Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/doc2/angle_dipole.html
fbfd916c6998efficient_neuronet

Last Change
Raw File

angle_dipole.html
View Options

<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>intel</I>, <I>kk</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-INTEL,
KOKKOS, 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>
c4science · Help