Consolidated doc of soft-core pair styles

The {pstyle} argument is the name of the pair style. For example,

{pstyle} could be specified as "lj/cut".  The {pparam} argument is the

name of the parameter to change.  This is a (non-exclusive) list of

name of the parameter to change.  This is a list of

pair styles and parameters that can be used with this compute.  See

the doc pages for individual pair styles and their energy formulas for

the meaning of these parameters:

"born"_pair_born.html: a,b,c: type pairs:

"buck"_pair_buck.html: a,c: type pairs:

"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:

"coul/cut"_pair_coul.html: scale: type pairs:

"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:

"coul/long, coul/msm"_pair_coul.html: scale: type pairs:

"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:

"eam"_pair_eam.html: scale: type pairs:

"gauss"_pair_gauss.html: a: type pairs:

"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:

"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:

"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:

"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:

"coul/long/soft"_pair_lj_soft.html: lambda: type pairs:

"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs:

"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"born"_pair_born.html: a,b,c: type pairs:

"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:)

"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:

"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:

"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:

"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:

"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:

"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:

"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:

"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:

"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:

"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)

Note that it is easy to add new potentials and their parameters to

this list.  All it typically takes is adding an extract() method to

[Related commands:]

"fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,

"pair_style lj/soft/coul/soft"_pair_lj_soft.html

"pair_fep_soft"_pair_fep_soft.html

[Default:]

"born"_pair_born.html: a,b,c: type pairs:

"buck"_pair_buck.html: a,c: type pairs:

"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:

"coul/cut"_pair_coul.html: scale: type pairs:

"coul/debye"_pair_coul.html: scale: type pairs:

"coul/long"_pair_coul.html: scale: type pairs:

"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:

"coul/long, coul/msm"_pair_coul.html: scale: type pairs:

"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:

"eam"_pair_eam.html: scale: type pairs:

"gauss"_pair_gauss.html: a: type pairs:

"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:

"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:

"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:

"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:

"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:

"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:

"lubricate"_pair_lubricate.html: mu: global:

"gauss"_pair_gauss.html: a: type pairs:

"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:

"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:

"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:

"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:

"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:

"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:

"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:

"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:

"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)

NOTE: It is easy to add new potentials and their parameters to this

list.  All it typically takes is adding an extract() method to the

pair_*.cpp file associated with the potential.

Some parameters are global settings for the pair style, e.g. the

viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.

Other parameters apply to atom type pairs within the pair style,

e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.

Note that for many of the potentials, the parameter that can be varied

is effectively a prefactor on the entire energy expression for the

potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"

[Related commands:]

"compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute

ti"_compute_ti.html

ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html

[Default:]

:line

A version of these styles with a soft core, {lj/cut/soft}, suitable for use in

free energy calculations, is part of the USER-FEP package and is documented with

the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is

only available if LAMMPS was built with that package. See the "Build

package"_Build_package.html doc page for more info.

:line

Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

functionally the same as the corresponding style without the suffix.

They have been optimized to run faster, depending on your available

[Related commands:]

"pair_coeff"_pair_coeff.html

"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html

[Default:] none

pair_style coul/long/soft/omp command :h3

pair_style tip4p/long/soft command :h3

pair_style tip4p/long/soft/omp command :h3

pair_style morse/soft command :h3

[Syntax:]

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 {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} 

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} or {morse/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

    qdist = distance from O atom to massless charge (distance units)

    n, alpha_C = parameters of the soft-core potential

    cutoff = global cutoff for Coulomb interactions (distance units)

  {morse/soft} args = n lf cutoff

    n = soft-core parameter

    lf = transformation range is lf < lambda < 1

    cutoff = global cutoff for Morse interactions (distance units)

:pre

[Examples:]

pair_coeff * * 0.28 3.1 1.0

pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre

pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5

pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5

pair_coeff * * 0.28 3.1 1.0

pair_coeff 1 1 0.28 3.1 0.0 10.0

pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre

pair_style coul/long/soft 1.0 10.0 9.5

pair_coeff * * 1.0

pair_coeff 1 1 1.0 9.5 :pre

pair_coeff * * 1.0

pair_coeff 1 1 1.0 9.5 :pre

pair_style morse/soft 4 0.9 10.0

pair_coeff * * 100.0 2.0 1.5 1.0

pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre

[Description:]

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

These pair styles have a soft repulsive core, tuneable by a parameter lambda,

in order to avoid singularities during free energy calculations when sites are

created or annihilated "(Beutler)"_#Beutler.  When lambda tends to 0 the pair

interaction vanishes with a soft repulsive core.  When lambda tends to 1, the pair

interaction approaches the normal, non-soft potential. 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.

