2007-04-20 07:25:27 +08:00
|
|
|
<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>pair_style gayberne command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style gayberne gamma upsilon mu cutoff
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>gamma = shift for potential minimum (typically 1)
|
|
|
|
|
<LI>upsilon = exponent for eta orientation-dependent energy function
|
|
|
|
|
<LI>mu = exponent for chi orientation-dependent energy function
|
|
|
|
|
<LI>cutoff = global cutoff for interactions (distance units)
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
|
|
|
|
|
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Style <I>gayberne</I> computes a Gay-Berne anisotropic LJ interaction
|
|
|
|
|
<A HREF = "#Beradi">(Beradi)</A> between pairs of ellipsoidal particles via the
|
|
|
|
|
formulas
|
|
|
|
|
</P>
|
|
|
|
|
<CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
|
|
|
|
|
</CENTER>
|
|
|
|
|
<P>where A1 and A2 are the transformation matrices from the simulation
|
|
|
|
|
box frame to the body frame and r12 is the center to center vector
|
|
|
|
|
between the particles. Ur controls the shifted distance dependent
|
|
|
|
|
interaction based on the distance of closest approach of the two
|
|
|
|
|
particles (h12) and the user-specified shift parameter gamma.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For large uniform molecules it has been shown that the energy
|
|
|
|
|
parameters are approximately representable in terms of local contact
|
|
|
|
|
curvatures <A HREF = "#Everaers">(Everaers)</A>:
|
|
|
|
|
</P>
|
|
|
|
|
<CENTER><IMG SRC = "Eqs/pair_gayberne2.jpg">
|
|
|
|
|
</CENTER>
|
|
|
|
|
<P>The variable names utilized as potential parameters are for the most
|
|
|
|
|
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
|
2007-06-20 20:56:17 +08:00
|
|
|
its RE-squared potential fix. Details on the upsilon and mu
|
|
|
|
|
parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>. Use of this pair style requires
|
|
|
|
|
the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
|
|
|
|
|
nve/asphere</A>) in order to integrate particle
|
2007-04-20 07:25:27 +08:00
|
|
|
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
|
2007-06-20 20:56:17 +08:00
|
|
|
be used since it defines the rotational state of the ellipsoidal
|
2007-04-20 07:25:27 +08:00
|
|
|
particles.
|
|
|
|
|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
|
|
|
|
|
|
2007-04-20 07:25:27 +08:00
|
|
|
<P>More details of the Gay-Berne formulation are given in the references
|
|
|
|
|
listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The following coefficients must be defined for each pair of atoms
|
|
|
|
|
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
|
|
|
|
|
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>epsilon = well depth (energy units)
|
|
|
|
|
<LI>sigma = minimum effective particle radii (distance units)
|
2007-06-20 20:56:25 +08:00
|
|
|
<LI>epsilon_i_a = relative well depth of I for side-to-side interactions
|
|
|
|
|
<LI>epsilon_i_b = relative well depth of I for face-to-face interactions
|
|
|
|
|
<LI>epsilon_i_c = relative well depth of I for end-to-end interactions
|
|
|
|
|
<LI>epsilon_j_a = relative well depth of J for side-to-side interactions
|
|
|
|
|
<LI>epsilon_j_b = relative well depth of J for face-to-face interactions
|
|
|
|
|
<LI>epsilon_j_c = relative well depth of J for end-to-end interactions
|
2007-04-20 07:25:27 +08:00
|
|
|
<LI>cutoff (distance units)
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The last coefficient is optional. If not specified, the global
|
|
|
|
|
cutoff specified in the pair_style command is used.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The epsilon and sigma parameters are mixed for I != J atom pairings
|
|
|
|
|
the same as Lennard-Jones parameters; see the <A HREF = "pair_modify.html">pair_modify
|
|
|
|
|
mix</A> documentation for details. The other parameters
|
|
|
|
|
(except cutoff) are really specific to a single atom type, and not a
|
|
|
|
|
pair of atoms. Thus they are applied to atom type I only.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>Can only be used if LAMMPS was built with the "asphere" package.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The use of this potential requires additional fixes as described
|
|
|
|
|
above. The "shift yes" option currently cannot be used with this
|
|
|
|
|
potential to shift energies to 0 at the cutoff due to the anisotropic
|
|
|
|
|
dependence of the interaction. Angular velocities are all set to zero
|
|
|
|
|
initially. The Gay-Berne potential does not become isotropic as r
|
2007-06-20 20:56:25 +08:00
|
|
|
increases <A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
|
|
|
|
|
approximation used by the code becomes less accurate as the shape of
|
|
|
|
|
ellipsoids becomes more dissimilar (high-aspect-ratio particles).
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
|
|
|
|
|
<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Everaers"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Berardi"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Berardi)</B> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Perram"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Perram)</B> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Allen"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Allen)</B> Allen and Germano, Mol Phys 104, 3225-3235 (2006).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
