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7
doc/pair_gayberne.html
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@ -51,17 +51,16 @@ curvatures <A HREF = "#Everaers">(Everaers)</A>:
<P>The variable names utilized as potential parameters are for the most <P>The variable names utilized as potential parameters are for the most
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu its RE-squared potential fix. Details on the upsilon and mu
parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>. Use of this pair style requires parameters are given <A HREF = "gbdoc">here</A>. Use of this pair style requires
the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
nve/asphere</A>) in order to integrate particle nve/asphere</A>) in order to integrate particle
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
be used since it defines the rotational state of the ellipsoidal be used since it defines the rotational state of the ellipsoidal
particles. particles.
</P> </P>
<P>More details of the Gay-Berne formulation are given in the references <P>More details of the Gay-Berne formulation are given in the references
listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>. listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this supplementary
document</A>.
</P> </P>
<P>The following coefficients must be defined for each pair of atoms <P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples

5
doc/pair_gayberne.txt
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@ -55,10 +55,9 @@ rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
be used since it defines the rotational state of the ellipsoidal be used since it defines the rotational state of the ellipsoidal
particles. particles.
:link(gbdoc,Eqs/pair_gayberne_extra.pdf)
More details of the Gay-Berne formulation are given in the references More details of the Gay-Berne formulation are given in the references
listed below and in "this document"_Eqs/pair_gayberne_extra.pdf. listed below and in "this supplementary
document"_Eqs/pair_gayberne_extra.pdf.
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples types via the "pair_coeff"_pair_coeff.html command as in the examples

100
doc/pair_resquared.html
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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
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Style <I>resquared</I> computes the RE-squared anisotropic interaction <P>Style <I>resquared</I> computes the RE-squared anisotropic interaction
<A HREF = "#Everaers">(Everaers,Babadi)</A> between pairs of ellipsoidal and/or <A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
spherical Lennard-Jones particles. For ellipsoidal interactions, ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
the potential considers the ellipsoid as being comprised of small interactions, the potential considers the ellipsoid as being comprised
spheres of size sigma. LJ particles are a single sphere of size of small spheres of size sigma. LJ particles are a single sphere of
sigma. The distinction is made to allow the pair style to make size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions. efficient calculations of ellipsoid/solvent interactions.
</P> </P>
<P>Details for the equations used are given in the references below and
in <A HREF = "Eqs/pair_resquqred_extra.pdf">this supplementary document</A>.
<P>Details for the equations used are given in the references below
and <A HREF = "#redoc">this document</A>.
</P> </P>
<P>Use of this pair style requires the NVE, NVT, or NPT fixes <P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
nve/asphere</A>) in order to integrate particle order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should ellipsoid</A> should be used since it defines the
be used since it defines the rotational state of the ellipsoidal rotational state of the ellipsoidal particles and the
particles and the <A HREF = "shape.html">shape</A> command should be used to <A HREF = "shape.html">shape</A> command should be used to specify ellipsoid
specify ellipsoid diameters. diameters.
</P> </P>
<P>The following coefficients must be defined for each pair of atoms <P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@ -61,52 +59,52 @@ commands:
<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions <LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
<LI>cutoff (distance units) <LI>cutoff (distance units)
</UL> </UL>
<P>The parameters used depend on the type of particles interacting - <P>The parameters used depend on the type of the interacting particles,
ellipsoid or LJ sphere. The type of particle is determined by i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the <A HREF = "shape.html">shape</A> the diameters specified with the <A HREF = "shape.html">shape</A> command. LJ
command. LJ spheres have diameters equal to zero and thus spheres have diameters equal to zero and thus represent a single
represent a single particle with size sigma. The epsilon_i_* or particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
epsilon_j_* parameters are ignored for LJ sphere interactions. are ignored for LJ sphere interactions. The interactions between two
The interactions between two LJ sphere particles are computed LJ sphere particles are computed using the standard Lennard-Jones
using the standard Lennard-Jones formula. formula.
</P> </P>
<P>A12 specifies the energy prefactor which depends on <P>A12 specifies the energy prefactor which depends on the type of
the type of particles interacting. For ellipsoid-ellipsoid particles interacting. For ellipsoid-ellipsoid interactions, A12 is
interactions, A12 is the Hamaker constant as described in the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
<A HREF = "#Everaers">(Everaers)</A>. In LJ units: units:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared.jpg">
</CENTER> </CENTER>
<P>where rho gives the number density of the spherical particles <P>where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the composing the ellipsoids and epsilon_LJ determines the interaction
interaction strength of the spherical particles. strength of the spherical particles.
