficients
|
|
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
|
|
|
|
Note that there are also additional dihedral styles submitted by users
|
|
which are included in the LAMMPS distribution. The list of these with
|
|
links to the individual styles are given in the dihedral section of
|
|
"this page"_Section_commands.html#cmd_5.
|
|
|
|
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
|
|
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
|
|
|
|
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
|
|
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
|
|
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
|
|
"dihedral_style helix"_dihedral_helix.html - helix dihedral
|
|
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
|
|
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
Dihedral styles can only be set for atom styles that allow dihedrals
|
|
to be defined.
|
|
|
|
Most dihedral styles are part of the MOLECULAR package. They are only
|
|
enabled if LAMMPS was built with that package. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|
The doc pages for individual dihedral potentials tell if it is part of
|
|
a package.
|
|
|
|
[Related commands:]
|
|
|
|
"dihedral_coeff"_dihedral_coeff.html
|
|
|
|
[Default:]
|
|
|
|
dihedral_style none
|