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>
|
2009-08-13 00:45:55 +08:00
|
|
|
<H3>pair_style gayberne/gpu command
|
|
|
|
|
</H3>
|
2014-08-15 00:30:25 +08:00
|
|
|
<H3>pair_style gayberne/intel command
|
|
|
|
|
</H3>
|
2011-10-07 01:32:51 +08:00
|
|
|
<H3>pair_style gayberne/omp command
|
|
|
|
|
</H3>
|
2007-04-20 07:25:27 +08:00
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style gayberne gamma upsilon mu cutoff
|
|
|
|
|
</PRE>
|
2011-06-09 05:26:06 +08:00
|
|
|
<UL><LI>gamma = shift for potential minimum (typically 1)
|
2007-04-20 07:25:27 +08:00
|
|
|
<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>
|
2009-08-13 00:45:55 +08:00
|
|
|
<P>The <I>gayberne</I> styles compute a Gay-Berne anisotropic LJ interaction
|
2008-02-02 00:28:24 +08:00
|
|
|
<A HREF = "#Berardi">(Berardi)</A> between pairs of ellipsoidal particles or an
|
2007-06-21 01:08:17 +08:00
|
|
|
ellipsoidal and spherical particle via the formulas
|
2007-04-20 07:25:27 +08:00
|
|
|
</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
|
2007-06-21 01:08:17 +08:00
|
|
|
particles (h12) and the user-specified shift parameter gamma. When
|
|
|
|
|
both particles are spherical, the formula reduces to the usual
|
|
|
|
|
Lennard-Jones interaction (see details below for when Gay-Berne treats
|
|
|
|
|
a particle as "spherical").
|
2007-04-20 07:25:27 +08:00
|
|
|
</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
|
2009-10-29 23:41:27 +08:00
|
|
|
the <A HREF = "pair_resquared.html">RE-squared pair potential</A>. Details on the
|
|
|
|
|
upsilon and mu parameters are given
|
|
|
|
|
<A HREF = "PDF/pair_resquared_extra.pdf">here</A>.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
|
|
|
|
<P>More details of the Gay-Berne formulation are given in the references
|
2008-05-18 06:33:11 +08:00
|
|
|
listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
|
2007-10-23 06:00:52 +08:00
|
|
|
document</A>.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
2009-05-19 22:43:06 +08:00
|
|
|
<P>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 rotation. Additionally, <A HREF = "atom_style.html">atom_style
|
|
|
|
|
ellipsoid</A> should be used since it defines the
|
2011-04-14 05:39:34 +08:00
|
|
|
rotational state and the size and shape of each ellipsoidal particle.
|
2009-05-19 22:43:06 +08:00
|
|
|
</P>
|
2007-04-20 07:25:27 +08:00
|
|
|
<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>
|
2007-06-26 08:03:39 +08:00
|
|
|
commands, or by mixing as described below:
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
|
|
|
|
<UL><LI>epsilon = well depth (energy units)
|
|
|
|
|
<LI>sigma = minimum effective particle radii (distance units)
|
2007-06-21 01:08:17 +08:00
|
|
|
<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
|
|
|
|
|
<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
|
|
|
|
|
<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
|
|
|
|
|
<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
|
|
|
|
|
<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
|
|
|
|
|
<LI>epsilon_j_c = relative well depth of type 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>
|
2011-04-14 05:39:34 +08:00
|
|
|
<P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
|
|
|
|
|
minimum of the 3 shape diameters of the particles involved in an I,I
|
|
|
|
|
interaction, though this is not required. Note that this is a
|
|
|
|
|
different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
|
|
|
|
|
resquared</A> potential uses.
|
2009-05-19 22:43:06 +08:00
|
|
|
</P>
|
2007-06-21 01:08:17 +08:00
|
|
|
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
|
|
|
|
|
types, not for pairs of atom types. Thus, in a series of pair_coeff
|
|
|
|
|
commands, they only need to be specified once for each atom type.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
|
|
|
|
|
non-zero, the three values are assigned to atom type I. If all the
|
|
|
|
|
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
|
|
|
|
|
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
|
2012-10-05 23:32:01 +08:00
|
|
|
to atom type J. If all three epsilon_j values are zero, they are
|
2007-06-21 01:08:17 +08:00
|
|
|
ignored. Thus the typical way to define the epsilon_i and epsilon_j
|
|
|
|
|
coefficients is to list their values in "pair_coeff I J" commands when
|
|
|
|
|
I = J, but set them to 0.0 when I != J. If you do list them when I !=
|
|
|
|
|
J, you should insure they are consistent with their values in other
|
2012-10-05 23:32:01 +08:00
|
|
|
pair_coeff commands, since only the last setting will be in effect.
|
2007-06-21 01:08:17 +08:00
|
|
|
</P>
|
|
|
|
|
<P>Note that if this potential is being used as a sub-style of
|
|
|
|
|
<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
|
|
|
|
|
setting made for Gay-Berne for a particular type I (because I-I
|
|
|
|
|
interactions are computed by another hybrid pair potential), then you
|
|
|
|
|
still need to insure the epsilon a,b,c coefficients are assigned to
|
2012-10-05 23:32:01 +08:00
|
|
|
that type. e.g. in a "pair_coeff I J" command.
