Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/src/dihedral_hybrid.txt
3b8ecd5c0634lammm-master-deprecated

Last Change
Raw File

dihedral_hybrid.txt
View Options

"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 hybrid command :h3
[Syntax:]
dihedral_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more dihedral styles :ul
[Examples:]
dihedral_style hybrid harmonic helix
dihedral_coeff 1 harmonic 6.0 1 3
dihedral_coeff 2* helix 10 10 10 :pre
[Description:]
The {hybrid} style enables the use of multiple dihedral styles in one
simulation. An dihedral style is assigned to each dihedral type. For
example, dihedrals in a polymer flow (of dihedral type 1) could be
computed with a {harmonic} potential and dihedrals in the wall
boundary (of dihedral type 2) could be computed with a {helix}
potential. The assignment of dihedral type to style is made via the
"dihedral_coeff"_dihedral_coeff.html command or in the data file.
In the dihedral_coeff commands, the name of a dihedral style must be
added after the dihedral type, with the remaining coefficients being
those appropriate to that style. In the example above, the 2
dihedral_coeff commands set dihedrals of dihedral type 1 to be
computed with a {harmonic} potential with coefficients 6.0, 1, 3 for
K, d, n. All other dihedral types (2-N) are computed with a {helix}
potential with coefficients 10, 10, 10 for A, B, C.
If dihedral coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "harmonic" or "helix", must be added after the dihedral type, for
each line in the "Dihedral Coeffs" section, e.g.
Dihedral Coeffs :pre
1 harmonic 6.0 1 3
2 helix 10 10 10
... :pre
If {class2} is one of the dihedral hybrid styles, the same rule holds
for specifying additional AngleTorsion (and EndBondTorsion, etc)
coefficients either via the input script or in the data file.
I.e. {class2} must be added to each line after the dihedral type. For
lines in the AngleTorsion (or EndBondTorsion, etc) section of the data
file for dihedral types that are not {class2}, you must use an
dihedral style of {skip} as a placeholder, e.g.
AngleTorsion Coeffs :pre
1 skip
2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
... :pre
Note that it is not necessary to use the dihedral style {skip} in the
input script, since AngleTorsion (or EndBondTorsion, etc) coefficients
need not be specified at all for dihedral types that are not {class2}.
A dihedral style of {none} with no additional coefficients can be used
in place of a dihedral style, either in a input script dihedral_coeff
command or in the data file, if you desire to turn off interactions
for specific dihedral types.
:line
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
c4science · Help