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236 lines
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<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>
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<H3>pair_style gayberne command
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</H3>
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<H3>pair_style gayberne/gpu command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style gayberne gamma upsilon mu cutoff
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</PRE>
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<PRE>pair_style gayberne/gpu gamma upsilon mu cutoff
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</PRE>
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<UL><LI>style = <I>gayberne</I> or <I>gayberne/gpu</I>
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<LI>gamma = shift for potential minimum (typically 1)
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<LI>upsilon = exponent for eta orientation-dependent energy function
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<LI>mu = exponent for chi orientation-dependent energy function
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<LI>cutoff = global cutoff for interactions (distance units)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
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pair_style gayberne/gpu 1.0 1.0 1.0 10.0
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pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>gayberne</I> styles compute a Gay-Berne anisotropic LJ interaction
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<A HREF = "#Berardi">(Berardi)</A> between pairs of ellipsoidal particles or an
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ellipsoidal and spherical particle via the formulas
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</P>
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<CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
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</CENTER>
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<P>where A1 and A2 are the transformation matrices from the simulation
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box frame to the body frame and r12 is the center to center vector
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between the particles. Ur controls the shifted distance dependent
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interaction based on the distance of closest approach of the two
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particles (h12) and the user-specified shift parameter gamma. When
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both particles are spherical, the formula reduces to the usual
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Lennard-Jones interaction (see details below for when Gay-Berne treats
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a particle as "spherical").
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</P>
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<P>Style <I>gayberne/gpu</I> is a GPU-enabled version of style <I>gayberne</I>.
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See more details below.
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</P>
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<P>For large uniform molecules it has been shown that the energy
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parameters are approximately representable in terms of local contact
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curvatures <A HREF = "#Everaers">(Everaers)</A>:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_gayberne2.jpg">
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</CENTER>
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<P>The variable names utilized as potential parameters are for the most
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part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
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the <A HREF = "pair_resquared.html">RE-squared pair potential</A>. Details on the
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upsilon and mu parameters are given
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<A HREF = "PDF/pair_resquared_extra.pdf">here</A>.
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</P>
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<P>More details of the Gay-Berne formulation are given in the references
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listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
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document</A>.
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</P>
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<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
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<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
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order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
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ellipsoid</A> should be used since it defines the
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rotational state of the ellipsoidal particles. The size and shape of
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the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
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command.
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</P>
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<P>The following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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</P>
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<UL><LI>epsilon = well depth (energy units)
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<LI>sigma = minimum effective particle radii (distance units)
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<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
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<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
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<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
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<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
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<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
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<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
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<LI>cutoff (distance units)
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</UL>
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<P>The last coefficient is optional. If not specified, the global
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cutoff specified in the pair_style command is used.
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</P>
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<P>It is typical for the Gay-Berne potential to define <I>sigma</I> as the
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minimum of the 3 "shape" diameters for a I,I interaction, though this
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is not required. Note that this is a different meaning for <I>sigma</I>
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than the <A HREF = "pair_resquared.html">pair_style resquared</A> potential uses.
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</P>
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<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
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types, not for pairs of atom types. Thus, in a series of pair_coeff
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commands, they only need to be specified once for each atom type.
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</P>
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<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
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non-zero, the three values are assigned to atom type I. If all the
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epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
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epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
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to atom type J. If all three epsilon_i values are zero, they are
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ignored. Thus the typical way to define the epsilon_i and epsilon_j
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coefficients is to list their values in "pair_coeff I J" commands when
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I = J, but set them to 0.0 when I != J. If you do list them when I !=
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J, you should insure they are consistent with their values in other
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pair_coeff commands.
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</P>
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<P>Note that if this potential is being used as a sub-style of
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<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
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setting made for Gay-Berne for a particular type I (because I-I
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interactions are computed by another hybrid pair potential), then you
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still need to insure the epsilon a,b,c coefficients are assigned to
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that type in a "pair_coeff I J" command.
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</P>
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<P>IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
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if the shape of the particle is spherical (see the <A HREF = "shape.html">shape</A>
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command), meaning the 3 diameters are all the same, then the particle
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is treated as "spherical" by the Gay-Berne potential. This is
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significant because if two "spherical" particles interact, then the
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simple Lennard-Jones formula is used to compute their interaction
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energy/force using epsilon and sigma, which is much cheaper to compute
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than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
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are set to 1.0 for spherical particle types and use epsilon and sigma
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to specify its interaction with other spherical particles.
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</P>
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<HR>
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<P>The <I>gayberne/gpu</I> style is identical to the <I>gayberne</I> style, except
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that each processor off-loads its pairwise calculations to a GPU chip.
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Depending on the hardware available on your system this can provide a
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significant speed-up, especially for the relatively expensive
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computations inherent in Gay-Berne interactions. See the <A HREF = "Section_start.html#2_8">Running on
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GPUs</A> section of the manual for more details
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about hardware and software requirements for using GPUs.
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</P>
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<P>More details about these settings and various possible hardware
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configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
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manual.
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</P>
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<P>Additional requirements in your input script to run with style
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<I>gayberne/gpu</I> are as follows:
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</P>
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<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
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<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
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essential GPU selection and initialization steps.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for this pair style can be mixed. The default mix
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value is <I>geometric</I>. See the "pair_modify" command for details.
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</P>
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<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
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option for the energy of the Lennard-Jones portion of the pair
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interaction, but only for sphere-sphere interactions. There is no
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shifting performed for ellipsoidal interactions due to the anisotropic
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dependence of the interaction.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
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for this pair style.
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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tail option for adding long-range tail corrections to energy and
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pressure.
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</P>
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<P>This pair style writes its information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>gayberne</I> style is part of the "asphere" package. The
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<I>gayberne/gpu</I> style is part of the "gpu" package. They are only
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enabled if LAMMPS was built with the those packages. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>This pair style requires that atoms store torque and a quaternion to
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represent their orientation, as defined by the
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<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
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<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
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diameter.
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</P>
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<P>Particles acted on by the potential can be extended aspherical or
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spherical particles, or point particles.
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</P>
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<P>The Gay-Berne potential does not become isotropic as r increases
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<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
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approximation used by LAMMPS becomes less accurate when high-aspect
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ratio ellipsoids are used.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
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<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_resquared.html">pair_style
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resquared</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Everaers"></A>
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<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
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</P>
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<A NAME = "Berardi"></A>
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<P><B>(Berardi)</B> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
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Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
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</P>
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<A NAME = "Perram"></A>
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<P><B>(Perram)</B> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
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</P>
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<A NAME = "Allen"></A>
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<P><B>(Allen)</B> Allen and Germano, Mol Phys 104, 3225-3235 (2006).
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</P>
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</HTML>
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