</P> </P>
<P>For ellipsoid-LJ sphere interactions, A12 gives the energy <P>For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
prefactor (see <A HREF = "Eqs/pair_resquared_extra.pdf">here</A> for details: (see <A HREF = "Eqs/pair_resquared_extra.pdf">here</A> for details:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
</CENTER> </CENTER>
<P>For LJ sphere-LJ sphere interactions, A12 is the standard <P>For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used
epsilon used in Lennard-Jones pair styles: in Lennard-Jones pair styles:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
</CENTER> </CENTER>
<P>sigma specifies the diameter of the continuous distribution of <P>sigma specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model constituent particles within each ellipsoid used to model the
the RE-squared potential. Therefore, the effective shape RE-squared potential. Therefore, the effective shape of an ellipsoid
of an ellipsoid is given by the specified diameters is given by the specified diameters (see the <A HREF = "shape.html">shape</A>
(see the <A HREF = "shape.html">shape</A> command) plus sigma. command) plus sigma.
</P> </P>
<P>For large uniform molecules it has been shown that the epsilon_*_* <P>For large uniform molecules it has been shown that the epsilon_*_*
energy parameters are approximately representable in terms of energy parameters are approximately representable in terms of local
local contact curvatures <A HREF = "#Everaers">(Everaers)</A>: contact curvatures <A HREF = "#Everaers">(Everaers)</A>:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared4.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared4.jpg">
</CENTER> </CENTER>
<P>where a, b, and c give the particle diameters. <P>where a, b, and c give the particle diameters.
</P> </P>
<P>The last coefficient is optional. If not specified, the global <P>The last coefficient is optional. If not specified, the global cutoff
cutoff specified in the pair_style command is used. specified in the pair_style command is used.
</P> </P>
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom <P>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 types, not for pairs of atom types. Thus, in a series of pair_coeff
@ -135,12 +133,14 @@ that type in a "pair_coeff I J" command.
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, <P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>: restart, rRESPA info</B>:
</P> </P>
<P>Automatic mixing is supported only between LJ sphere <P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
pairs due to the different meanings of the energy prefactors used and cutoff distance can be mixed, but only for LJ sphere pairs. The
to calculate the interactions and the implicit dependance of default mix value is <I>geometric</I>. See the "pair_modify" command for
the ellipsoid-LJ sphere interaction on the equation for the details. Other type pairs cannot be mixed, due to the different
Hamaker constant presented here. Mixing of sigma and epsilon meanings of the energy prefactors used to calculate the interactions
followed by calculation of the energy prefactors using the and the implicit dependance of the ellipsoid-LJ sphere interaction on
the equation for the Hamaker constant presented here. Mixing of sigma
and epsilon followed by calculation of the energy prefactors using the
equations above is recommended. equations above is recommended.
</P> </P>
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift <P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift

100
doc/pair_resquared.txt
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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
[Description:] [Description:]
Style {resquared} computes the RE-squared anisotropic interaction Style {resquared} computes the RE-squared anisotropic interaction
"(Everaers,Babadi)"_#Everaers between pairs of ellipsoidal and/or "(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of
spherical Lennard-Jones particles. For ellipsoidal interactions, ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
the potential considers the ellipsoid as being comprised of small interactions, the potential considers the ellipsoid as being comprised
spheres of size sigma. LJ particles are a single sphere of size of small spheres of size sigma. LJ particles are a single sphere of
sigma. The distinction is made to allow the pair style to make size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions. efficient calculations of ellipsoid/solvent interactions.
:link(redoc,Eqs/pair_resquared_extra.pdf) Details for the equations used are given in the references below and
in "this supplementary document"_Eqs/pair_resquqred_extra.pdf.
Details for the equations used are given in the references below Use of this pair style requires the NVE, NVT, or NPT fixes with the
and "this document"_#redoc. {asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
Use of this pair style requires the NVE, NVT, or NPT fixes ellipsoid"_atom_style.html should be used since it defines the
with the {asphere} extension (e.g. "fix rotational state of the ellipsoidal particles and the
nve/asphere"_fix_nve_asphere.html) in order to integrate particle "shape"_shape.html command should be used to specify ellipsoid
rotation. Additionally, "atom_style ellipsoid"_atom_style.html should diameters.
be used since it defines the rotational state of the ellipsoidal
particles and the "shape"_shape.html command should be used to
specify ellipsoid diameters.
