Commit a6ecd3d0 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into... 

Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates

Resolved Conflicts:
	doc/src/compute_fep.txt
	doc/src/fix_adapt_fep.txt
parents 1be589fb 0bfb3438

doc/src/compute_fep.txt

+18 −30
Original line number Diff line number Diff line
@@ -128,52 +128,40 @@ commands to be changed, if the pair style supports it. 


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:

"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:

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

"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:

"buck/mdf"_pair_mdf.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/debye"_pair_coul.html: scale: type pairs:

"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:

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

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

"eam, eam/alloy, eam/fs"_pair_eam.html: scale: 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: A,B: 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,coulombic_cutoff: 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, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:

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

"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:

"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: 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:

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

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

"lubricate"_pair_lubricate.html: mu: global:

"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: 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,m,n: type pairs:

"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:

"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:

"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:

"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:

"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:

"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:

"table"_pair_table.html: table_cutoff: type pairs:

"ufm"_pair_ufm.html: epsilon,sigma: 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

the pair_*.cpp file associated with the potential.
@@ -263,7 +251,7 @@ package"_Build_package.html doc page for more info. 
[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:]

doc/src/fix_adapt_fep.txt

+17 −33
Original line number Diff line number Diff line
@@ -113,54 +113,38 @@ can be varied by this fix. 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:

"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:

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

"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:

"buck/mdf"_pair_mdf.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/debye"_pair_coul.html: scale: type pairs:

"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:

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

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

"eam, eam/alloy, eam/fs"_pair_eam.html: scale: 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: A,B: 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,coulombic_cutoff: 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, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:

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

"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:

"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: 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:

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

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

"lubricate"_pair_lubricate.html: mu: global:

"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: 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,m,n: type pairs:

"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:

"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:

"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:

"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:

"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:

"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:

"table"_pair_table.html: table_cutoff: type pairs:

"ufm"_pair_ufm.html: epsilon,sigma: 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"
@@ -282,7 +266,7 @@ minimization"_minimize.html. 
[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:]

doc/src/pair_class2.txt

+9 −1
Original line number Diff line number Diff line
@@ -99,6 +99,14 @@ cutoff distance. 


: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
@@ -159,7 +167,7 @@ package"_Build_package.html doc page for more info. 


[Related commands:]



"pair_coeff"_pair_coeff.html

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



[Default:] none

doc/src/pair_lj_soft.txt→doc/src/pair_fep_soft.txt

+154 −72

File changed and moved.

Preview size limit exceeded, changes collapsed.

doc/src/pair_lj.txt

+8 −0
Original line number Diff line number Diff line
@@ -260,6 +260,14 @@ pair_style command. 


: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

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