+ +
pair_style resquared command +
+Syntax: +
+pair_style resquared cutoff ++
- cutoff = global cutoff for interactions (distance units) +
Examples: +
+pair_style resquared 10.0 +pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 ++
Description: +
+Style resquared computes the RE-squared anisotropic interaction +(Everaers,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. +
+ + +Details for the equations used are given in the references below +and this document. +
+Use of this pair style requires the NVE, NVT, or NPT fixes +with the asphere extension (e.g. fix +nve/asphere) in order to integrate particle +rotation. Additionally, atom_style ellipsoid should +be used since it defines the rotational state of the ellipsoidal +particles and the shape command should be used to +specify ellipsoid diameters. +
+The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above, or in the data file or restart files read by the +read_data or read_restart +commands: +
+- A12 = Energy Prefactor/Hamaker constant (energy units) +
- sigma = atomic interaction diameter (distance units) +
- epsilon_i_a = relative well depth of type I for side-to-side interactions +
- epsilon_i_b = relative well depth of type I for face-to-face interactions +
- epsilon_i_c = relative well depth of type I for end-to-end interactions +
- epsilon_j_a = relative well depth of type J for side-to-side interactions +
- 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) +
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. +
+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. +
+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: +
+
+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): +
+
+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 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 +commands, they only need to be specified once for each atom type. +
+Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are +non-zero, the three values are assigned to atom type I. If all the +epsilon_i values are zero, they are ignored. If any of epsilon_j_a, +epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned +to atom type J. If all three epsilon_i values are zero, they are +ignored. Thus the typical way to define the epsilon_i and epsilon_j +coefficients is to list their values in "pair_coeff I J" commands when +I = J, but set them to 0.0 when I != J. If you do list them when I != +J, you should insure they are consistent with their values in other +pair_coeff commands. +
+Note that if this potential is being used as a sub-style of +pair_style hybrid, and there is no "pair_coeff I I" +setting made for RE-squared for a particular type I (because I-I +interactions are computed by another hybrid pair potential), then you +still need to insure the epsilon a,b,c coefficients are assigned to +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 +equations above is recommended. +
+This pair styles supports the pair_modify shift +option for the energy of the Lennard-Jones portion of the pair +interaction, but only for sphere-sphere interactions. There is no +shifting performed for ellipsoidal interactions due to the anisotropic +dependence of the interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +
+This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords of the run_style +command. +
++ +
Restrictions: +
+This style is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. +
+The distance-of-closest-approach approximation used by LAMMPS becomes +less accurate when high-aspect ratio ellipsoids are used. +
+Related commands: +
+pair_coeff, fix nve/asphere, +compute temp/asphere +
+Default: none +
++ + + +
(Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). +
+ + +(Berardi) Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). +
+ diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt new file mode 100755 index 0000000000..c3e3ff0864 --- /dev/null +++ b/doc/pair_resquared.txt @@ -0,0 +1,194 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style resquared command :h3 + +[Syntax:] + +pair_style resquared cutoff :pre + +cutoff = global cutoff for interactions (distance units) :ul + +[Examples:] + +pair_style resquared 10.0 +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 +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 "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. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +A12 = Energy Prefactor/Hamaker constant (energy units) +sigma = atomic interaction diameter (distance units) +epsilon_i_a = relative well depth of type I for side-to-side interactions +epsilon_i_b = relative well depth of type I for face-to-face interactions +epsilon_i_c = relative well depth of type I for end-to-end interactions +epsilon_j_a = relative well depth of type J for side-to-side interactions +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. + +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. + +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: + +: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. + +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 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 +commands, they only need to be specified once for each atom type. + +Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are +non-zero, the three values are assigned to atom type I. If all the +epsilon_i values are zero, they are ignored. If any of epsilon_j_a, +epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned +to atom type J. If all three epsilon_i values are zero, they are +ignored. Thus the typical way to define the epsilon_i and epsilon_j +coefficients is to list their values in "pair_coeff I J" commands when +I = J, but set them to 0.0 when I != J. If you do list them when I != +J, you should insure they are consistent with their values in other +pair_coeff commands. + +Note that if this potential is being used as a sub-style of +"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I" +setting made for RE-squared for a particular type I (because I-I +interactions are computed by another hybrid pair potential), then you +still need to insure the epsilon a,b,c coefficients are assigned to +that type in a "pair_coeff I J" command. + +:line + +[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 +equations above is recommended. + +This pair styles supports the "pair_modify"_pair_modify.html shift +option for the energy of the Lennard-Jones portion of the pair +interaction, but only for sphere-sphere interactions. There is no +shifting performed for ellipsoidal interactions due to the anisotropic +dependence of the interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords of the "run_style +command"_run_style.html. + +:line + +[Restrictions:] + +This style is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +The distance-of-closest-approach approximation used by LAMMPS becomes +less accurate when high-aspect ratio ellipsoids are used. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html, +"compute temp/asphere"_compute_temp_asphere.html + +[Default:] none + +:line + +:link(Everaers) +[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). + +:link(Babadi) +[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). diff --git a/doc/pair_style.html b/doc/pair_style.html index 22bae93db1..7bd27d802b 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -131,6 +131,7 @@ the pair_style command, and coefficients specified by the associated
+
+