forked from lijiext/lammps
210 lines
8.3 KiB
Plaintext
Executable File
210 lines
8.3 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 resquared command :h3
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[Syntax:]
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pair_style resquared cutoff :pre
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cutoff = global cutoff for interactions (distance units) :ul
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[Examples:]
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pair_style resquared 10.0
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pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre
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[Description:]
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Style {resquared} computes the RE-squared anisotropic interaction
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"(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of
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ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
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interactions, the potential considers the ellipsoid as being comprised
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of small spheres of size sigma. LJ particles are a single sphere of
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size sigma. The distinction is made to allow the pair style to make
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efficient calculations of ellipsoid/solvent interactions.
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Details for the equations used are given in the references below and
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in "this supplementary document"_PDF/pair_resquared_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:
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A12 = Energy Prefactor/Hamaker constant (energy units)
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sigma = atomic interaction diameter (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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As described above, {sigma} is the size of the small spheres which are
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integrated over to create the potential. Note that this is a
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different meaning for {sigma} than the "pair_style
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gayberne"_pair_gayberne.html potential uses.
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The parameters used depend on the type of the interacting particles,
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i.e. ellipsoid or LJ sphere. The type of particle is determined by
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the diameters specified with the "shape"_shape.html command. LJ
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spheres have diameters equal to zero and thus represent a single
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particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
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are ignored for LJ sphere interactions. The interactions between two
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LJ sphere particles are computed using the standard Lennard-Jones
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formula.
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For ellipsoid-LJ sphere interactions, a correction to the distance-
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of-closest approach equation has been implemented to reduce the error
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from disparate sizes; see "this supplementary
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document"_PDF/pair_resquared_extra.pdf.
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A12 specifies the energy prefactor which depends on the type of
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particles interacting. For ellipsoid-ellipsoid interactions, A12 is
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the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
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units:
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:c,image(Eqs/pair_resquared.jpg)
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where rho gives the number density of the spherical particles
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composing the ellipsoids and epsilon_LJ determines the interaction
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strength of the spherical particles.
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For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
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(see "here"_PDF/pair_resquared_extra.pdf for details:
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:c,image(Eqs/pair_resquared2.jpg)
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For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used
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in Lennard-Jones pair styles:
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:c,image(Eqs/pair_resquared3.jpg)
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sigma specifies the diameter of the continuous distribution of
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constituent particles within each ellipsoid used to model the
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RE-squared potential.
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For large uniform molecules it has been shown that the epsilon_*_*
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energy parameters are approximately representable in terms of local
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contact curvatures "(Everaers)"_#Everaers:
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:c,image(Eqs/pair_resquared4.jpg)
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where a, b, and c give the particle diameters.
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The last coefficient is optional. If not specified, the global cutoff
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specified in the pair_style command is used.
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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 RE-squared 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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: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 can be mixed, but only for LJ sphere pairs. The
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default mix value is {geometric}. See the "pair_modify" command for
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details. Other type pairs cannot be mixed, due to the different
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meanings of the energy prefactors used to calculate the interactions
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and the implicit dependence of the ellipsoid-LJ sphere interaction on
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the equation for the Hamaker constant presented here. Mixing of sigma
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and epsilon followed by calculation of the energy prefactors using the
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equations above is recommended.
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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 of the "run_style
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command"_run_style.html.
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:line
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[Restrictions:]
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This style is part of the "asphere" package. It is only enabled if
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LAMMPS was built with that package. 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 distance-of-closest-approach approximation used by LAMMPS becomes
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less accurate when high-aspect 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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gayberne"_pair_gayberne.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(Babadi)
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[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
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