forked from lijiext/lammps
252 lines
10 KiB
Plaintext
Executable File
252 lines
10 KiB
Plaintext
Executable File
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style gayberne command :h3
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pair_style gayberne/gpu command :h3
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[Syntax:]
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pair_style gayberne gamma upsilon mu cutoff :pre
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pair_style gayberne/gpu gpuflag gpunum gamma upsilon mu cutoff :pre
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style = {gayberne} or {gayberne/gpu}
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gpuflag = {one/node} or {one/gpu} or {multi/gpu}, only used with gayberne/gpu
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gpunum = gpu ID or quantity, only used with gayberne/gpu
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gamma = shift for potential minimum (typically 1)
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upsilon = exponent for eta orientation-dependent energy function
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mu = exponent for chi orientation-dependent energy function
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cutoff = global cutoff for interactions (distance units) :ul
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[Examples:]
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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 :pre
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[Description:]
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The {gayberne} styles compute a Gay-Berne anisotropic LJ interaction
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"(Berardi)"_#Berardi between pairs of ellipsoidal particles or an
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ellipsoidal and spherical particle via the formulas
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:c,image(Eqs/pair_gayberne.jpg)
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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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Style {gayberne/gpu} is a GPU-enabled version of style {gayberne} that
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should give identical answers. Depending on system size and the GPU
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processor you have on your system, it may be 100x faster (for the
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pairwise portion of the run time). See more details below.
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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 "(Everaers)"_#Everaers:
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:c,image(Eqs/pair_gayberne2.jpg)
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The variable names utilized as potential parameters are for the most
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part taken from "(Everaers)"_#Everaers in order to be consistent with
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its RE-squared potential fix. Details on the upsilon and mu
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parameters are given "here"_gbdoc.
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More details of the Gay-Berne formulation are given in the references
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listed below and in "this supplementary
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document"_PDF/pair_gayberne_extra.pdf.
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Use of this pair style requires the NVE, NVT, or NPT fixes with the
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{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
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order to integrate particle rotation. Additionally, "atom_style
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ellipsoid"_atom_style.html 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 "shape"_shape.html
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command.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html 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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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon = well depth (energy units)
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sigma = minimum effective particle radii (distance units)
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epsilon_i_a = relative well depth of type I for side-to-side interactions
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epsilon_i_b = relative well depth of type I for face-to-face interactions
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epsilon_i_c = relative well depth of type I for end-to-end interactions
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epsilon_j_a = relative well depth of type J for side-to-side interactions
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epsilon_j_b = relative well depth of type J for face-to-face interactions
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epsilon_j_c = relative well depth of type J for end-to-end interactions
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cutoff (distance units) :ul
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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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It is typical for the Gay-Berne potential to define {sigma} 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 {sigma}
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than the "pair_style resquared"_pair_resquared.html potential uses.
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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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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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Note that if this potential is being used as a sub-style of
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"pair_style hybrid"_pair_hybrid.html, 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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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 "shape"_shape.html
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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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:line
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The {gayberne/gpu} style is identical to the {gayberne} 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, espcially for the relatively expensive
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computations inherent in Gay-Berne interactions. See the "Running on
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GPUs"_Section_start.html#2_8 section of the manual for more details
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about hardware and software requirements for using GPUs.
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The {gpuflag} and {gpunum} settings in the pair_style command refer to
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how the GPUs on your system are configured.
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Set {gpuflag} to {one/node} if you have a single compute "node" on
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your system, which may have multiple cores and/or GPUs. {Gpunum}
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should be set to the ID of the (first) GPU you wish to use with LAMMPS
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(another GPU might be driving your display).
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Set {gpuflag} to {one/gpu} if you have multiple compute "nodes" on
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your system, with one GPU per node. {Gpunum} should be set to the ID
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of the GPU.
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Set {gpuflag} to {multi/gpu} if you have multiple compute "nodes" on
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your system, each with multiple GPUs. {Gpunum} should be set to the
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number of GPUs per node.
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More details about these settings and various possible hardware
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configuration are in "this section"_Section_start.html#2_8 of the
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manual.
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Additional requirements in your input script to run with style
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{gayberne/gpu} are as follows:
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The "newton pair"_newton.html setting must be {off}.
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You should use the "neigh_modify one"_neigh_modify.html command and
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set its value to something close (but slightly larger) than the number
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of pairwise neighbors/atom you expect to have in your model. This is
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a function of the pairwise cutoff. Note that the default for this
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setting is 2000, which is much larger than most models need. Unlike
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neighbor lists in LAMMPS itself, the GPU version of this pair style
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uses that setting to allocate memory on the GPU for neighbor
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information. If the setting is too large, it will limit the number of
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atoms that can be stored on the GPU.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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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 {geometric}. See the "pair_modify" command for details.
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This pair styles supports the "pair_modify"_pair_modify.html 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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The "pair_modify"_pair_modify.html table option is not relevant
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for this pair style.
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This pair style does not support the "pair_modify"_pair_modify.html
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tail option for adding long-range tail corrections to energy and
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pressure.
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This pair style writes its information to "binary restart
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files"_restart.html, 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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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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The {gayberne} style is part of the "asphere" package. The
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{gayberne/gpu} 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 "Making
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LAMMPS"_Section_start.html#2_3 section for more info.
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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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"atom_style"_atom_style.html. It also require they store a per-type
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"shape"_shape.html. The particles cannot store a per-particle
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diameter.
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Particles acted on by the potential can be extended aspherical or
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spherical particles, or point particles.
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The Gay-Berne potential does not become isotropic as r increases
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"(Everaers)"_#Everaers. 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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[Related commands:]
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"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html,
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"compute temp/asphere"_compute_temp_asphere.html, "pair_style
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resquared"_pair_resquared.html
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[Default:] none
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:line
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:link(Everaers)
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[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
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:link(Berardi)
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[(Berardi)] 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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:link(Perram)
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[(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
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:link(Allen)
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[(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006).
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