|
2007-06-21 01:08:17 +08:00
|
|
|
</P>
|
2011-04-15 03:17:39 +08:00
|
|
|
<P>IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the
|
|
|
|
|
shape of the particle itself is spherical, meaning its 3 shape
|
2011-04-14 05:39:34 +08:00
|
|
|
parameters are all the same, then the particle is treated as an LJ
|
|
|
|
|
sphere by the Gay-Berne potential. This is significant because if two
|
|
|
|
|
LJ spheres interact, then the simple Lennard-Jones formula is used to
|
2011-04-15 03:17:39 +08:00
|
|
|
compute their interaction energy/force using the specified epsilon and
|
|
|
|
|
sigma as the standard LJ parameters. This is much cheaper to compute
|
|
|
|
|
than the full Gay-Berne formula. To treat the particle as a LJ sphere
|
|
|
|
|
with sigma = D, you should normally set epsilon a = b = c = 1.0, set
|
|
|
|
|
the pair_coeff sigma = D, and also set the 3 shape parameters for the
|
|
|
|
|
particle to D. The one exception is that if the 3 shape parameters
|
|
|
|
|
are set to 0.0, which is a valid way in LAMMPS to specify a point
|
|
|
|
|
particle, then the Gay-Berne potential will treat that as shape
|
|
|
|
|
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
|
|
|
|
|
requires finite-size particles. In this case you should still set the
|
|
|
|
|
pair_coeff sigma to 1.0 as well.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2014-08-15 00:30:25 +08:00
|
|
|
<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.
|
2011-06-09 05:26:06 +08:00
|
|
|
</P>
|
|
|
|
|
<P>You can specify the accelerated styles explicitly in your input script
|
2012-01-28 07:39:14 +08:00
|
|
|
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
2011-08-26 00:46:23 +08:00
|
|
|
switch</A> when you invoke LAMMPS, or you can
|
|
|
|
|
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
2011-06-09 05:26:06 +08:00
|
|
|
</P>
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
|
|
|
|
more instructions on how to use the accelerated styles effectively.
|
2009-08-13 00:45:55 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2008-01-22 02:12:34 +08:00
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
|
|
|
|
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
|
|
|
|
and cutoff distance for this pair style can be mixed. The default mix
|
|
|
|
|
value is <I>geometric</I>. See the "pair_modify" command for details.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
|
|
|
|
|
option for the energy of the Lennard-Jones portion of the pair
|
|
|
|
|
interaction, but only for sphere-sphere interactions. There is no
|
|
|
|
|
shifting performed for ellipsoidal interactions due to the anisotropic
|
|
|
|
|
dependence of the interaction.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
|
|
|
|
|
for this pair style.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
|
|
|
|
tail option for adding long-range tail corrections to energy and
|
|
|
|
|
pressure.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
|
|
|
|
|
files</A>, so pair_style and pair_coeff commands do not need
|
|
|
|
|
to be specified in an input script that reads a restart file.
|
|
|
|
|
</P>
|
2007-10-04 08:21:14 +08:00
|
|
|
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
|
|
|
|
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
2007-10-12 07:09:49 +08:00
|
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
2007-10-04 08:21:14 +08:00
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-04-20 07:25:27 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2011-08-27 02:53:00 +08:00
|
|
|
<P>The <I>gayberne</I> style is part of the ASPHERE package. It is only
|
2011-08-26 00:46:23 +08:00
|
|
|
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
2009-06-27 02:22:33 +08:00
|
|
|
LAMMPS</A> section for more info.
|
|
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<P>These pair style require that atoms store torque and a quaternion to
|
2009-06-27 02:22:33 +08:00
|
|
|
represent their orientation, as defined by the
|
|
|
|
|
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
|
|
|
|
|
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
|
|
|
|
|
diameter.
|
|
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<P>This pair style requires that atoms be ellipsoids as defined by the
|
|
|
|
|
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
|
|
|
|
|
</P>
|
2013-02-01 08:24:05 +08:00
|
|
|
<P>Particles acted on by the potential can be finite-size aspherical or
|
2011-04-14 05:39:34 +08:00
|
|
|
spherical particles, or point particles. Spherical particles have all
|
|
|
|
|
3 of their shape parameters equal to each other. Point particles have
|
|
|
|
|
all 3 of their shape parameters equal to 0.0.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>The Gay-Berne potential does not become isotropic as r increases
|
|
|
|
|
<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
|
|
|
|
|
approximation used by LAMMPS becomes less accurate when high-aspect
|
|
|
|
|
ratio ellipsoids are used.
|
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>,
|
2008-02-02 00:42:26 +08:00
|
|
|
<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_resquared.html">pair_style
|
|
|
|
|
resquared</A>
|
2007-04-20 07:25:27 +08:00
|
|
|
</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).
|
2008-02-02 00:28:24 +08:00
|
|
|
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
|
2007-04-20 07:25:27 +08:00
|
|
|
</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>
|
