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This commit is contained in:
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parent
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e5bb1dec27
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@ -51,17 +51,16 @@ curvatures <A HREF = "#Everaers">(Everaers)</A>:
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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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its RE-squared potential fix. Details on the upsilon and mu
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parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>. Use of this pair style requires
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parameters are given <A HREF = "gbdoc">here</A>. Use of this pair style requires
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the NVE, NVT, or NPT fixes 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.
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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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listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>.
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listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this supplementary
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document</A>.
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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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@ -55,10 +55,9 @@ rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
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be used since it defines the rotational state of the ellipsoidal
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particles.
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:link(gbdoc,Eqs/pair_gayberne_extra.pdf)
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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 document"_Eqs/pair_gayberne_extra.pdf.
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listed below and in "this supplementary
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document"_Eqs/pair_gayberne_extra.pdf.
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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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@ -25,25 +25,23 @@ pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
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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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<A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> 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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</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>Details for the equations used are given in the references below and
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in <A HREF = "Eqs/pair_resquqred_extra.pdf">this supplementary 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>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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rotational state of the ellipsoidal particles and the
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<A HREF = "shape.html">shape</A> command should be used to specify ellipsoid
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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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@ -61,52 +59,52 @@ commands:
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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>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 <A HREF = "shape.html">shape</A> 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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</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>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 <A HREF = "#Everaers">(Everaers)</A>. In LJ
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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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composing the ellipsoids and epsilon_LJ determines the interaction
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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>For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
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(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>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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</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>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. Therefore, the effective shape of an ellipsoid
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is given by the specified diameters (see the <A HREF = "shape.html">shape</A>
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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>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 <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>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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</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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@ -135,12 +133,14 @@ that type in a "pair_coeff I J" command.
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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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<P>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 <I>geometric</I>. 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 dependance 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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</P>
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<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
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@ -22,25 +22,23 @@ 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,Babadi)"_#Everaers 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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"(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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:link(redoc,Eqs/pair_resquared_extra.pdf)
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Details for the equations used are given in the references below and
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in "this supplementary document"_Eqs/pair_resquqred_extra.pdf.
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Details for the equations used are given in the references below
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and "this document"_#redoc.
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Use of this pair style requires the NVE, NVT, or NPT fixes
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with the {asphere} extension (e.g. "fix
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nve/asphere"_fix_nve_asphere.html) in order to integrate particle
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rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
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be used since it defines the rotational state of the ellipsoidal
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particles and the "shape"_shape.html command should be used to
|
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specify ellipsoid diameters.
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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 and the
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"shape"_shape.html command should be used to specify ellipsoid
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diameters.
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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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@ -58,52 +56,52 @@ 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 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 "shape"_shape.html
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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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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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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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"(Everaers)"_#Everaers. In LJ units:
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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
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interaction strength 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
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prefactor (see "here"_Eqs/pair_resquared_extra.pdf for details:
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For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
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(see "here"_Eqs/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
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epsilon used in Lennard-Jones pair styles:
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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
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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 "shape"_shape.html command) plus sigma.
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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. Therefore, the effective shape of an ellipsoid
|
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is given by the specified diameters (see the "shape"_shape.html
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command) plus sigma.
|
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|
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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
|
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local contact curvatures "(Everaers)"_#Everaers:
|
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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
|
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cutoff specified in the pair_style command is used.
|
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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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|
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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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|
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@ -132,12 +130,14 @@ that type in a "pair_coeff I J" command.
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[Mixing, shift, table, tail correction, per-atom energy/stress,
|
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restart, rRESPA info]:
|
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|
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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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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
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
|
||||
details. Other type pairs cannot be mixed, due to the different
|
||||
meanings of the energy prefactors used to calculate the interactions
|
||||
and the implicit dependance of the ellipsoid-LJ sphere interaction on
|
||||
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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|
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Loading…
Reference in New Issue