forked from lijiext/lammps
242 lines
10 KiB
HTML
242 lines
10 KiB
HTML
<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 resquared command
|
|
</H3>
|
|
<H3>pair_style resquared/gpu command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>pair_style resquared cutoff
|
|
</PRE>
|
|
<UL><LI>cutoff = global cutoff for interactions (distance units)
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>pair_style resquared 10.0
|
|
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Style <I>resquared</I> computes the RE-squared anisotropic interaction
|
|
<A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
|
|
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
|
|
interactions, the potential considers the ellipsoid as being comprised
|
|
of small spheres of size sigma. LJ particles are a single sphere of
|
|
size sigma. The distinction is made to allow the pair style to make
|
|
efficient calculations of ellipsoid/solvent interactions.
|
|
</P>
|
|
<P>Details for the equations used are given in the references below and
|
|
in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
|
|
</P>
|
|
<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
|
|
rotational state and the size and shape of each ellipsoidal particle.
|
|
</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>A12 = Energy Prefactor/Hamaker constant (energy units)
|
|
<LI>sigma = atomic interaction diameter (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 parameters used depend on the type of the interacting particles,
|
|
i.e. ellipsoids or LJ spheres. The type of a particle is determined
|
|
by the diameters specified for its 3 shape paramters. If all 3 shape
|
|
parameters = 0.0, then the particle is treated as an LJ sphere. The
|
|
epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
|
|
the 3 shape paraemters are > 0.0, then the particle is treated as an
|
|
ellipsoid (even if the 3 parameters are equal to each other).
|
|
</P>
|
|
<P>A12 specifies the energy prefactor which depends on the types of the
|
|
two interacting particles.
|
|
</P>
|
|
<P>For ellipsoid/ellipsoid interactions, the interaction is computed by
|
|
the formulas in the supplementary docuement referenced above. A12 is
|
|
the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
|
|
units:
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_resquared.jpg">
|
|
</CENTER>
|
|
<P>where rho gives the number density of the spherical particles
|
|
composing the ellipsoids and epsilon_LJ determines the interaction
|
|
strength of the spherical particles.
|
|
</P>
|
|
<P>For ellipsoid/LJ sphere interactions, the interaction is also computed
|
|
by the formulas in the supplementary docuement referenced above. A12
|
|
has a modifed form (see <A HREF = "PDF/pair_resquared_extra.pdf">here</A> for
|
|
details):
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
|
|
</CENTER>
|
|
<P>For ellipsoid/LJ sphere interactions, a correction to the distance-
|
|
of-closest approach equation has been implemented to reduce the error
|
|
from two particles of disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary
|
|
document</A>.
|
|
</P>
|
|
<P>For LJ sphere/LJ sphere interactions, the interaction is computed
|
|
using the standard Lennard-Jones formula, which is much cheaper to
|
|
compute than the ellipsoidal formulas. A12 is used as epsilon in the
|
|
standard LJ formula:
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
|
|
</CENTER>
|
|
<P>and the specified <I>sigma</I> is used as the sigma in the standard LJ
|
|
formula.
|
|
</P>
|
|
<P>When one of both of the interacting particles are ellipsoids, then
|
|
<I>sigma</I> specifies the diameter of the continuous distribution of
|
|
constituent particles within each ellipsoid used to model the
|
|
RE-squared potential. Note that this is a different meaning for
|
|
<I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_style gayberne</A> potential
|
|
uses.
|
|
</P>
|
|
<P>The epsilon_i and epsilon_j coefficients are 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 RE-squared 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>For large uniform molecules it has been shown that the epsilon_*_*
|
|
energy parameters are approximately representable in terms of local
|
|
contact curvatures <A HREF = "#Everaers">(Everaers)</A>:
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_resquared4.jpg">
|
|
</CENTER>
|
|
<P>where a, b, and c give the particle diameters.
|
|
</P>
|
|
<P>The last coefficient is optional. If not specified, the global cutoff
|
|
specified in the pair_style command is used.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</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">this section</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", and "opt"
|
|
packages respectively. They are only enabled if LAMMPS was built with
|
|
those packages. See the <A HREF = "Section_start.html#2_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#2_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">this section</A> of the manual for more
|
|
instructions on how to use the accelerated styles effectively.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
|
</P>
|
|
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
|
and cutoff distance can be mixed, but only for sphere pairs. The
|
|
default mix value is <I>geometric</I>. See the "pair_modify" command for
|
|
details. Other type pairs cannot be mixed, due to the different
|
|
meanings of the energy prefactors used to calculate the interactions
|
|
and the implicit dependence of the ellipsoid-sphere interaction on the
|
|
equation for the Hamaker constant presented here. Mixing of sigma and
|
|
epsilon followed by calculation of the energy prefactors using the
|
|
equations above is recommended.
|
|
</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>
|
|
<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
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
|
|
command</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This style is part of the "asphere" package. It is only enabled if
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P>This pair style requires that atoms be ellipsoids as defined by the
|
|
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
|
|
</P>
|
|
<P>Particles acted on by the potential can be extended aspherical or
|
|
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.
|
|
</P>
|
|
<P>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>, <A HREF = "pair_gayberne.html">pair_style
|
|
gayberne</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 = "Babadi"></A>
|
|
|
|
<P><B>(Berardi)</B> Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
|
|
</P>
|
|
</HTML>
|