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rLAMMPS lammps
angle_dipole.html
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<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
angle_style dipole command
</H3>
<H3>
angle_style dipole/omp command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
angle_style dipole
</PRE>
<P><B>
Examples:
</B>
</P>
<PRE>
angle_style dipole
angle_coeff 6 2.1 180.0
</PRE>
<P><B>
Description:
</B>
</P>
<P>
The
<I>
dipole
</I>
angle style is used to control the orientation of a dipolar
atom within a molecule
<A
HREF =
"#Orsi"
>
(Orsi)
</A>
. Specifically, the
<I>
dipole
</I>
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).
</P>
<P>
It is convenient to define an angle gamma between the 'free' vector mu_j
and the reference (bond) vector r_ij:
</P>
<CENTER><IMG
SRC =
"Eqs/angle_dipole_gamma.jpg"
>
</CENTER>
<P>
The
<I>
dipole
</I>
angle style uses the potential:
</P>
<CENTER><IMG
SRC =
"Eqs/angle_dipole_potential.jpg"
>
</CENTER>
<P>
where K is a rigidity constant and gamma0 is an equilibrium (reference)
angle.
</P>
<P>
The torque on the dipole can be obtained by differentiating the
potential using the 'chain rule' as in appendix C.3 of
<A
HREF =
"#Allen"
>
(Allen)
</A>
:
</P>
<CENTER><IMG
SRC =
"Eqs/angle_dipole_torque.jpg"
>
</CENTER>
<P>
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').
</P>
<P>
Note that the angle dipole potential does not give rise to any force,
because it does not depend on the distance between i and j (it only
depends on the angle between mu_j and r_ij).
</P>
<P>
The following coefficients must be defined for each angle type via the
<A
HREF =
"angle_coeff.html"
>
angle_coeff
</A>
command as in the example above, or in
the data file or restart files read by the
<A
HREF =
"read_data.html"
>
read_data
</A>
or
<A
HREF =
"read_restart.html"
>
read_restart
</A>
commands:
</P>
<UL><LI>
K (energy)
<LI>
gamma0 (degrees)
</UL>
<HR>
<P>
Styles with a
<I>
cuda
</I>
,
<I>
gpu
</I>
,
<I>
omp
</I>
, or
<I>
opt
</I>
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
<A
HREF =
"Section_accelerate.html"
>
Section_accelerate
</A>
of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the
<A
HREF =
"Section_start.html#start_3"
>
Making LAMMPS
</A>
section for more info.
</P>
<P>
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the
<A
HREF =
"Section_start.html#start_6"
>
-suffix command-line
switch
</A>
when you invoke LAMMPS, or you can
use the
<A
HREF =
"suffix.html"
>
suffix
</A>
command in your input script.
</P>
<P>
See
<A
HREF =
"Section_accelerate.html"
>
Section_accelerate
</A>
of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<P><B>
Restrictions:
</B>
</P>
<P>
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the
<A
HREF =
"Section_start.html#2_3"
>
Making LAMMPS
</A>
section for more info on packages.
</P>
<P>
IMPORTANT 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
</P>
<P>
The "newton" command for intramolecular interactions must be "on"
(which is the default).
</P>
<P>
This angle style should not be used with SHAKE.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"angle_coeff.html"
>
angle_coeff
</A>
,
<A
HREF =
"angle_hybrid.html"
>
angle_hybrid
</A>
</P>
<P><B>
Default:
</B>
none
</P>
<HR>
<A
NAME =
"Orsi"
></A>
<P><B>
(Orsi)
</B>
Orsi
&
Essex, The ELBA force field for coarse-grain modeling of
lipid membranes, PloS ONE 6(12): e28637, 2011.
</P>
<A
NAME =
"Allen"
></A>
<P><B>
(Allen)
</B>
Allen
&
Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.
</P>
</HTML>
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