diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index b498e6bfdadc348034e849839c505d866af1639c..b18d852c09900f5b47ddc21b801b2a0d6d11996c 100644
--- a/doc/src/Commands_pair.txt
+++ b/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,
@@ -114,32 +114,35 @@ 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,
"lj/class2 (gko)"_pair_class2.html,
"lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/cut/soft"_pair_fep_soft.html,
"lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/class2/coul/long/soft"_pair_fep_soft.html,
+"lj/class2/soft"_pair_fep_soft.html,
"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,
@@ -170,7 +173,7 @@ OPT.
"momb"_pair_momb.html,
"morse (gkot)"_pair_morse.html,
"morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_morse.html,
+"morse/soft"_pair_fep_soft.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
@@ -230,7 +233,7 @@ 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,
diff --git a/doc/src/Install_git.txt b/doc/src/Install_git.txt
index 80ec3e34785a09bba8d0274920ca1b1869a0be0e..bae5bef94f2c72aa71bc2d7339dfe6597cefaa5a 100644
--- a/doc/src/Install_git.txt
+++ b/doc/src/Install_git.txt
@@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above.
between them at any time using "git checkout <branch name>".)
Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir). You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included. They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
diff --git a/doc/src/Install_svn.txt b/doc/src/Install_svn.txt
index 7a0211ab65fa39a41985e74198f7a7cdd145b0b2..84a46865f3361d8ca13e12d2e762a2b20e5c382d 100644
--- a/doc/src/Install_svn.txt
+++ b/doc/src/Install_svn.txt
@@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on
your machine.
Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir). You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included. They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index ebfe01d8a73a2cfbda9057cd761131313b3d0041..7d3d6d13e2edbc846454b689909958d0bd7d6284 100644
--- a/doc/src/Packages_details.txt
+++ b/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
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 5b3a6915dd4a6c3c442be5034caa03b7fb709602..a46ab5b8d333233db5278394059964071998dc85 100644
--- a/doc/src/compute_fep.txt
+++ b/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: a,c: 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: 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: 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:]
diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt
index 0ca28fb8694c6c5c4d4c2d39ab649dc79a9152a3..fe86f49b258d15a257d88c55eef38684d3c5331d 100644
--- a/doc/src/fix_adapt.txt
+++ b/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_*:i,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
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 7e30a1d29d5b4354b7fae0761f50fc7d8d6e8dd3..9a9255db06c9289ab5caa38c5c48c7ed5a5514cb 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/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: a,c: 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: 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: 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:]
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 049c3aa558d5b35218389fe7955e0a84905217fc..e1f799a6c9c632dffde46d3b63f786e4f003f49d 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -370,8 +370,7 @@ of these styles.
All of the kspace styles are part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
-package"_Build_package.html doc page for more info. Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 5ae3456ad4be214edce5fc66e0d55b4e6418db26..02a55e38103ff08c4d9dc7c087c98f9ed6dc3185 100644
--- a/doc/src/lammps.book
+++ b/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
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 7f3a959ad620a39db19c466ad7012b6412740cc6..ff27f6b0056698f2737ec57afc2e90f47e5da623 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -154,8 +154,7 @@ details.
This style is part of the KSPACE package. It is only enabled if
LAMMPS was built with that package. See the "Build
-package"_Build_package.html doc page for more info. Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 7f0104266c1cdedf994233a618c1f0cb54b03bbb..f5344b752f7b30de8e11245341673dc51591a94f 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -249,8 +249,7 @@ All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
of the MOLECULE package. All the styles with {coul/long} style are
part of the KSPACE package. They 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 MOLECULE and KSPACE packages are
-installed by default.
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 5fc42e78f9f9b4a34d854e30d9bd96999177252b..8d4aa486026070124ffee6077bd0b1f3113a3f62 100644
--- a/doc/src/pair_class2.txt
+++ b/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
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_fep_soft.txt
similarity index 51%
rename from doc/src/pair_lj_soft.txt
rename to doc/src/pair_fep_soft.txt
index 4e400d1c0aa226220057b450e5977820b3afde7f..d5e848cd1e86d6afde83c49a7d565ba857529b39 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_fep_soft.txt
@@ -16,18 +16,21 @@ 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
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 {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
@@ -51,6 +54,17 @@ 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)
@@ -63,6 +77,10 @@ args = list of arguments for a particular style :ul
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:]
@@ -93,6 +111,12 @@ pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
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
@@ -101,17 +125,31 @@ pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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 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,
+These pair styles have a soft repulsive core, tunable 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)
@@ -119,34 +157,32 @@ In the Coulomb part C is an energy-conversion constant, q_i and q_j
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 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
@@ -160,24 +196,29 @@ since it has no Coulombic terms. For the {coul/cut/soft} and
{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/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
@@ -189,7 +230,7 @@ occur. These sub-styles are suitable to represent charges embedded in
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
@@ -202,6 +243,31 @@ Waals site is present during the free-energy route, thus avoiding
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
@@ -228,40 +294,57 @@ instructions on how to use the accelerated styles effectively.
[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.
-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.
+The {morse/soft} pair style does not support mixing. Thus, coefficients for all
+LJ pairs must be specified explicitly.
-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.
+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.
-:line
+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.
-[Restrictions:]
+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. The errors due to
+this approximation should be negligible. For example, for a cutoff of 2.5 sigma
+this approximation leads to maximum relative errors in tail corrections of the
+order of 1e-4 for energy and virial (alpha_LJ = 0.5, n = 2). The error vanishes
+when lambda approaches 0 or 1. Note that these are the errors affecting the
+long-range tail (itself a correction to the interaction energy) which includes
+other approximations, namely that the system is homogeneous (local density equal
+the average density) beyond the cutoff.
+
+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 requires 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.
[Related commands:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index 40730d67a721cc3d36d1996e17e50b0d436650cc..8dce8383e5db0e91d920c37a54b43d668f44a9d2 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -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
@@ -321,8 +329,7 @@ The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
package. 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.
+more info.
[Related commands:]
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 9f95fc0347bd5133cfe735f924b02f589a9277fa..4e8410d062069aa8f40470d742a8f15c906bea84 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -154,6 +154,14 @@ specified in the 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
@@ -211,8 +219,7 @@ different levels of the rRESPA hierarchy. See the
These styles are part of the KSPACE package. They are only enabled if
LAMMPS was built with that package. See the "Build
-package"_Build_package.html doc page for more info. Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 68894f691384d7445196aa4783dbb882964d6b3f..7faa6ab7852f41a7dd5ec399f04858339220a998 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -12,7 +12,6 @@ pair_style morse/omp command :h3
pair_style morse/opt command :h3
pair_style morse/smooth/linear command :h3
pair_style morse/smooth/linear/omp command :h3
-pair_style morse/soft command :h3
pair_style morse/kk command :h3
[Syntax:]
@@ -25,10 +24,6 @@ args = list of arguments for a particular style :ul
cutoff = global cutoff for Morse interactions (distance units)
{morse/smooth/linear} args = cutoff
cutoff = global cutoff for Morse 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:]
@@ -38,10 +33,6 @@ pair_style morse/smooth/linear 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0 :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:]
Style {morse} computes pairwise interactions with the formula
@@ -77,24 +68,11 @@ the {morse} and {morse/smooth/linear} styles.
:line
-The {morse/soft} variant is similar to the {lj/cut/soft} pair style
-in that it modifies the potential at short range to have a soft core.
-This helps to avoid singularities during free energy calculation in
-which sites are created or annihilated. The formula differs from that
-of {lj/cut/soft}, 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)
-lamda (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.
+A version of the {morse} style with a soft core, {morse/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
@@ -151,12 +129,8 @@ The {morse/smooth/linear} pair style is only enabled if LAMMPS was
built with the USER-MISC package. See the "Build
package"_Build_package.html doc page for more info.
-The {morse/soft} pair style is only enabled if LAMMPS was built with
-the USER-FEP package. See the "Build 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
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 978277245607446d9a1abb3214dfbc6949035276..f6fcd110d803cda0886c9d7103d55c20db080f9e 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -130,13 +130,13 @@ accelerated styles exist.
"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
"coul/cut"_pair_coul.html - cutoff Coulombic potential
-"coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core
+"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
"coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity
"coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model
"coul/long"_pair_coul.html - long-range Coulombic potential
"coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell
-"coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core
+"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core
"coul/msm"_pair_coul.html - long-range MSM Coulombics
"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
@@ -181,31 +181,34 @@ accelerated styles exist.
"lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"lj/charmm/coul/long/soft"_pair_lj_soft.html - CHARMM with long-range Coulomb and a soft core
+"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core
"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
+"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
+"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
+"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"lj/cut/coul/cut/soft"_pair_lj_soft.html - LJ with cutoff Coulomb with a soft core
+"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
-"lj/cut/coul/long/soft"_pair_lj_soft.html - LJ with long-range Coulombics with a soft core
+"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"lj/cut/soft"_pair_lj_soft.html - LJ with a soft core
+"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"lj/cut/tip4p/long/soft"_pair_lj_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
@@ -296,7 +299,7 @@ accelerated styles exist.
"thole"_pair_thole.html - Coulomb interactions with thole damping
"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
-"tip4p/long/soft"_pair_lj_soft.html -
+"tip4p/long/soft"_pair_fep_soft.html -
"tri/lj"_pair_tri_lj.html - LJ potential between triangles
"ufm"_pair_ufm.html -
"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 62cbb7f56d018662c260feae935e7343994b1453..09c310a11083817020c4fa3dde5ac9a24fcdfd64 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -38,6 +38,7 @@ Pair Styles :h1
pair_eim
pair_exp6_rx
pair_extep
+ pair_fep_soft
pair_gauss
pair_gayberne
pair_gran
@@ -60,7 +61,6 @@ Pair Styles :h1
pair_lj_long
pair_lj_smooth
pair_lj_smooth_linear
- pair_lj_soft
pair_lj_switch3_coulgauss
pair_lubricate
pair_lubricateU
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 8807b2d680766839db90849a37662f5f53d02b6d..9cf3c7467f5a6898c0fd7ab23b70829e71cd4847 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -891,6 +891,8 @@ fz
Gahler
gainsboro
Galindo
+gamA
+gamR
gammaA
gammaFactor
gammaR
@@ -2730,6 +2732,7 @@ ttm
tu
Tuckerman
tue
+tunable
Turkand
Tutein
tweakable
diff --git a/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane b/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane
new file mode 100644
index 0000000000000000000000000000000000000000..6483512de163bc579b7de75d2b2ef67e86f7e9f6
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane
@@ -0,0 +1,2783 @@
+LAMMPS data file via write_data, version 27 Nov 2018, timestep = 1100100
+
+383 atoms
+8 atom types
+342 bonds
+9 bond types
+562 angles
+14 angle types
+534 dihedrals
+11 dihedral types
+348 impropers
+11 improper types
+
+-5.0514130135769175e-01 1.5783110029075640e+01 xlo xhi
+-8.0620338035756767e-01 1.5482047948350324e+01 ylo yhi
+-8.6275306635756799e-01 1.5425498262350324e+01 zlo zhi
+
+Masses
+
+1 12.0112
+2 12.0112
+3 15.9994
+4 1.00797
+5 1.00797
+6 12.0112
+7 12.0112
+8 1.00797
+
+Pair Coeffs # lj/class2/coul/long
+
+1 lj/class2/coul/long 0.054 4.01
+2 lj/class2/coul/long 0.054 4.01
+3 lj/class2/coul/long 0.24 3.535
+4 lj/class2/coul/long 0.02 2.995
+5 lj/class2/coul/long 0.013 1.098
+6 lj/class2/coul/long 0.054 4.01
+7 lj/class2/coul/long 0.054 4.01
+8 lj/class2/coul/long 0.02 2.995
+
+Bond Coeffs # class2
+
+1 1.53 299.67 -501.77 679.81
+2 1.101 345 -691.89 844.6
+3 1.101 345 -691.89 844.6
+4 1.42 400.395 -835.195 1313.01
+5 0.965 532.506 -1282.9 2004.77
+6 1.53 299.67 -501.77 679.81
+7 1.101 345 -691.89 844.6
+8 1.53 299.67 -501.77 679.81
+9 1.101 345 -691.89 844.6
+
+Angle Coeffs # class2
+
+1 110.77 41.453 -10.604 5.129
+2 107.66 39.641 -12.921 -2.4318
+3 110.77 41.453 -10.604 5.129
+4 111.27 54.5381 -8.3642 -13.0838
+5 107.66 39.641 -12.921 -2.4318
+6 108.728 58.5446 -10.8088 -12.4006
+7 105.8 52.7061 -12.109 -9.8681
+8 110.77 41.453 -10.604 5.129
+9 107.66 39.641 -12.921 -2.4318
+10 112.67 39.516 -7.443 -9.5583
+11 110.77 41.453 -10.604 5.129
+12 110.77 41.453 -10.604 5.129
+13 107.66 39.641 -12.921 -2.4318
+14 112.67 39.516 -7.443 -9.5583
+
+BondBond Coeffs
+
+1 3.3872 1.53 1.101
+2 5.3316 1.101 1.101
+3 3.3872 1.53 1.101
+4 11.4318 1.53 1.42
+5 5.3316 1.101 1.101
+6 23.1979 1.42 1.101
+7 -9.6879 1.42 0.965
+8 3.3872 1.53 1.101
+9 5.3316 1.101 1.101
+10 0 1.53 1.53
+11 3.3872 1.53 1.101
+12 3.3872 1.53 1.101
+13 5.3316 1.101 1.101
+14 0 1.53 1.53
+
+BondAngle Coeffs
+
+1 20.754 11.421 1.53 1.101
+2 18.103 18.103 1.101 1.101
+3 20.754 11.421 1.53 1.101
+4 2.6868 20.4033 1.53 1.42
+5 18.103 18.103 1.101 1.101
+6 55.327 4.6189 1.42 1.101
+7 28.58 18.9277 1.42 0.965
+8 20.754 11.421 1.53 1.101
+9 18.103 18.103 1.101 1.101
+10 8.016 8.016 1.53 1.53
+11 20.754 11.421 1.53 1.101
+12 20.754 11.421 1.53 1.101
+13 18.103 18.103 1.101 1.101
+14 8.016 8.016 1.53 1.53
+
+Dihedral Coeffs # class2
+
+1 -0.1432 0 0.0617 0 -0.1083 0
+2 -0.1435 0 0.253 0 -0.0905 0
+3 -0.6732 0 -0.4778 0 -0.167 0
+4 0.1863 0 -0.4338 0 -0.2121 0
+5 0 0 0.0316 0 -0.1681 0
+6 -0.1432 0 0.0617 0 -0.1083 0
+7 0 0 0.0514 0 -0.143 0
+8 0 0 0.0316 0 -0.1681 0
+9 0 0 0.0316 0 -0.1681 0
+10 -0.1432 0 0.0617 0 -0.1083 0
+11 0 0 0.0514 0 -0.143 0
+
+AngleAngleTorsion Coeffs
+
+1 -12.564 110.77 110.77
+2 -20.2006 110.77 111.27
+3 -12.1038 111.27 105.8
+4 -10.5093 108.728 105.8
+5 -16.164 110.77 112.67
+6 -12.564 110.77 110.77
+7 -22.045 112.67 112.67
+8 -16.164 112.67 110.77
+9 -16.164 112.67 110.77
+10 -12.564 110.77 110.77
+11 -22.045 112.67 112.67
+
+EndBondTorsion Coeffs
+
+1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.101 1.42
+3 -0.58 0.9004 0 0 0.5343 0.9025 1.53 0.965
+4 -1.7554 1.3145 0.2263 0.2493 0.6803 0 1.101 0.965
+5 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
+6 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+7 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+8 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+9 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+10 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+11 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+
+MiddleBondTorsion Coeffs
+
+1 -14.261 -0.5322 -0.4864 1.53
+2 -16.7975 -1.2296 -0.275 1.53
+3 1.2472 0 0.7485 1.42
+4 0 0.9241 -0.5889 1.42
+5 -14.879 -3.6581 -0.3138 1.53
+6 -14.261 -0.5322 -0.4864 1.53
+7 -17.787 -7.1877 0 1.53
+8 -14.879 -3.6581 -0.3138 1.53
+9 -14.879 -3.6581 -0.3138 1.53
+10 -14.261 -0.5322 -0.4864 1.53
+11 -17.787 -7.1877 0 1.53
+
+BondBond13 Coeffs
+
+1 0 1.101 1.101
+2 0 1.101 1.42
+3 0 1.53 0.965
