The parameters used depend on the type of particles interacting - -ellipsoid or LJ sphere. The type of particle is determined by -the diameters specified with the shape -command. LJ spheres have diameters equal to zero and thus -represent a single particle with size sigma. The epsilon_i_* or -epsilon_j_* parameters are ignored for LJ sphere interactions. -The interactions between two LJ sphere particles are computed -using the standard Lennard-Jones formula. +
The parameters used depend on the type of the interacting particles, +i.e. ellipsoid or LJ sphere. The type of particle is determined by +the diameters specified with the shape command. LJ +spheres have diameters equal to zero and thus represent a single +particle with size sigma. The epsilon_i_* or epsilon_j_* parameters +are ignored for LJ sphere interactions. The interactions between two +LJ sphere particles are computed using the standard Lennard-Jones +formula.
-A12 specifies the energy prefactor which depends on -the type of particles interacting. For ellipsoid-ellipsoid -interactions, A12 is the Hamaker constant as described in -(Everaers). In LJ units: +
A12 specifies the energy prefactor which depends on the type of +particles interacting. For ellipsoid-ellipsoid interactions, A12 is +the Hamaker constant as described in (Everaers). In LJ +units:
where rho gives the number density of the spherical particles -composing the ellipsoids and epsilon_LJ determines the -interaction strength of the spherical particles. +composing the ellipsoids and epsilon_LJ determines the interaction +strength of the spherical particles.
-For ellipsoid-LJ sphere interactions, A12 gives the energy -prefactor (see here for details: +
For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor +(see here for details:
For LJ sphere-LJ sphere interactions, A12 is the standard -epsilon used in Lennard-Jones pair styles: +
For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used +in Lennard-Jones pair styles:
sigma specifies the diameter of the continuous distribution of -constituent particles within each ellipsoid used to model -the RE-squared potential. Therefore, the effective shape -of an ellipsoid is given by the specified diameters -(see the shape command) plus sigma. +
sigma specifies the diameter of the continuous distribution of +constituent particles within each ellipsoid used to model the +RE-squared potential. Therefore, the effective shape of an ellipsoid +is given by the specified diameters (see the shape +command) plus sigma.
-For large uniform molecules it has been shown that the epsilon_*_* -energy parameters are approximately representable in terms of -local contact curvatures (Everaers): +
For large uniform molecules it has been shown that the epsilon_*_* +energy parameters are approximately representable in terms of local +contact curvatures (Everaers):
where a, b, and c give the particle diameters.
-The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. +
The last coefficient is optional. If not specified, the global cutoff +specified in the pair_style command is used.
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 @@ -135,12 +133,14 @@ that type in a "pair_coeff I J" command.
Mixing, shift, table, tail correction, per-atom energy/stress, restart, rRESPA info:
-Automatic mixing is supported only between LJ sphere -pairs 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 and epsilon -followed by calculation of the energy prefactors using the +
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 +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 +and epsilon followed by calculation of the energy prefactors using the equations above is recommended.
This pair styles supports the pair_modify shift diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt index c3e3ff0864..8697ebf28a 100755 --- a/doc/pair_resquared.txt +++ b/doc/pair_resquared.txt @@ -22,25 +22,23 @@ pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre [Description:] Style {resquared} computes the RE-squared anisotropic interaction -"(Everaers,Babadi)"_#Everaers between pairs of ellipsoidal and/or -spherical Lennard-Jones particles. For ellipsoidal interactions, -the potential considers the ellipsoid as being comprised of small -spheres of size sigma. LJ particles are a single sphere of size -sigma. The distinction is made to allow the pair style to make +"(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of +ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal +interactions, the potential considers the ellipsoid as being comprised +of small spheres of size sigma. LJ particles are a single sphere of +size sigma. The distinction is made to allow the pair style to make 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 -and "this document"_#redoc. - -Use of this pair style requires the NVE, NVT, or NPT fixes -with the {asphere} extension (e.g. "fix -nve/asphere"_fix_nve_asphere.html) in order to integrate particle -rotation. Additionally, "atom_style ellipsoid"_atom_style.html should -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. +Use of this pair style requires the NVE, NVT, or NPT fixes with the +{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in +order to integrate particle rotation. Additionally, "atom_style +ellipsoid"_atom_style.html should 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 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 cutoff (distance units) :ul -The parameters used depend on the type of particles interacting - -ellipsoid or LJ sphere. The type of particle is determined by -the diameters specified with the "shape"_shape.html -command. LJ spheres have diameters equal to zero and thus -represent a single particle with size sigma. The epsilon_i_* or -epsilon_j_* parameters are ignored for LJ sphere interactions. -The interactions between two LJ sphere particles are computed -using the standard Lennard-Jones formula. +The parameters used depend on the type of the interacting particles, +i.e. ellipsoid or LJ sphere. The type of particle is determined by +the diameters specified with the "shape"_shape.html command. LJ +spheres have diameters equal to zero and thus represent a single +particle with size sigma. The epsilon_i_* or epsilon_j_* parameters +are ignored for LJ sphere interactions. The interactions between two +LJ sphere particles are computed using the standard Lennard-Jones +formula. -A12 specifies the energy prefactor which depends on -the type of particles interacting. For ellipsoid-ellipsoid -interactions, A12 is the Hamaker constant as described in -"(Everaers)"_#Everaers. In LJ units: +A12 specifies the energy prefactor which depends on the type of +particles interacting. For ellipsoid-ellipsoid interactions, A12 is +the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ +units: :c,image(Eqs/pair_resquared.jpg) where rho gives the number density of the spherical particles -composing the ellipsoids and epsilon_LJ determines the -interaction strength of the spherical particles. +composing the ellipsoids and epsilon_LJ determines the interaction +strength of the spherical particles. -For ellipsoid-LJ sphere interactions, A12 gives the energy -prefactor (see "here"_Eqs/pair_resquared_extra.pdf for details: +For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor +(see "here"_Eqs/pair_resquared_extra.pdf for details: :c,image(Eqs/pair_resquared2.jpg) -For LJ sphere-LJ sphere interactions, A12 is the standard -epsilon used in Lennard-Jones pair styles: +For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used +in Lennard-Jones pair styles: :c,image(Eqs/pair_resquared3.jpg) -sigma specifies the diameter of the continuous distribution of -constituent particles within each ellipsoid used to model -the RE-squared potential. Therefore, the effective shape -of an ellipsoid is given by the specified diameters -(see the "shape"_shape.html command) plus sigma. +sigma specifies the diameter of the continuous distribution of +constituent particles within each ellipsoid used to model the +RE-squared potential. Therefore, the effective shape of an ellipsoid +is given by the specified diameters (see the "shape"_shape.html +command) plus sigma. -For large uniform molecules it has been shown that the epsilon_*_* -energy parameters are approximately representable in terms of -local contact curvatures "(Everaers)"_#Everaers: +For large uniform molecules it has been shown that the epsilon_*_* +energy parameters are approximately representable in terms of local +contact curvatures "(Everaers)"_#Everaers: :c,image(Eqs/pair_resquared4.jpg) where a, b, and c give the particle diameters. -The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. +The last coefficient is optional. If not specified, the global cutoff +specified in the pair_style command is used. 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 @@ -132,12 +130,14 @@ that type in a "pair_coeff I J" command. [Mixing, shift, table, tail correction, per-atom energy/stress, restart, rRESPA info]: -Automatic mixing is supported only between LJ sphere -pairs 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 and epsilon -followed by calculation of the energy prefactors using the +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 +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 +and epsilon followed by calculation of the energy prefactors using the equations above is recommended. This pair styles supports the "pair_modify"_pair_modify.html shift