The {lj/cut/soft} style and related sub-styles compute the 12-6 Lennard-Jones

and Coulomb potentials modified by a soft core, with the functional form

:c,image(Eqs/pair_lj_soft.jpg)

Coulomb interactions are also damped with a soft core at short

distance,

The {lj/class2/soft} style is a 9-6 potential with the exponent of the

denominator of the first term in brackets taking the value 1.5 instead of 2

(other details differ, see the form of the potential in

"pair_class2"_pair_class2.html).

Coulomb interactions can also be damped with a soft core at short distance,

:c,image(Eqs/pair_coul_soft.jpg)

are the charges on the 2 atoms, and epsilon is the dielectric constant

which can be set by the "dielectric"_dielectric.html command.

The coefficient lambda is an activation parameter. When lambda = 1 the

pair potential is identical to a Lennard-Jones term or a Coulomb term

or a combination of both. When lambda = 0 the interactions are

deactivated. The transition between these two extrema is smoothed by a

soft repulsive core in order to avoid singularities in potential

energy and forces when sites are created or annihilated and can overlap

"(Beutler)"_#Beutler.

The coefficient lambda is an activation parameter. When lambda = 1 the pair

potential is identical to a Lennard-Jones term or a Coulomb term or a

combination of both. When lambda = 0 the interactions are deactivated. The

transition between these two extrema is smoothed by a soft repulsive core in

order to avoid singularities in potential energy and forces when sites are

created or annihilated and can overlap "(Beutler)"_#Beutler.

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 12/6 LJ and Coulomb terms are shown

below, for lambda ranging from 1 to 0 every 0.1.

"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 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)

:c

For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,

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, or by mixing as described below:

For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, as well

as for the equivalent {class2} versions, 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, or

by mixing as described below:

epsilon (energy units)

sigma (distance units)

lambda (activation parameter between 0 and 1)

lambda (activation parameter, between 0 and 1)

cutoff1 (distance units)

cutoff2 (distance units) :ul

{coul/long/soft} only lambda and the optional cutoff2 are to be

specified.

Style {lj/cut/tip4p/long/soft} implements a soft-core version of the

TIP4P water model. The usage of this pair style is documented in the

"pair_lj"_pair_lj.html styles. The soft-core version introduces the

lambda parameter to the list of arguments, after epsilon and sigma in

the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ

and alpha_C are set in the "pair_style"_pair_style.html command,

before the cutoffs.

Style {lj/charmm/coul/long/soft} implements a soft-core version of the

CHARMM version of LJ interactions with an additional switching

function S(r) that ramps the energy and force smoothly to zero between

an inner and outer cutoff. The usage of this pair style is documented

in the "pair_charmm"_pair_charmm.html styles. The soft-core version

introduces the lambda parameter to the list of arguments, after

epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and

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. 

Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water

model. The usage of the TIP4P pair style is documented in the

"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ

and alpha_C are set in the "pair_style"_pair_style.html command, after the

specific parameters of the TIP4P water model and before the cutoffs. The

activation parameter lambda is supplied as an argument of the the

"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the

optional cutoffs.

Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified

12-6 LJ potential used in CHARMM and documented in the

"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,

alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before

the global cutoffs. The activation parameter lambda is introduced as an argument

of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and

before the optional eps14 and sigma14.

Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in

"pair_class2"_pair_class2.html. In the soft version the parameters n, alpha_LJ

and alpha_C are set in the "pair_style"_pair_style.html command, before the

global cutoffs. The activation parameter lambda is introduced as an argument of

the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before

the optional cutoffs.

The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles

are designed to be combined with other pair potentials via the

the Lennard-Jones radius of another site (for example hydrogen atoms

in several water models).

NOTES: When using the soft-core Coulomb potentials with long-range

NOTE: When using the soft-core Coulomb potentials with long-range

solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.)  in a free

energy calculation in which sites holding electrostatic charges are

being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html

overlap of the charges. Examples are provided in the LAMMPS source

directory tree, under examples/USER/fep.