+4 0 1.101 0.965
+5 0 1.101 1.53
+6 0 1.101 1.101
+7 0 1.53 1.53
+8 0 1.53 1.101
+9 0 1.53 1.101
+10 0 1.101 1.101
+11 0 1.53 1.53
+
+AngleTorsion Coeffs
+
+1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+2 2.3668 2.492 -1.0122 -0.1892 0.4918 0.7273 110.77 111.27
+3 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.27 105.8
+4 -3.406 1.6396 0.0737 0 -0.281 -0.5944 108.728 105.8
+5 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
+6 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+7 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+8 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+9 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+10 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+11 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+
+Improper Coeffs # class2
+
+1 0 0
+2 0 0
+3 0 0
+4 0 0
+5 0 0
+6 0 0
+7 0 0
+8 0 0
+9 0 0
+10 0 0
+11 0 0
+
+AngleAngle Coeffs
+
+1 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
+3 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+4 0.1689 2.5926 3.9177 111.27 108.728 110.77
+5 2.4259 2.1283 2.4259 108.728 107.66 108.728
+6 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+7 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
+8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+9 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+10 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+11 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+
+Atoms # full
+
+266 1 4 5.2999999999999999e-02 1.6864256263249984e+00 3.9338060620105360e+00 2.1660446484538451e+00 3 2 1
+369 3 8 5.2999999999999999e-02 3.3919511835590943e-01 3.0096236406752253e+00 -2.5770783759613225e-01 -6 -4 1
+262 1 1 -1.5900000000000000e-01 6.5498274037974347e-01 4.1907594188897948e+00 2.4050161328305437e+00 3 2 1
+32 1 4 5.2999999999999999e-02 2.7301623259329730e+00 5.8422246585345166e+00 5.5163771763213223e+00 5 -1 -2
+109 1 1 -1.5900000000000000e-01 2.7961551958578061e+00 -2.2969882281549192e-01 3.2188699615959901e+00 3 2 -1
+368 3 8 5.2999999999999999e-02 2.0712023208108077e+00 3.0177796852734509e+00 -5.8999253600034041e-01 -6 -4 1
+265 1 4 5.2999999999999999e-02 3.9700241923613155e-01 3.7910255338969643e+00 3.3987341741926453e+00 3 2 1
+33 1 4 5.2999999999999999e-02 1.2162576164780894e+00 6.7486742879722721e+00 5.3541920309475231e+00 5 -1 -2
+263 1 2 2.7000000000000000e-02 4.8103594949677597e-01 5.7557856279469517e+00 2.3868716152095644e+00 3 2 1
+39 1 3 -5.5710000000000004e-01 2.2521850090997195e+00 1.3947926015289074e+00 6.8621803249373796e+00 1 1 -3
+112 1 4 5.2999999999999999e-02 2.4856857509546786e+00 5.1057788440507146e-01 3.9725913564313755e+00 3 2 -1
+120 1 3 -5.5710000000000004e-01 1.2419834017083919e-01 -2.8040716156599221e-01 5.5372267728894133e+00 2 0 -1
+264 1 3 -5.5710000000000004e-01 7.8020608557254234e-01 6.5188794064615569e+00 1.1877308855805855e+00 3 2 1
+270 1 5 4.2409999999999998e-01 1.7403462539394239e+00 6.4832110763225046e+00 1.1734811625841393e+00 3 2 1
+267 1 4 5.2999999999999999e-02 1.1704177676301275e-02 3.6374346744456014e+00 1.7121920952086365e+00 3 2 1
+268 1 4 5.2999999999999999e-02 1.1685372696766843e+00 6.1221409798979280e+00 3.1734573248995028e+00 3 2 1
+45 1 5 4.2409999999999998e-01 3.0067261615845320e+00 1.7753804307094345e+00 6.4118946885558064e+00 1 1 -3
+31 1 4 5.2999999999999999e-02 2.2064050697036626e+00 6.6971086605071743e+00 7.0117703687360011e+00 5 -1 -2
+126 1 5 4.2409999999999998e-01 9.0902656336434240e-01 2.4613225741733991e-01 5.7163101931818154e+00 2 0 -1
+28 1 1 -1.5900000000000000e-01 2.1879824905767289e+00 6.7120777486652399e+00 5.8681805243073955e+00 5 -1 -2
+114 1 4 5.2999999999999999e-02 2.5999606312665224e+00 1.7579021287431351e-01 2.2402962094249448e+00 3 2 -1
+273 1 3 -5.5710000000000004e-01 3.5334785972957876e+00 6.4187908708259780e+00 8.3840175214941537e-01 3 -2 0
+258 1 4 5.2999999999999999e-02 2.9621482858284094e+00 3.8660247181975240e+00 1.3019528905914020e+01 0 2 -1
+37 1 1 -1.5900000000000000e-01 1.0598521129795269e+00 3.0842438875120148e+00 8.2204006884588523e+00 1 1 -3
+38 1 2 2.7000000000000000e-02 2.1712614298592863e+00 2.1008262983928208e+00 8.0540118733527279e+00 1 1 -3
+41 1 4 5.2999999999999999e-02 1.0703671263629493e+00 3.7702137135715805e+00 7.3735977277148770e+00 1 1 -3
+257 1 4 5.2999999999999999e-02 1.7278164571316088e+00 4.7177234027880157e+00 1.2063346879485389e+01 0 2 -1
+42 1 4 5.2999999999999999e-02 1.2265876394911785e+00 3.6636674713028308e+00 9.1605331578946778e+00 1 1 -3
+370 3 8 5.2999999999999999e-02 9.2116275250916879e-01 4.1227962814687666e+00 1.4820928762308647e+01 -6 -4 0
+40 1 4 5.2999999999999999e-02 5.2495487796965445e-02 2.6229951455138050e+00 8.2848891549388437e+00 1 1 -3
+375 3 8 5.2999999999999999e-02 -4.9489330077790628e-01 3.6053192991211880e-01 1.2651600307530902e+01 -6 -4 0
+376 3 8 5.2999999999999999e-02 8.3275310657087132e-01 1.0348745969202238e+00 1.1656725334364307e+01 -6 -4 0
+373 3 8 5.2999999999999999e-02 3.4813445141000299e-01 3.2104872018562682e+00 1.2429232235348742e+01 -6 -4 0
+372 3 8 5.2999999999999999e-02 1.8720848803887398e+00 1.6196739445964643e+00 1.3755288219666763e+01 -6 -4 0
+371 3 8 5.2999999999999999e-02 5.1521194340731657e-01 1.0583762045930640e+00 1.4722003701038862e+01 -6 -4 0
+367 3 6 -1.5900000000000000e-01 -6.3602171946119113e-02 -5.1524032249274621e-01 9.5686066785259367e+00 -6 -4 0
+361 3 6 -1.5900000000000000e-01 1.1055962223046736e+00 3.0718618123315631e+00 1.5223515082094190e+01 -6 -4 0
+362 3 7 -1.0600000000000000e-01 9.2517651947552504e-01 1.9594163698683427e+00 1.4169307339497134e+01 -6 -4 0
+58 1 4 5.2999999999999999e-02 -1.0797825339466011e-01 6.0503146158064398e+00 9.8664400533903684e+00 2 -1 1
+253 1 1 -1.5900000000000000e-01 2.8283162006044194e+00 4.5709670497798092e+00 1.2154328606987141e+01 0 2 -1
+364 3 7 -1.0600000000000000e-01 -1.7830350547990370e-01 1.2321897052899029e+00 1.2030731564906919e+01 -6 -4 0
+363 3 7 -1.0600000000000000e-01 -2.2293502066847992e-02 2.3269152812887848e+00 1.3058793538777712e+01 -6 -4 0
+55 1 1 -1.5900000000000000e-01 -3.4547620768957216e-01 6.7052614343524413e+00 8.9800035885703497e+00 2 -1 1
+43 1 4 5.2999999999999999e-02 2.2289826718804684e+00 1.3826800188016928e+00 8.8857303442604341e+00 1 1 -3
+44 1 4 5.2999999999999999e-02 3.1106725954525829e+00 2.6936260484123027e+00 8.2445169299102297e+00 1 1 -3
