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pair_style gayberne command

Syntax:

pair_style gayberne gamma upsilon mu cutoff 

Examples:

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 

Description:

Style gayberne computes a Gay-Berne anisotropic LJ interaction (Beradi) between pairs of ellipsoidal particles or an ellipsoidal and spherical particle via the formulas

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").

For large uniform molecules it has been shown that the energy parameters are approximately representable in terms of local contact curvatures (Everaers):

The variable names utilized as potential parameters are for the most part taken from (Everaers) in order to be consistent with its RE-squared potential fix. Details on the upsilon and mu parameters are given here. Use of this pair style requires the NVE, NVT, or NPT fixes with the asphere extension (e.g. fix nve/asphere) in order to integrate particle rotation. Additionally, atom_style ellipsoid should be used since it defines the rotational state of the ellipsoidal particles.

More details of the Gay-Berne formulation are given in the references listed below and in this supplementary document.

The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below:

The last coefficient is optional. If not specified, the global cutoff specified in the pair_style command is used.

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.

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.

Note that if this potential is being used as a sub-style of pair_style hybrid, 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.

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 shape 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.


Mixing, shift, table, tail correction, per-atom energy/stress, restart, rRESPA info:

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 geometric. See the "pair_modify" command for details.

This pair styles supports the pair_modify 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.

The pair_modify table option is not relevant for this pair style.

This pair style does not support the pair_modify tail option for adding long-range tail corrections to energy and pressure.

This pair style does not calculate per-atom energy and stress, as used by the compute epair/atom, compute stress/atom, and dump custom commands.

This pair style writes its information to binary restart files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file.

This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.


Restrictions:

This style is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

The Gay-Berne potential does not become isotropic as r increases (Everaers). The distance-of-closest-approach approximation used by LAMMPS becomes less accurate when high-aspect ratio ellipsoids are used.

Related commands:

pair_coeff, fix nve/asphere, compute temp/asphere

Default: none


(Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).

(Berardi) Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).

(Perram) Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).

(Allen) Allen and Germano, Mol Phys 104, 3225-3235 (2006).