Combined USER-FEP related updates

doc/src/Commands_pair.txt

@@ -63,13 +63,13 @@ OPT.
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
 "coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/dsf (gko)"_pair_coul.html,
 "coul/long (gko)"_pair_coul.html,
 "coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/long/soft (o)"_pair_fep_soft.html,
 "coul/msm (o)"_pair_coul.html,
 "coul/shield"_pair_coul_shield.html,
 "coul/streitz"_pair_coul.html,
@@ -114,7 +114,7 @@ OPT.
 "lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/charmm/coul/msm (o)"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@@ -124,22 +124,22 @@ OPT.
 "lj/cubic (go)"_pair_lj_cubic.html,
 "lj/cut (gikot)"_pair_lj.html,
 "lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/debye (gko)"_pair_lj.html,
 "lj/cut/coul/dsf (gko)"_pair_lj.html,
 "lj/cut/coul/long (gikot)"_pair_lj.html,
 "lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/msm (go)"_pair_lj.html,
 "lj/cut/coul/wolf (o)"_pair_lj.html,
 "lj/cut/dipole/cut (go)"_pair_dipole.html,
 "lj/cut/dipole/long (g)"_pair_dipole.html,
 "lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/thole/long (o)"_pair_thole.html,
 "lj/cut/tip4p/cut (o)"_pair_lj.html,
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/expand/coul/long (g)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
@@ -230,7 +230,7 @@ OPT.
 "thole"_pair_thole.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tip4p/long/soft (o)"_pair_fep_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
 "vashishta (gko)"_pair_vashishta.html,

doc/src/Packages_details.txt

@@ -1306,7 +1306,7 @@ src/USER-FEP: filenames -> commands
 src/USER-FEP/README
 "fix adapt/fep"_fix_adapt_fep.html
 "compute fep"_compute_fep.html
-"pair_style */soft"_pair_lj_soft.html
+"pair_style */soft"_pair_fep_soft.html
 examples/USER/fep
 tools/fep/README
 tools/fep :ul

doc/src/compute_fep.txt

@@ -128,24 +128,39 @@ 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:
 
-"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/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=:)
+"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_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_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_fep_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_fep_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_fep_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:
+"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
@@ -236,7 +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.txt

@@ -112,17 +112,43 @@ 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:
 "coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
 "coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_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_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs:
 "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: A,B: 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/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_fep_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_fep_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:
-"gauss"_pair_gauss.html: a: type pairs:
-"morse"_pair_morse.html: d0,r0,alpha: type pairs:
+"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:
 "soft"_pair_soft.html: a: type pairs:
 "kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
 
@@ -217,6 +243,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are
 
+"gromos"_bond_gromos.html: k, r0: type bonds:
 "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
 
 :line

doc/src/fix_adapt_fep.txt

@@ -114,24 +114,37 @@ 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/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_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_fep_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_fep_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_fep_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"
@@ -253,7 +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/lammps.book

@@ -595,7 +595,7 @@ pair_lj_expand.html
 pair_lj_long.html
 pair_lj_smooth.html
 pair_lj_smooth_linear.html
-pair_lj_soft.html
+pair_fep_soft.html
 pair_lj_switch3_coulgauss.html
 pair_lubricate.html
 pair_lubricateU.html

doc/src/pair_class2.txt

@@ -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