+256 1 4 5.2999999999999999e-02 3.0815299500044633e+00 4.1798256626747667e+00 1.1170970686950326e+01 0 2 -1
+383 3 8 5.2999999999999999e-02 6.6060041795775071e-01 1.8687930716221879e-01 9.0559595439783092e+00 -6 -4 0
+59 1 4 5.2999999999999999e-02 4.7264429449302814e-01 6.6355010886654773e+00 8.3125090991278423e+00 2 -1 1
+259 1 4 5.2999999999999999e-02 3.3035090800840821e+00 6.2970068335297444e+00 1.3411452602206555e+01 0 2 -1
+260 1 4 5.2999999999999999e-02 3.4815907559267174e+00 6.5487893364255791e+00 1.1673290002180893e+01 0 2 -1
+246 1 3 -5.5710000000000004e-01 5.9360453663246515e-01 1.2888335162908080e+01 4.9194654955102726e+00 0 1 1
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+336 2 355 352 356 357
+337 3 226 227 232 233
+338 4 226 227 228 232
+339 4 226 227 228 233
+340 5 228 227 233 232
+341 1 74 73 76 77
+342 1 74 73 76 78
+343 1 74 73 77 78
+344 2 76 73 77 78
+345 1 290 289 292 293
+346 1 290 289 292 294
+347 1 290 289 293 294
+348 2 292 289 293 294
diff --git a/examples/USER/fep/C7inEthanol/fep01/in.insertion b/examples/USER/fep/C7inEthanol/fep01/in.insertion
new file mode 100644
index 0000000000000000000000000000000000000000..243d83751504fd7bfba0e26f65d429012329437d
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep01/in.insertion
@@ -0,0 +1,57 @@
+# LAMMPS atomistic input script
+
+echo screen
+units real
+atom_style full
+
+pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5
+bond_style class2
+angle_style class2
+dihedral_style class2
+improper_style class2
+pair_modify mix sixthpower tail yes
+special_bonds lj/coul 0 0 1
+
+read_data data.init_conf_without_heptane
+
+pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 0.0
+pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 0.0
+pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
+pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
+pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0
+
+pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 0.0
+pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 0.0
+pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
+pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
+pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0
+
+pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
+pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
+pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 0.0
+pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 0.0
+pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 0.0
+
+timestep 1.0
+kspace_style pppm 1.0e-5
+
+variable lambda equal ramp(0.0,1.0)
+variable q1 equal -0.1590*v_lambda
+variable q2 equal -0.1060*v_lambda
+variable q3 equal 0.0530*v_lambda
+
+fix ADAPT all adapt/fep 10 &
+ pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda &
+ atom charge 6 v_q1 &
+ atom charge 7 v_q2 &
+ atom charge 8 v_q3 &
+ after yes
+
+thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_modify line one
+thermo 100
+
+fix 1 all nvt temp 300 300 100
+run 100000
+
+write_data data.after_heptane_insertion
diff --git a/examples/USER/fep/C7inEthanol/fep01/log.lammps b/examples/USER/fep/C7inEthanol/fep01/log.lammps
new file mode 100644
index 0000000000000000000000000000000000000000..fbd4a49a3e18722a2e7424f47938351fb09e33c8
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep01/log.lammps
@@ -0,0 +1,1125 @@
+LAMMPS (27 Nov 2018)
+# LAMMPS atomistic input script
+
+echo screen
+ orthogonal box = (-0.505141 -0.806203 -0.862753) to (15.7831 15.482 15.4255)
+ 4 by 2 by 2 MPI processor grid
+WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:580)
+ reading atoms ...
+ 383 atoms
+ reading velocities ...
+ 383 velocities
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 9 = max dihedrals/atom
+ scanning impropers ...
+ 4 = max impropers/atom
+ reading bonds ...
+ 342 bonds
+ reading angles ...
+ 562 angles
+ reading dihedrals ...
+ 534 dihedrals
+ reading impropers ...
+ 348 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 10 = max # of special neighbors
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.288287
+ grid = 10 10 10
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00279394
+ estimated relative force accuracy = 8.41388e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 1296 90
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.5
+ ghost atom cutoff = 11.5
+ binsize = 5.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair lj/class2/coul/long, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/class2/coul/long/soft, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.61 | 13.92 | 14.89 Mbytes
+Step S/CPU Temp Press Volume TotEng PotEng v_lambda v_q1 v_q2 v_q3
+ 0 0 301.82904 533.3184 4321.3892 -79.144423 -422.82793 1 -0.159 -0.106 0.053
+ 100 799.51858 297.06821 2966.9114 4321.3892 -67.550969 -405.81346 0.999 -0.158841 -0.105894 0.052947
+ 200 1111.1841 310.89475 -1076.6004 4321.3892 -32.998901 -387.00525 0.998 -0.158682 -0.105788 0.052894
+ 300 1459.1789 313.65424 320.85082 4321.3892 -29.026776 -386.17527 0.997 -0.158523 -0.105682 0.052841
+ 400 1415.1559 311.37233 -4525.9921 4321.3892 -43.910969 -398.46112 0.996 -0.158364 -0.105576 0.052788
+ 500 1489.9869 288.38744 -1783.6133 4321.3892 -59.978436 -388.3564 0.995 -0.158205 -0.10547 0.052735
+ 600 1372.2162 300.78589 2406.4287 4321.3892 -58.529306 -401.025 0.994 -0.158046 -0.105364 0.052682
+ 700 1273.4802 302.48787 1188.4083 4321.3892 -19.664773 -364.09847 0.993 -0.157887 -0.105258 0.052629
+ 800 1379.5701 324.19685 3525.573 4321.3892 -6.5601902 -375.71324 0.992 -0.157728 -0.105152 0.052576
+ 900 1417.4117 302.20264 580.80929 4321.3892 -31.492626 -375.60153 0.991 -0.157569 -0.105046 0.052523
+ 1000 1423.0943 288.09813 -3390.5518 4321.3892 -50.795041 -378.84358 0.99 -0.15741 -0.10494 0.05247
+ 1100 1339.6567 279.41478 -1585.8135 4321.3892 -65.305421 -383.46649 0.989 -0.157251 -0.104834 0.052417
+ 1200 1283.0804 297.57659 -5628.1846 4321.3892 -61.457533 -400.2989 0.988 -0.157092 -0.104728 0.052364
+ 1300 1374.8154 302.95867 2800.3971 4321.3892 -25.223933 -370.19371 0.987 -0.156933 -0.104622 0.052311
+ 1400 1548.7979 314.63757 169.32405 4321.3892 -9.2461401 -367.51433 0.986 -0.156774 -0.104516 0.052258
+ 1500 1543.4384 302.78598 2667.3171 4321.3892 -28.872419 -373.64556 0.985 -0.156615 -0.10441 0.052205
+ 1600 1505.9924 307.4754 -3144.1719 4321.3892 -42.805804 -392.91864 0.984 -0.156456 -0.104304 0.052152