NOTE: To avoid division by zero do not set sigma = 0 in the {lj/cut/soft} and

related styles; use the lambda parameter instead to activate/deactivate

interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not

interact though the Lennard-Jones term the {coul/long/soft} or similar sub-style

can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command.

:line

The {morse/soft} variant modifies the "pair_morse"_pair_morse.html style at

short range to have a soft core. The functional form differs from that of the

{lj/soft} styles, and is instead given by:

:c,image(Eqs/pair_morse_soft.jpg)

The {morse/soft} style requires the following pair coefficients:

D0 (energy units)

alpha (1/distance units)

r0 (distance units)

lambda (unitless, between 0.0 and 1.0)

cutoff (distance units) :ul

The last coefficient is optional. If not specified, the global morse cutoff is

used.

:line

Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

[Mixing, shift, tail correction, restart info]:

For atom type pairs I,J and I != J, the epsilon and sigma coefficients

and cutoff distance for this pair style can be mixed.

The default mix value is {geometric}.  See the "pair_modify" command

for details.

The different versions of the {lj/cut/soft} pair styles support mixing.  For atom

type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff

distance for these pair style can be mixed.  The default mix value is

{geometric} for 12-6 styles.

These pair styles support the "pair_modify"_pair_modify.html shift

option for the energy of the Lennard-Jones portion of the pair

interaction.

The mixing rule for epsilon and sigma for {lj/class2/soft} 9-6 potentials is to use the

{sixthpower} formulas. The "pair_modify mix"_pair_modify.html setting is thus

ignored for class2 potentials for epsilon and sigma. However it is still

followed for mixing the cutoff distance. See the "pair_modify"_pair_modify.html

command for details.

The {morse/soft} pair style does not support mixing. Thus, coefficients for all

LJ pairs must be specified explicitly.

These pair styles support the "pair_modify"_pair_modify.html tail

option for adding a long-range tail correction to the energy and

pressure for the Lennard-Jones portion of the pair interaction.

All of the pair styles with soft core support the "pair_modify"_pair_modify.html

shift option for the energy of the Lennard-Jones portion of the pair

interaction.

These pair styles write 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.

The different versions of the {lj/cut/soft} pair styles support the

"pair_modify"_pair_modify.html tail option for adding a long-range tail

correction to the energy and pressure for the Lennard-Jones portion of the pair

interaction.

:line

NOTE: The analytical form of the tail corrections for energy and pressure used

in the {lj/cut/soft} potentials are approximate, being identical to that of the

corresponding non-soft potentials scaled by a factor lambda^n. For real-space

cutoffs greater than 2.5 sigma and alpha_LJ = 0.5, the error affecting the tail

correction is below 0.2% when lambda = 0 (worse case). This error disappears as

lambda approaches 1. Note that this is the error affecting the long-range tail

(itself a correction to the interaction energy) which includes other

approximations, namely that the system is homogenous (local density equal the

average density) beyond the cutoff.

[Restrictions:]

The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html

tail option for adding long-range tail corrections to energy and pressure.

To avoid division by zero do not set sigma = 0; use the lambda

parameter instead to activate/deactivate interactions, or use

epsilon = 0 and sigma = 1. Alternatively, when sites do not

interact though the Lennard-Jones term the {coul/long/soft} or

similar sub-style can be used via the

"pair_style hybrid/overlay"_pair_hybrid.html command.

All of these pair styles write 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.

:line

All of the plain {soft} pair styles are part of the USER-FEP package.

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.

[Restrictions:]

The pair styles with soft core are only enabled if LAMMPS was built with the

USER-FEP package. The {long} versions also require the KSPACE package to be

installed. The soft {tip4p} versions also require the MOLECULE package to be

installed. These styles are only enabled if LAMMPS was built with those

packages.  See the "Build package"_Build_package.html doc page for more

info. Note that the KSPACE and MOLECULE packages are installed by default.

[Related commands:]

:line

A version of these styles with a soft core, {lj/cut/soft}, suitable for use in

free energy calculations, is part of the USER-FEP package and is documented with

the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is

only available if LAMMPS was built with that package. See the "Build

package"_Build_package.html doc page for more info.

:line

Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

functionally the same as the corresponding style without the suffix.

They have been optimized to run faster, depending on your available