2007-04-20 07:25:27 +08:00
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<HTML>
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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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<HR>
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<H3>pair_style gayberne command
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</H3>
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2009-08-13 00:45:55 +08:00
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<H3>pair_style gayberne/gpu command
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</H3>
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2011-10-07 01:32:51 +08:00
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<H3>pair_style gayberne/omp command
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</H3>
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2007-04-20 07:25:27 +08:00
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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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2011-06-09 05:26:06 +08:00
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<UL><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_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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2009-08-13 00:45:55 +08:00
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<P>The <I>gayberne</I> styles compute a Gay-Berne anisotropic LJ interaction
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2008-02-02 00:28:24 +08:00
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<A HREF = "#Berardi">(Berardi)</A> between pairs of ellipsoidal particles or an
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2007-06-21 01:08:17 +08:00
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ellipsoidal and spherical particle via the formulas
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2007-04-20 07:25:27 +08:00
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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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2007-06-21 01:08:17 +08:00
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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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2007-04-20 07:25:27 +08:00
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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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2009-10-29 23:41:27 +08:00
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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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2007-04-20 07:25:27 +08:00
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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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2008-05-18 06:33:11 +08:00
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listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
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2007-10-23 06:00:52 +08:00
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document</A>.
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2007-04-20 07:25:27 +08:00
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</P>
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2009-05-19 22:43:06 +08:00
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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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2011-04-14 05:39:34 +08:00
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rotational state and the size and shape of each ellipsoidal particle.
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2009-05-19 22:43:06 +08:00
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</P>
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2007-04-20 07:25:27 +08:00
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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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2007-06-26 08:03:39 +08:00
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commands, or by mixing as described below:
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2007-04-20 07:25:27 +08:00
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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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2011-04-14 05:39:34 +08:00
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<P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
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minimum of the 3 shape diameters of the particles involved in an I,I
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interaction, though this is not required. Note that this is a
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different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
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resquared</A> potential uses.
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2009-05-19 22:43:06 +08:00
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</P>
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2007-06-21 01:08:17 +08:00
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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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2011-04-15 03:17:39 +08:00
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<P>IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the
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shape of the particle itself is spherical, meaning its 3 shape
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2011-04-14 05:39:34 +08:00
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parameters are all the same, then the particle is treated as an LJ
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sphere by the Gay-Berne potential. This is significant because if two
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LJ spheres interact, then the simple Lennard-Jones formula is used to
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2011-04-15 03:17:39 +08:00
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compute their interaction energy/force using the specified epsilon and
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sigma as the standard LJ parameters. This is much cheaper to compute
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than the full Gay-Berne formula. To treat the particle as a LJ sphere
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with sigma = D, you should normally set epsilon a = b = c = 1.0, set
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the pair_coeff sigma = D, and also set the 3 shape parameters for the
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particle to D. The one exception is that if the 3 shape parameters
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are set to 0.0, which is a valid way in LAMMPS to specify a point
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particle, then the Gay-Berne potential will treat that as shape
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parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
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requires finite-size particles. In this case you should still set the
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pair_coeff sigma to 1.0 as well.
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2007-04-20 07:25:27 +08:00
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</P>
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2007-06-25 22:36:36 +08:00
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<HR>
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2011-12-14 04:35:35 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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2011-06-09 05:26:06 +08:00
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</P>
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2011-10-07 01:32:51 +08:00
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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2011-08-26 00:46:23 +08:00
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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2011-06-09 05:26:06 +08:00
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-08-26 00:46:23 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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2011-06-09 05:26:06 +08:00
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2009-08-13 00:45:55 +08:00
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</P>
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<HR>
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2008-01-22 02:12:34 +08:00
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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2007-06-25 22:36:36 +08:00
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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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2007-10-04 08:21:14 +08:00
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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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2007-10-12 07:09:49 +08:00
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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2007-10-04 08:21:14 +08:00
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</P>
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2007-06-25 22:36:36 +08:00
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<HR>
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2007-04-20 07:25:27 +08:00
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<P><B>Restrictions:</B>
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</P>
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2011-08-27 02:53:00 +08:00
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<P>The <I>gayberne</I> style is part of the ASPHERE package. It is only
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2011-08-26 00:46:23 +08:00
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enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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2009-06-27 02:22:33 +08:00
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LAMMPS</A> section for more info.
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</P>
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2011-04-14 05:39:34 +08:00
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<P>These pair style require that atoms store torque and a quaternion to
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2009-06-27 02:22:33 +08:00
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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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2011-04-14 05:39:34 +08:00
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<P>This pair style requires that atoms be ellipsoids as defined by the
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<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
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</P>
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2009-06-27 02:22:33 +08:00
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<P>Particles acted on by the potential can be extended aspherical or
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2011-04-14 05:39:34 +08:00
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spherical particles, or point particles. Spherical particles have all
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3 of their shape parameters equal to each other. Point particles have
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all 3 of their shape parameters equal to 0.0.
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2007-04-20 07:25:27 +08:00
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</P>
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2007-06-25 22:36:36 +08:00
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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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2007-04-20 07:25:27 +08:00
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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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2008-02-02 00:42:26 +08:00
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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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2007-04-20 07:25:27 +08:00
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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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2008-02-02 00:28:24 +08:00
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Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
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2007-04-20 07:25:27 +08:00
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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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