+ 1700 1519.2347 291.11376 -51.878589 4321.3892 -44.622256 -376.1046 0.983 -0.156297 -0.104198 0.052099
+ 1800 1442.3107 297.91891 1568.4932 4321.3892 -38.314165 -377.54533 0.982 -0.156138 -0.104092 0.052046
+ 1900 1416.7513 299.44141 -3439.0539 4321.3892 -34.396006 -375.36079 0.981 -0.155979 -0.103986 0.051993
+ 2000 1320.1308 311.55135 -4036.9906 4321.3892 -38.635681 -393.38969 0.98 -0.15582 -0.10388 0.05194
+ 2100 1352.1874 294.77184 1722.2251 4321.3892 -52.682147 -388.32983 0.979 -0.155661 -0.103774 0.051887
+ 2200 1398.9382 275.77965 -798.41267 4321.3892 -87.333361 -401.35522 0.978 -0.155502 -0.103668 0.051834
+ 2300 1401.8526 288.31697 1440.4268 4321.3892 -95.443884 -423.7416 0.977 -0.155343 -0.103562 0.051781
+ 2400 1410.2793 300.6133 1047.3407 4321.3892 -67.450573 -409.74975 0.976 -0.155184 -0.103456 0.051728
+ 2500 1342.2665 304.4924 4512.7456 4321.3892 -46.485002 -393.20119 0.975 -0.155025 -0.10335 0.051675
+ 2600 1399.6709 304.59021 -1440.2459 4321.3892 -41.296463 -388.12403 0.974 -0.154866 -0.103244 0.051622
+ 2700 1393.5595 307.63992 1801.3517 4321.3892 -35.974699 -386.27487 0.973 -0.154707 -0.103138 0.051569
+ 2800 1416.1276 301.99824 680.3111 4321.3892 -37.283922 -381.16009 0.972 -0.154548 -0.103032 0.051516
+ 2900 1467.076 290.21584 -655.51621 4321.3892 -55.113989 -385.5739 0.971 -0.154389 -0.102926 0.051463
+ 3000 1507.7721 284.82664 2047.2406 4321.3892 -81.291143 -405.61453 0.97 -0.15423 -0.10282 0.05141
+ 3100 1470.3382 285.07726 -4149.6477 4321.3892 -85.012313 -409.62108 0.969 -0.154071 -0.102714 0.051357
+ 3200 1514.1911 299.64651 1428.5333 4321.3892 -52.958903 -394.15722 0.968 -0.153912 -0.102608 0.051304
+ 3300 1511.3429 311.60785 36.886282 4321.3892 -40.626937 -395.44527 0.967 -0.153753 -0.102502 0.051251
+ 3400 1570.8737 299.11947 3828.1184 4321.3892 -43.612199 -384.2104 0.966 -0.153594 -0.102396 0.051198
+ 3500 1588.4825 297.08441 2021.8438 4321.3892 -52.83333 -391.11427 0.965 -0.153435 -0.10229 0.051145
+ 3600 1514.3641 294.38448 510.47993 4321.3892 -76.148011 -411.35462 0.964 -0.153276 -0.102184 0.051092
+ 3700 1579.6325 267.42535 1976.3472 4321.3892 -92.292608 -396.80168 0.963 -0.153117 -0.102078 0.051039
+ 3800 1579.4417 305.93263 -2594.8587 4321.3892 -60.46367 -408.8198 0.962 -0.152958 -0.101972 0.050986
+ 3900 1556.0604 295.41636 -2413.3469 4321.3892 -39.598538 -375.98011 0.961 -0.152799 -0.101866 0.050933
+ 4000 1480.4195 291.39244 23.97447 4321.3892 -39.171532 -370.9712 0.96 -0.15264 -0.10176 0.05088
+ 4100 1427.5893 302.95007 -136.92129 4321.3892 -61.300632 -406.26062 0.959 -0.152481 -0.101654 0.050827
+ 4200 1507.0531 290.0336 -1924.0805 4321.3892 -78.49136 -408.74376 0.958 -0.152322 -0.101548 0.050774
+ 4300 1530.443 301.52983 1346.5118 4321.3892 -65.981817 -409.32462 0.957 -0.152163 -0.101442 0.050721
+ 4400 1522.4039 296.09695 2033.2832 4321.3892 -38.949103 -376.10565 0.956 -0.152004 -0.101336 0.050668
+ 4500 1469.3288 299.67261 -2870.5264 4321.3892 -36.881907 -378.10995 0.955 -0.151845 -0.10123 0.050615
+ 4600 1476.1078 317.35258 -43.577562 4321.3892 -46.136233 -407.49591 0.954 -0.151686 -0.101124 0.050562
+ 4700 1521.8164 285.69675 -2599.4101 4321.3892 -67.71719 -393.03135 0.953 -0.151527 -0.101018 0.050509
+ 4800 1567.0075 297.89711 -3002.7695 4321.3892 -82.138424 -421.34476 0.952 -0.151368 -0.100912 0.050456
+ 4900 1603.8725 292.54174 392.88991 4321.3892 -77.729344 -410.83769 0.951 -0.151209 -0.100806 0.050403
+ 5000 1596.5842 324.83308 522.49599 4321.3892 -37.736703 -407.6142 0.95 -0.15105 -0.1007 0.05035
+ 5100 1606.1392 312.9193 -878.4909 4321.3892 -35.650262 -391.96191 0.949 -0.150891 -0.100594 0.050297
+ 5200 1596.9711 301.10369 4932.6479 4321.3892 -53.77998 -396.63755 0.948 -0.150732 -0.100488 0.050244
+ 5300 1465.77 299.48781 -279.78852 4321.3892 -74.767934 -415.78555 0.947 -0.150573 -0.100382 0.050191
+ 5400 1373.2951 283.80778 -213.42159 4321.3892 -98.619463 -421.78271 0.946 -0.150414 -0.100276 0.050138
+ 5500 1420.5231 264.12997 -2228.6488 4321.3892 -130.10614 -430.86286 0.945 -0.150255 -0.10017 0.050085
+ 5600 1515.9938 266.04428 -2171.6706 4321.3892 -108.55638 -411.49288 0.944 -0.150096 -0.100064 0.050032
+ 5700 1549.72 276.23021 1058.2904 4321.3892 -77.55162 -392.08652 0.943 -0.149937 -0.099958 0.049979
+ 5800 1522.7747 296.33023 2834.8108 4321.3892 -52.620617 -390.0428 0.942 -0.149778 -0.099852 0.049926
+ 5900 1501.6416 310.56588 2024.1237 4321.3892 -35.466522 -389.0984 0.941 -0.149619 -0.099746 0.049873
+ 6000 1518.1573 305.31866 90.498107 4321.3892 -37.024388 -384.68142 0.94 -0.14946 -0.09964 0.04982
+ 6100 1492.5011 298.08903 1653.7952 4321.3892 -59.680839 -399.1057 0.939 -0.149301 -0.099534 0.049767
+ 6200 1441.766 282.17236 -1566.1626 4321.3892 -77.565829 -398.86687 0.938 -0.149142 -0.099428 0.049714
+ 6300 1425.2832 297.96681 -2194.5697 4321.3892 -58.623811 -397.90951 0.937 -0.148983 -0.099322 0.049661
+ 6400 1555.6883 320.41355 286.39321 4321.3892 -19.662831 -384.50795 0.936 -0.148824 -0.099216 0.049608
+ 6500 1569.0293 301.95644 -1411.1846 4321.3892 -24.09389 -367.92246 0.935 -0.148665 -0.09911 0.049555
+ 6600 1459.2486 303.94603 428.05651 4321.3892 -48.559803 -394.65386 0.934 -0.148506 -0.099004 0.049502
+ 6700 1407.3379 307.53794 1933.383 4321.3892 -65.054887 -415.23894 0.933 -0.148347 -0.098898 0.049449
+ 6800 1396.4378 283.43758 -1552.7689 4321.3892 -67.772351 -390.51406 0.932 -0.148188 -0.098792 0.049396
+ 6900 1312.334 294.20856 -86.309891 4321.3892 -60.748487 -395.75478 0.931 -0.148029 -0.098686 0.049343
+ 7000 1328.9804 309.35057 -1620.5208 4321.3892 -35.894847 -388.14288 0.93 -0.14787 -0.09858 0.04929
+ 7100 1271.3608 307.56399 -1880.8175 4321.3892 -18.413736 -368.62745 0.929 -0.147711 -0.098474 0.049237
+ 7200 1280.4326 306.93914 -851.36608 4321.3892 -46.917022 -396.41924 0.928 -0.147552 -0.098368 0.049184
+ 7300 1365.3317 299.9729 828.31029 4321.3892 -75.239942 -416.80992 0.927 -0.147393 -0.098262 0.049131
+ 7400 1450.2442 315.71577 -2258.2975 4321.3892 -77.889538 -437.38543 0.926 -0.147234 -0.098156 0.049078
+ 7500 1506.8723 300.07141 -1066.1338 4321.3892 -81.309686 -422.99183 0.925 -0.147075 -0.09805 0.049025
+ 7600 1479.5677 300.46763 2522.7745 4321.3892 -59.141607 -401.27491 0.924 -0.146916 -0.097944 0.048972
+ 7700 1486.7071 313.96637 534.54997 4321.3892 -32.408256 -389.91217 0.923 -0.146757 -0.097838 0.048919