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -58,52 +56,52 @@ epsilon_j_b = relative well depth of type J for face-to-face interactions
epsilon_j_c = relative well depth of type J for end-to-end interactions epsilon_j_c = relative well depth of type J for end-to-end interactions
cutoff (distance units) :ul cutoff (distance units) :ul
The parameters used depend on the type of particles interacting - The parameters used depend on the type of the interacting particles,
ellipsoid or LJ sphere. The type of particle is determined by i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the "shape"_shape.html the diameters specified with the "shape"_shape.html command. LJ
command. LJ spheres have diameters equal to zero and thus spheres have diameters equal to zero and thus represent a single
represent a single particle with size sigma. The epsilon_i_* or particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
epsilon_j_* parameters are ignored for LJ sphere interactions. are ignored for LJ sphere interactions. The interactions between two
The interactions between two LJ sphere particles are computed LJ sphere particles are computed using the standard Lennard-Jones
using the standard Lennard-Jones formula. formula.
A12 specifies the energy prefactor which depends on A12 specifies the energy prefactor which depends on the type of
the type of particles interacting. For ellipsoid-ellipsoid particles interacting. For ellipsoid-ellipsoid interactions, A12 is
interactions, A12 is the Hamaker constant as described in the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
"(Everaers)"_#Everaers. In LJ units: units:
:c,image(Eqs/pair_resquared.jpg) :c,image(Eqs/pair_resquared.jpg)
where rho gives the number density of the spherical particles where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the composing the ellipsoids and epsilon_LJ determines the interaction
interaction strength of the spherical particles. strength of the spherical particles.
For ellipsoid-LJ sphere interactions, A12 gives the energy For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
prefactor (see "here"_Eqs/pair_resquared_extra.pdf for details: (see "here"_Eqs/pair_resquared_extra.pdf for details:
:c,image(Eqs/pair_resquared2.jpg) :c,image(Eqs/pair_resquared2.jpg)
For LJ sphere-LJ sphere interactions, A12 is the standard For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used
epsilon used in Lennard-Jones pair styles: in Lennard-Jones pair styles:
:c,image(Eqs/pair_resquared3.jpg) :c,image(Eqs/pair_resquared3.jpg)
sigma specifies the diameter of the continuous distribution of sigma specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model constituent particles within each ellipsoid used to model the
the RE-squared potential. Therefore, the effective shape RE-squared potential. Therefore, the effective shape of an ellipsoid
of an ellipsoid is given by the specified diameters is given by the specified diameters (see the "shape"_shape.html
(see the "shape"_shape.html command) plus sigma. command) plus sigma.
For large uniform molecules it has been shown that the epsilon_*_* For large uniform molecules it has been shown that the epsilon_*_*
energy parameters are approximately representable in terms of energy parameters are approximately representable in terms of local
local contact curvatures "(Everaers)"_#Everaers: contact curvatures "(Everaers)"_#Everaers:
:c,image(Eqs/pair_resquared4.jpg) :c,image(Eqs/pair_resquared4.jpg)
where a, b, and c give the particle diameters. where a, b, and c give the particle diameters.
The last coefficient is optional. If not specified, the global The last coefficient is optional. If not specified, the global cutoff
cutoff specified in the pair_style command is used. specified in the pair_style command is used.
The epsilon_i and epsilon_j coefficients are actually defined for atom 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 types, not for pairs of atom types. Thus, in a series of pair_coeff
@ -132,12 +130,14 @@ that type in a "pair_coeff I J" command.
[Mixing, shift, table, tail correction, per-atom energy/stress, [Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]: restart, rRESPA info]:
Automatic mixing is supported only between LJ sphere For atom type pairs I,J and I != J, the epsilon and sigma coefficients
pairs due to the different meanings of the energy prefactors used and cutoff distance can be mixed, but only for LJ sphere pairs. The
to calculate the interactions and the implicit dependance of default mix value is {geometric}. See the "pair_modify" command for
the ellipsoid-LJ sphere interaction on the equation for the details. Other type pairs cannot be mixed, due to the different
Hamaker constant presented here. Mixing of sigma and epsilon meanings of the energy prefactors used to calculate the interactions
followed by calculation of the energy prefactors using the and the implicit dependance of the ellipsoid-LJ sphere interaction on
the equation for the Hamaker constant presented here. Mixing of sigma
and epsilon followed by calculation of the energy prefactors using the
equations above is recommended. equations above is recommended.
This pair styles supports the "pair_modify"_pair_modify.html shift This pair styles supports the "pair_modify"_pair_modify.html shift