Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/src/angle_dipole.txt
39d713b5a307lammm-master

Last Change
Raw File

angle_dipole.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
angle_style dipole command :h3
angle_style dipole/omp command :h3
[Syntax:]
angle_style dipole :pre
[Examples:]
angle_style dipole
angle_coeff 6 2.1 180.0 :pre
[Description:]
The {dipole} angle style is used to control the orientation of a dipolar
atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
style restrains the orientation of a point dipole mu_j (embedded in atom
'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
is another atom of the same molecule (typically, 'i' and 'j' are also
covalently bonded).
It is convenient to define an angle gamma between the 'free' vector mu_j
and the reference (bond) vector r_ij:
:c,image(Eqs/angle_dipole_gamma.jpg)
The {dipole} angle style uses the potential:
:c,image(Eqs/angle_dipole_potential.jpg)
where K is a rigidity constant and gamma0 is an equilibrium (reference)
angle.
The torque on the dipole can be obtained by differentiating the
potential using the 'chain rule' as in appendix C.3 of
"(Allen)"_#Allen:
:c,image(Eqs/angle_dipole_torque.jpg)
Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference
direction defined by the (bond) vector r_ij (in other words, mu_j is
restrained to point towards atom 'i').
The dipolar torque T_j must be counterbalanced in order to conserve
the local angular momentum. This is achieved via an additional force
couple generating a torque equivalent to the opposite of T_j:
:c,image(Eqs/angle_dipole_couple.jpg)
where F_i and F_j are applied on atoms i and j, respectively.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
gamma0 (degrees) :ul
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
section for more info on packages.
NOTE: In the "Angles" section of the data file, the atom ID 'j'
corresponding to the dipole to restrain must come before the atom ID
of the reference atom 'i'. A third atom ID 'k' must also be provided,
although 'k' is just a 'dummy' atom which can be any atom; it may be
useful to choose a convention (e.g., 'k'='i') and adhere to it. For
example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
reference atom, the corresponding line in the "Angles" section of the
data file would read: X X 1 2 2
The "newton" command for intramolecular interactions must be "on"
(which is the default).
This angle style should not be used with SHAKE.
[Related commands:]
"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html
[Default:] none
:line
:link(Orsi)
[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
lipid membranes, PloS ONE 6(12): e28637, 2011.
:link(Allen)
[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.
c4science · Help