+ 7800 1460.0973 321.9645 5106.3828 4321.3892 -36.110275 -402.72141 0.922 -0.146598 -0.097732 0.048866
+ 7900 1473.6768 307.50736 -3942.5615 4321.3892 -65.330897 -415.48013 0.921 -0.146439 -0.097626 0.048813
+ 8000 1504.0498 294.39848 -1832.9535 4321.3892 -70.459732 -405.68229 0.92 -0.14628 -0.09752 0.04876
+ 8100 1468.7781 304.28718 -189.43195 4321.3892 -55.133331 -401.61584 0.919 -0.146121 -0.097414 0.048707
+ 8200 1557.1646 319.02283 4230.5317 4321.3892 -47.629777 -410.89132 0.918 -0.145962 -0.097308 0.048654
+ 8300 1556.6952 293.4999 181.18352 4321.3892 -69.981799 -404.18117 0.917 -0.145803 -0.097202 0.048601
+ 8400 1451.0615 274.30746 1400.9176 4321.3892 -92.417033 -404.76255 0.916 -0.145644 -0.097096 0.048548
+ 8500 1390.1269 299.11094 -1413.3952 4321.3892 -73.457265 -414.04575 0.915 -0.145485 -0.09699 0.048495
+ 8600 1526.8274 293.96637 -966.76211 4321.3892 -62.221729 -396.95226 0.914 -0.145326 -0.096884 0.048442
+ 8700 1502.3239 300.59003 2603.3929 4321.3892 -51.141883 -393.41456 0.913 -0.145167 -0.096778 0.048389
+ 8800 1477.6603 308.15475 -3167.6166 4321.3892 -51.633564 -402.51996 0.912 -0.145008 -0.096672 0.048336
+ 8900 1404.4793 281.16982 486.65033 4321.3892 -84.815835 -404.97531 0.911 -0.144849 -0.096566 0.048283
+ 9000 1424.7846 298.03984 -324.86358 4321.3892 -100.12166 -439.49052 0.91 -0.14469 -0.09646 0.04823
+ 9100 1459.1724 296.61591 2439.8998 4321.3892 -85.458332 -423.2058 0.909 -0.144531 -0.096354 0.048177
+ 9200 1531.9879 285.76254 -703.26192 4321.3892 -70.24585 -395.63492 0.908 -0.144372 -0.096248 0.048124
+ 9300 1531.1159 309.08622 480.80176 4321.3892 -59.014943 -410.96197 0.907 -0.144213 -0.096142 0.048071
+ 9400 1364.9221 302.81366 4047.2007 4321.3892 -46.537085 -391.34175 0.906 -0.144054 -0.096036 0.048018
+ 9500 1319.5761 315.47312 -2178.3733 4321.3892 -40.286299 -399.5059 0.905 -0.143895 -0.09593 0.047965
+ 9600 1391.9897 283.75501 5823.4447 4321.3892 -60.734392 -383.83755 0.904 -0.143736 -0.095824 0.047912
+ 9700 1404.1358 290.17475 -1708.2225 4321.3892 -80.431455 -410.84458 0.903 -0.143577 -0.095718 0.047859
+ 9800 1445.6242 292.05836 44.59996 4321.3892 -62.767593 -395.32553 0.902 -0.143418 -0.095612 0.047806
+ 9900 1365.5774 298.31941 -223.25286 4321.3892 -35.976309 -375.6635 0.901 -0.143259 -0.095506 0.047753
+ 10000 1343.7083 299.18429 1708.9208 4321.3892 -34.382217 -375.05423 0.9 -0.1431 -0.0954 0.0477
+ 10100 1282.9797 308.71854 -652.52818 4321.3892 -46.004329 -397.5327 0.899 -0.142941 -0.095294 0.047647
+ 10200 1278.3479 312.09094 2652.1454 4321.3892 -67.04801 -422.41643 0.898 -0.142782 -0.095188 0.047594
+ 10300 1253.7734 284.06759 4280.0315 4321.3892 -101.02383 -424.48292 0.897 -0.142623 -0.095082 0.047541
+ 10400 1213.7166 279.67797 3325.4782 4321.3892 -118.3233 -436.78406 0.896 -0.142464 -0.094976 0.047488
+ 10500 1328.4058 300.54216 4902.639 4321.3892 -84.105683 -426.32386 0.895 -0.142305 -0.09487 0.047435
+ 10600 1465.8074 301.81404 -2332.3657 4321.3892 -68.683729 -412.35015 0.894 -0.142146 -0.094764 0.047382
+ 10700 1497.7154 299.59422 -974.5001 4321.3892 -48.852191 -389.99098 0.893 -0.141987 -0.094658 0.047329
+ 10800 1508.0315 297.19353 -2907.1175 4321.3892 -32.148071 -370.55326 0.892 -0.141828 -0.094552 0.047276
+ 10900 1506.1204 313.07882 2531.8457 4321.3892 -35.85479 -392.34808 0.891 -0.141669 -0.094446 0.047223
+ 11000 1485.6 299.93491 -671.40624 4321.3892 -69.205125 -410.73184 0.89 -0.14151 -0.09434 0.04717
+ 11100 1508.5851 288.40496 1294.2822 4321.3892 -77.440587 -405.8385 0.889 -0.141351 -0.094234 0.047117
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+ 99200 1152.1594 314.46538 -138.58309 4321.3892 -26.023578 -384.09569 0.008 -0.001272 -0.000848 0.000424
+ 99300 1195.7914 294.0181 2065.5118 4321.3892 -49.077056 -383.86648 0.007 -0.001113 -0.000742 0.000371
+ 99400 1266.2656 287.47157 -2921.4005 4321.3892 -65.534324 -392.86941 0.006 -0.000954 -0.000636 0.000318
+ 99500 1269.4126 292.64019 -2312.8277 4321.3892 -58.326345 -391.54679 0.005 -0.000795 -0.00053 0.000265
+ 99600 1296.8191 302.22068 2864.3077 4321.3892 -44.992409 -389.12186 0.004 -0.000636 -0.000424 0.000212
+ 99700 1410.231 300.25576 552.56231 4321.3892 -32.773166 -374.66523 0.003 -0.000477 -0.000318 0.000159
+ 99800 1435.524 336.9684 -1254.1072 4321.3892 -4.899367 -388.59499 0.002 -0.000318 -0.000212 0.000106
+ 99900 1433.3697 319.25818 3463.0802 4321.3892 8.0883629 -355.44117 0.001 -0.000159 -0.000106 5.3e-05
+ 100000 1318.7622 291.43698 -2961.7602 4321.3892 -27.295831 -359.14621 0 -0 -0 0
+Loop time of 78.283 on 16 procs for 100000 steps with 383 atoms
+
+Performance: 110.369 ns/day, 0.217 hours/ns, 1277.417 timesteps/s
+94.1% CPU use with 16 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 15.43 | 19.194 | 29.637 | 81.5 | 24.52
+Bond | 3.2625 | 3.4917 | 4.0461 | 11.0 | 4.46
+Kspace | 29.911 | 40.821 | 44.717 | 57.6 | 52.14
+Neigh | 0.96168 | 0.96819 | 0.97633 | 0.5 | 1.24
+Comm | 10.348 | 10.581 | 10.846 | 4.3 | 13.52
+Output | 0.030217 | 0.031298 | 0.040418 | 1.3 | 0.04
+Modify | 1.8451 | 1.9233 | 1.9863 | 3.6 | 2.46
+Other | | 1.273 | | | 1.63
+
+Nlocal: 23.9375 ave 37 max 16 min
+Histogram: 3 3 2 2 1 2 0 1 1 1
+Nghost: 2317.44 ave 2369 max 2273 min
+Histogram: 3 3 1 1 0 1 2 1 2 2
+Neighs: 5966.62 ave 8863 max 4086 min
+Histogram: 4 2 2 0 2 1 2 1 0 2
+
+Total # of neighbors = 95466
+Ave neighs/atom = 249.258
+Ave special neighs/atom = 4.72063
+Neighbor list builds = 3058
+Dangerous builds = 0
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.288285
+ grid = 10 10 10
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00277417
+ estimated relative force accuracy = 8.35432e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 1296 90
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.5
+ ghost atom cutoff = 11.5
+ binsize = 5.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair lj/class2/coul/long, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/class2/coul/long/soft, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Total wall time: 0:01:18
diff --git a/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane b/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane
new file mode 100644
index 0000000000000000000000000000000000000000..6483512de163bc579b7de75d2b2ef67e86f7e9f6
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane
@@ -0,0 +1,2783 @@
