Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/pair_gayberne.html
b704a82dafc5efficient_neuronet

Last Change
Raw File

pair_gayberne.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>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 or an
ellipsoidal and spherical particle 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. 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").
</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
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
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
be used since it defines the rotational state of the ellipsoidal
particles.
</P>
<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)
<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
<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.
</P>
<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
to atom type J. If all three epsilon_i values are zero, they are
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
pair_coeff commands.
</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
that type in a "pair_coeff I J" command.
</P>
<P>IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
if the shape of the particle is spherical (see the <A HREF = "shape.html">shape</A>
command), meaning the 3 diameters are all the same, then the particle
is treated as "spherical" by the Gay-Berne potential. This is
significant because if two "spherical" particles interact, then the
simple Lennard-Jones formula is used to compute their interaction
energy/force using epsilon and sigma, which is much cheaper to compute
than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
are set to 1.0 for spherical particle types and use epsilon and sigma
to specify its interaction with other spherical particles.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package.
</P>
<P>The "shift yes" option in <A HREF = "pair_modify.html">pair_modify</A> only applies
to sphere-sphere interactions for this potential; there is no shifting
performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction. 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.
</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>
c4science · Help