forked from lijiext/lammps
202 lines
8.3 KiB
HTML
202 lines
8.3 KiB
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 resquared 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 resquared cutoff
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</PRE>
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<UL><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 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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>resquared</I> computes the RE-squared anisotropic interaction
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<A HREF = "#Everaers">(Everaers,Babadi)</A> between pairs of ellipsoidal and/or
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spherical Lennard-Jones particles. For ellipsoidal interactions,
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the potential considers the ellipsoid as being comprised of small
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spheres of size sigma. LJ particles are a single sphere of size
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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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</P>
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<P>Details for the equations used are given in the references below
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and <A HREF = "#redoc">this document</A>.
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</P>
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<P>Use of this pair style requires the NVE, NVT, or NPT fixes
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with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
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nve/asphere</A>) in order to integrate particle
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rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
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be used since it defines the rotational state of the ellipsoidal
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particles and the <A HREF = "shape.html">shape</A> command should be used to
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specify ellipsoid diameters.
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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:
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</P>
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<UL><LI>A12 = Energy Prefactor/Hamaker constant (energy units)
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<LI>sigma = atomic interaction diameter (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 parameters used depend on the type of particles interacting -
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ellipsoid or LJ sphere. The type of particle is determined by
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the diameters specified with the <A HREF = "shape.html">shape</A>
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command. LJ spheres have diameters equal to zero and thus
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represent a single particle with size sigma. The epsilon_i_* or
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epsilon_j_* parameters are ignored for LJ sphere interactions.
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The interactions between two LJ sphere particles are computed
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using the standard Lennard-Jones formula.
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</P>
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<P>A12 specifies the energy prefactor which depends on
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the type of particles interacting. For ellipsoid-ellipsoid
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interactions, A12 is the Hamaker constant as described in
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<A HREF = "#Everaers">(Everaers)</A>. In LJ units:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_resquared.jpg">
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</CENTER>
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<P>where rho gives the number density of the spherical particles
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composing the ellipsoids and epsilon_LJ determines the
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interaction strength of the spherical particles.
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</P>
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<P>For ellipsoid-LJ sphere interactions, A12 gives the energy
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prefactor (see <A HREF = "Eqs/pair_resquared_extra.pdf">here</A> for details:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
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</CENTER>
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<P>For LJ sphere-LJ sphere interactions, A12 is the standard
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epsilon used in Lennard-Jones pair styles:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
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</CENTER>
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<P>sigma specifies the diameter of the continuous distribution of
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constituent particles within each ellipsoid used to model
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the RE-squared potential. Therefore, the effective shape
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of an ellipsoid is given by the specified diameters
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(see the <A HREF = "shape.html">shape</A> command) plus sigma.
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</P>
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<P>For large uniform molecules it has been shown that the epsilon_*_*
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energy parameters are approximately representable in terms of
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local contact curvatures <A HREF = "#Everaers">(Everaers)</A>:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_resquared4.jpg">
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</CENTER>
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<P>where a, b, and c give the particle diameters.
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</P>
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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>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 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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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
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restart, rRESPA info</B>:
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</P>
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<P>Automatic mixing is supported only between LJ sphere
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pairs due to the different meanings of the energy prefactors used
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to calculate the interactions and the implicit dependance of
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the ellipsoid-LJ sphere interaction on the equation for the
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Hamaker constant presented here. Mixing of sigma and epsilon
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followed by calculation of the energy prefactors using the
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equations above is recommended.
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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 does not calculate per-atom energy and stress, as used
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by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
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stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
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commands.
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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 of the <A HREF = "run_style.html">run_style
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command</A>.
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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>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 <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>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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</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>
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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 = "Babadi"></A>
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<P><B>(Berardi)</B> Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
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</P>
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</HTML>
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