+LAMMPS data file via write_data, version 27 Nov 2018, timestep = 1100100
+
+383 atoms
+8 atom types
+342 bonds
+9 bond types
+562 angles
+14 angle types
+534 dihedrals
+11 dihedral types
+348 impropers
+11 improper types
+
+-5.0514130135769175e-01 1.5783110029075640e+01 xlo xhi
+-8.0620338035756767e-01 1.5482047948350324e+01 ylo yhi
+-8.6275306635756799e-01 1.5425498262350324e+01 zlo zhi
+
+Masses
+
+1 12.0112
+2 12.0112
+3 15.9994
+4 1.00797
+5 1.00797
+6 12.0112
+7 12.0112
+8 1.00797
+
+Pair Coeffs # lj/class2/coul/long
+
+1 lj/class2/coul/long 0.054 4.01
+2 lj/class2/coul/long 0.054 4.01
+3 lj/class2/coul/long 0.24 3.535
+4 lj/class2/coul/long 0.02 2.995
+5 lj/class2/coul/long 0.013 1.098
+6 lj/class2/coul/long 0.054 4.01
+7 lj/class2/coul/long 0.054 4.01
+8 lj/class2/coul/long 0.02 2.995
+
+Bond Coeffs # class2
+
+1 1.53 299.67 -501.77 679.81
+2 1.101 345 -691.89 844.6
+3 1.101 345 -691.89 844.6
+4 1.42 400.395 -835.195 1313.01
+5 0.965 532.506 -1282.9 2004.77
+6 1.53 299.67 -501.77 679.81
+7 1.101 345 -691.89 844.6
+8 1.53 299.67 -501.77 679.81
+9 1.101 345 -691.89 844.6
+
+Angle Coeffs # class2
+
+1 110.77 41.453 -10.604 5.129
+2 107.66 39.641 -12.921 -2.4318
+3 110.77 41.453 -10.604 5.129
+4 111.27 54.5381 -8.3642 -13.0838
+5 107.66 39.641 -12.921 -2.4318
+6 108.728 58.5446 -10.8088 -12.4006
+7 105.8 52.7061 -12.109 -9.8681
+8 110.77 41.453 -10.604 5.129
+9 107.66 39.641 -12.921 -2.4318
+10 112.67 39.516 -7.443 -9.5583
+11 110.77 41.453 -10.604 5.129
+12 110.77 41.453 -10.604 5.129
+13 107.66 39.641 -12.921 -2.4318
+14 112.67 39.516 -7.443 -9.5583
+
+BondBond Coeffs
+
+1 3.3872 1.53 1.101
+2 5.3316 1.101 1.101
+3 3.3872 1.53 1.101
+4 11.4318 1.53 1.42
+5 5.3316 1.101 1.101
+6 23.1979 1.42 1.101
+7 -9.6879 1.42 0.965
+8 3.3872 1.53 1.101
+9 5.3316 1.101 1.101
+10 0 1.53 1.53
+11 3.3872 1.53 1.101
+12 3.3872 1.53 1.101
+13 5.3316 1.101 1.101
+14 0 1.53 1.53
+
+BondAngle Coeffs
+
+1 20.754 11.421 1.53 1.101
+2 18.103 18.103 1.101 1.101
+3 20.754 11.421 1.53 1.101
+4 2.6868 20.4033 1.53 1.42
+5 18.103 18.103 1.101 1.101
+6 55.327 4.6189 1.42 1.101
+7 28.58 18.9277 1.42 0.965
+8 20.754 11.421 1.53 1.101
+9 18.103 18.103 1.101 1.101
+10 8.016 8.016 1.53 1.53
+11 20.754 11.421 1.53 1.101
+12 20.754 11.421 1.53 1.101
+13 18.103 18.103 1.101 1.101
+14 8.016 8.016 1.53 1.53
+
+Dihedral Coeffs # class2
+
+1 -0.1432 0 0.0617 0 -0.1083 0
+2 -0.1435 0 0.253 0 -0.0905 0
+3 -0.6732 0 -0.4778 0 -0.167 0
+4 0.1863 0 -0.4338 0 -0.2121 0
+5 0 0 0.0316 0 -0.1681 0
+6 -0.1432 0 0.0617 0 -0.1083 0
+7 0 0 0.0514 0 -0.143 0
+8 0 0 0.0316 0 -0.1681 0
+9 0 0 0.0316 0 -0.1681 0
+10 -0.1432 0 0.0617 0 -0.1083 0
+11 0 0 0.0514 0 -0.143 0
+
+AngleAngleTorsion Coeffs
+
+1 -12.564 110.77 110.77
+2 -20.2006 110.77 111.27
+3 -12.1038 111.27 105.8
+4 -10.5093 108.728 105.8
+5 -16.164 110.77 112.67
+6 -12.564 110.77 110.77
+7 -22.045 112.67 112.67
+8 -16.164 112.67 110.77
+9 -16.164 112.67 110.77
+10 -12.564 110.77 110.77
+11 -22.045 112.67 112.67
+
+EndBondTorsion Coeffs
+
+1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.101 1.42
+3 -0.58 0.9004 0 0 0.5343 0.9025 1.53 0.965
+4 -1.7554 1.3145 0.2263 0.2493 0.6803 0 1.101 0.965
+5 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
+6 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+7 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+8 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+9 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+10 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+11 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+
+MiddleBondTorsion Coeffs
+
+1 -14.261 -0.5322 -0.4864 1.53
+2 -16.7975 -1.2296 -0.275 1.53
+3 1.2472 0 0.7485 1.42
+4 0 0.9241 -0.5889 1.42
+5 -14.879 -3.6581 -0.3138 1.53
+6 -14.261 -0.5322 -0.4864 1.53
+7 -17.787 -7.1877 0 1.53
+8 -14.879 -3.6581 -0.3138 1.53
+9 -14.879 -3.6581 -0.3138 1.53
+10 -14.261 -0.5322 -0.4864 1.53
+11 -17.787 -7.1877 0 1.53
+
+BondBond13 Coeffs
+
+1 0 1.101 1.101
+2 0 1.101 1.42
+3 0 1.53 0.965
+4 0 1.101 0.965
+5 0 1.101 1.53
+6 0 1.101 1.101
+7 0 1.53 1.53
+8 0 1.53 1.101
+9 0 1.53 1.101
+10 0 1.101 1.101
+11 0 1.53 1.53
+
+AngleTorsion Coeffs
+
+1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+2 2.3668 2.492 -1.0122 -0.1892 0.4918 0.7273 110.77 111.27
+3 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.27 105.8
+4 -3.406 1.6396 0.0737 0 -0.281 -0.5944 108.728 105.8
+5 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
+6 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+7 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+8 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+9 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+10 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+11 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+
+Improper Coeffs # class2
+
+1 0 0
+2 0 0
+3 0 0
+4 0 0
+5 0 0
+6 0 0
+7 0 0
+8 0 0
+9 0 0
+10 0 0
+11 0 0
+
+AngleAngle Coeffs
+
+1 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
+3 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+4 0.1689 2.5926 3.9177 111.27 108.728 110.77
+5 2.4259 2.1283 2.4259 108.728 107.66 108.728
+6 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+7 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
+8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+9 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+10 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+11 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+
+Atoms # full
+
+266 1 4 5.2999999999999999e-02 1.6864256263249984e+00 3.9338060620105360e+00 2.1660446484538451e+00 3 2 1
+369 3 8 5.2999999999999999e-02 3.3919511835590943e-01 3.0096236406752253e+00 -2.5770783759613225e-01 -6 -4 1
+262 1 1 -1.5900000000000000e-01 6.5498274037974347e-01 4.1907594188897948e+00 2.4050161328305437e+00 3 2 1
+32 1 4 5.2999999999999999e-02 2.7301623259329730e+00 5.8422246585345166e+00 5.5163771763213223e+00 5 -1 -2
+109 1 1 -1.5900000000000000e-01 2.7961551958578061e+00 -2.2969882281549192e-01 3.2188699615959901e+00 3 2 -1
+368 3 8 5.2999999999999999e-02 2.0712023208108077e+00 3.0177796852734509e+00 -5.8999253600034041e-01 -6 -4 1
+265 1 4 5.2999999999999999e-02 3.9700241923613155e-01 3.7910255338969643e+00 3.3987341741926453e+00 3 2 1
+33 1 4 5.2999999999999999e-02 1.2162576164780894e+00 6.7486742879722721e+00 5.3541920309475231e+00 5 -1 -2
+263 1 2 2.7000000000000000e-02 4.8103594949677597e-01 5.7557856279469517e+00 2.3868716152095644e+00 3 2 1
