diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_fep_soft.txt similarity index 86% rename from doc/src/pair_lj_soft.txt rename to doc/src/pair_fep_soft.txt index 4e400d1c0a..df013f0c9c 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_fep_soft.txt @@ -16,7 +16,10 @@ pair_style lj/cut/tip4p/long/soft command :h3 pair_style lj/cut/tip4p/long/soft/omp command :h3 pair_style lj/charmm/coul/long/soft command :h3 pair_style lj/charmm/coul/long/soft/omp command :h3 -pair_style coul/cut/soft command :h3 +pair_style lj/class2/soft command :h3 +pair_style lj/class2/coul/cut/soft command :h3 +pair_style lj/class2/coul/long/soft command :h3 + pair_style coul/cut/soft command :h3 pair_style coul/cut/soft/omp command :h3 pair_style coul/long/soft command :h3 pair_style coul/long/soft/omp command :h3 @@ -27,7 +30,9 @@ pair_style tip4p/long/soft/omp command :h3 pair_style style args :pre -style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} +style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or +{lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {lj/class2/soft} or {lj/class2/coul/cut/soft} or {lj/class2/coul/long/soft} or {coul/cut/soft} or +{coul/long/soft} or {tip4p/long/soft} args = list of arguments for a particular style :ul {lj/cut/soft} args = n alpha_lj cutoff n, alpha_LJ = parameters of soft-core potential @@ -51,6 +56,17 @@ args = list of arguments for a particular style :ul n, alpha_LJ, alpha_C = parameters of the soft-core potential inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args) cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args) + {lj/class2/soft} args = n alpha_lj cutoff + n, alpha_LJ = parameters of soft-core potential + cutoff = global cutoff for Lennard-Jones interactions (distance units) + {lj/class2/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) + n, alpha_LJ, alpha_C = parameters of soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + {lj/class2/coul/long/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) + n, alpha_LJ, alpha_C = parameters of soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {coul/cut/soft} args = n alpha_C cutoff n, alpha_C = parameters of the soft-core potential cutoff = global cutoff for Coulomb interactions (distance units) @@ -103,10 +119,13 @@ pair_coeff 1 1 1.0 9.5 :pre [Description:] -The {lj/cut/soft} style and sub-styles compute the 12/6 Lennard-Jones -and Coulomb potential modified by a soft core, in order to avoid -singularities during free energy calculations when sites are created -or annihilated "(Beutler)"_#Beutler, +The {lj/cut/soft} style and sub-styles compute the 12/6 or 9/6 Lennard-Jones and +Coulomb potentials modified by a soft core, in order to avoid singularities +during free energy calculations when sites are created or annihilated +"(Beutler)"_#Beutler. These pair styles are suited for "alchemical" free energy +calculations using the "fix adapt/fep"_fix_adapt_fep.html and "compute +fep"_compute_fep.html commands. For example, the 12-6 Lennard-Jones modified +with a soft core has functional form :c,image(Eqs/pair_lj_soft.jpg) @@ -131,7 +150,7 @@ The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are -appropriate choices. Plots of the LJ and Coulomb terms are shown +appropriate choices. Plots of the 12/6 LJ and Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. :image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) @@ -179,6 +198,9 @@ before the optional eps14 and sigma14). The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. +Style {lj/class2/soft} implements a soft-core version of the 9/6 potential used +in the COMPASS class2 force field. + The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles are designed to be combined with other pair potentials via the "pair_style hybrid/overlay"_pair_hybrid.html command. This is because @@ -259,7 +281,7 @@ similar sub-style can be used via the :line All of the plain {soft} pair styles are part of the USER-FEP package. -The {long} styles also requires the KSPACE package to be installed. +The {long} styles also require the KSPACE package to be installed. They are only enabled if LAMMPS was built with those packages. See the "Build package"_Build_package.html doc page for more info.