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Consolidated doc for soft pair styles

This commit is contained in:
Agilio Padua 2019-01-23 12:02:23 +00:00
parent a5ce656c32
commit 012d5a55bf
1 changed files with 30 additions and 8 deletions
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38
doc/src/pair_lj_soft.txt → doc/src/pair_fep_soft.txt
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@ -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.