+39 1 3 -5.5710000000000004e-01 2.2521850090997195e+00 1.3947926015289074e+00 6.8621803249373796e+00 1 1 -3
+112 1 4 5.2999999999999999e-02 2.4856857509546786e+00 5.1057788440507146e-01 3.9725913564313755e+00 3 2 -1
+120 1 3 -5.5710000000000004e-01 1.2419834017083919e-01 -2.8040716156599221e-01 5.5372267728894133e+00 2 0 -1
+264 1 3 -5.5710000000000004e-01 7.8020608557254234e-01 6.5188794064615569e+00 1.1877308855805855e+00 3 2 1
+270 1 5 4.2409999999999998e-01 1.7403462539394239e+00 6.4832110763225046e+00 1.1734811625841393e+00 3 2 1
+267 1 4 5.2999999999999999e-02 1.1704177676301275e-02 3.6374346744456014e+00 1.7121920952086365e+00 3 2 1
+268 1 4 5.2999999999999999e-02 1.1685372696766843e+00 6.1221409798979280e+00 3.1734573248995028e+00 3 2 1
+45 1 5 4.2409999999999998e-01 3.0067261615845320e+00 1.7753804307094345e+00 6.4118946885558064e+00 1 1 -3
+31 1 4 5.2999999999999999e-02 2.2064050697036626e+00 6.6971086605071743e+00 7.0117703687360011e+00 5 -1 -2
+126 1 5 4.2409999999999998e-01 9.0902656336434240e-01 2.4613225741733991e-01 5.7163101931818154e+00 2 0 -1
+28 1 1 -1.5900000000000000e-01 2.1879824905767289e+00 6.7120777486652399e+00 5.8681805243073955e+00 5 -1 -2
+114 1 4 5.2999999999999999e-02 2.5999606312665224e+00 1.7579021287431351e-01 2.2402962094249448e+00 3 2 -1
+273 1 3 -5.5710000000000004e-01 3.5334785972957876e+00 6.4187908708259780e+00 8.3840175214941537e-01 3 -2 0
+258 1 4 5.2999999999999999e-02 2.9621482858284094e+00 3.8660247181975240e+00 1.3019528905914020e+01 0 2 -1
+37 1 1 -1.5900000000000000e-01 1.0598521129795269e+00 3.0842438875120148e+00 8.2204006884588523e+00 1 1 -3
+38 1 2 2.7000000000000000e-02 2.1712614298592863e+00 2.1008262983928208e+00 8.0540118733527279e+00 1 1 -3
+41 1 4 5.2999999999999999e-02 1.0703671263629493e+00 3.7702137135715805e+00 7.3735977277148770e+00 1 1 -3
+257 1 4 5.2999999999999999e-02 1.7278164571316088e+00 4.7177234027880157e+00 1.2063346879485389e+01 0 2 -1
+42 1 4 5.2999999999999999e-02 1.2265876394911785e+00 3.6636674713028308e+00 9.1605331578946778e+00 1 1 -3
+370 3 8 5.2999999999999999e-02 9.2116275250916879e-01 4.1227962814687666e+00 1.4820928762308647e+01 -6 -4 0
+40 1 4 5.2999999999999999e-02 5.2495487796965445e-02 2.6229951455138050e+00 8.2848891549388437e+00 1 1 -3
+375 3 8 5.2999999999999999e-02 -4.9489330077790628e-01 3.6053192991211880e-01 1.2651600307530902e+01 -6 -4 0
+376 3 8 5.2999999999999999e-02 8.3275310657087132e-01 1.0348745969202238e+00 1.1656725334364307e+01 -6 -4 0
+373 3 8 5.2999999999999999e-02 3.4813445141000299e-01 3.2104872018562682e+00 1.2429232235348742e+01 -6 -4 0
+372 3 8 5.2999999999999999e-02 1.8720848803887398e+00 1.6196739445964643e+00 1.3755288219666763e+01 -6 -4 0
+371 3 8 5.2999999999999999e-02 5.1521194340731657e-01 1.0583762045930640e+00 1.4722003701038862e+01 -6 -4 0
+367 3 6 -1.5900000000000000e-01 -6.3602171946119113e-02 -5.1524032249274621e-01 9.5686066785259367e+00 -6 -4 0
+361 3 6 -1.5900000000000000e-01 1.1055962223046736e+00 3.0718618123315631e+00 1.5223515082094190e+01 -6 -4 0
+362 3 7 -1.0600000000000000e-01 9.2517651947552504e-01 1.9594163698683427e+00 1.4169307339497134e+01 -6 -4 0
+58 1 4 5.2999999999999999e-02 -1.0797825339466011e-01 6.0503146158064398e+00 9.8664400533903684e+00 2 -1 1
+253 1 1 -1.5900000000000000e-01 2.8283162006044194e+00 4.5709670497798092e+00 1.2154328606987141e+01 0 2 -1
+364 3 7 -1.0600000000000000e-01 -1.7830350547990370e-01 1.2321897052899029e+00 1.2030731564906919e+01 -6 -4 0
+363 3 7 -1.0600000000000000e-01 -2.2293502066847992e-02 2.3269152812887848e+00 1.3058793538777712e+01 -6 -4 0
+55 1 1 -1.5900000000000000e-01 -3.4547620768957216e-01 6.7052614343524413e+00 8.9800035885703497e+00 2 -1 1
+43 1 4 5.2999999999999999e-02 2.2289826718804684e+00 1.3826800188016928e+00 8.8857303442604341e+00 1 1 -3
+44 1 4 5.2999999999999999e-02 3.1106725954525829e+00 2.6936260484123027e+00 8.2445169299102297e+00 1 1 -3
+256 1 4 5.2999999999999999e-02 3.0815299500044633e+00 4.1798256626747667e+00 1.1170970686950326e+01 0 2 -1
+383 3 8 5.2999999999999999e-02 6.6060041795775071e-01 1.8687930716221879e-01 9.0559595439783092e+00 -6 -4 0
+59 1 4 5.2999999999999999e-02 4.7264429449302814e-01 6.6355010886654773e+00 8.3125090991278423e+00 2 -1 1
+259 1 4 5.2999999999999999e-02 3.3035090800840821e+00 6.2970068335297444e+00 1.3411452602206555e+01 0 2 -1
+260 1 4 5.2999999999999999e-02 3.4815907559267174e+00 6.5487893364255791e+00 1.1673290002180893e+01 0 2 -1
+246 1 3 -5.5710000000000004e-01 5.9360453663246515e-01 1.2888335162908080e+01 4.9194654955102726e+00 0 1 1
+194 1 4 5.2999999999999999e-02 1.5982974629307658e+00 1.0794069696699315e+01 2.7568796416622536e+00 -1 2 -2
+306 2 5 4.2409999999999998e-01 1.9607698791782062e+00 1.3490896316592197e+01 6.1148592423624670e+00 0 -2 0
+169 1 4 5.2999999999999999e-02 2.5814274148450411e+00 8.9353531619117117e+00 -7.1860299310229192e-01 1 1 0
+29 1 2 2.7000000000000000e-02 2.9715974167913686e+00 7.9074772360655281e+00 5.4078205795204184e+00 5 -1 -2
+347 2 4 5.2999999999999999e-02 -1.2145719128731031e-01 1.4316297751241606e+01 1.9542178483600749e+00 1 -2 -1
+245 1 2 2.7000000000000000e-02 -3.1943890227418781e-02 1.1653109988263420e+01 5.3021998249174400e+00 0 1 1
+346 2 4 5.2999999999999999e-02 1.1648612308654103e+00 1.3546593415196059e+01 1.1513387013498551e+00 1 -2 -1
+105 1 4 5.2999999999999999e-02 2.4984252378209559e+00 1.2561039259960308e+01 -7.4563758375880484e-01 -2 1 3
+190 1 1 -1.5900000000000000e-01 2.5442573818340546e+00 1.0336093395312226e+01 2.4142884402883711e+00 -1 2 -2
+252 1 5 4.2409999999999998e-01 -8.4868098238746081e-02 1.3527901602376835e+01 4.7408105763897623e+00 0 1 1
+195 1 4 5.2999999999999999e-02 2.7444617280772605e+00 9.5155123532255175e+00 3.0995750636190915e+00 -1 2 -2
+193 1 4 5.2999999999999999e-02 2.2759583286797103e+00 9.8854073073173439e+00 1.3997372539430004e+00 -1 2 -2
+251 1 4 5.2999999999999999e-02 7.0682971683056928e-01 1.0855419453551940e+01 5.4815682983141318e+00 0 1 1
+113 1 4 5.2999999999999999e-02 2.1365548120446012e+00 1.5110693884482084e+01 3.3157191792030547e+00 3 1 -1
+35 1 4 5.2999999999999999e-02 2.8218901511510834e+00 7.8331847645831392e+00 4.3648254807178608e+00 5 -1 -2
+34 1 4 5.2999999999999999e-02 2.6112645111197019e+00 8.8482268099249133e+00 5.8786736247116984e+00 5 -1 -2
+300 2 3 -5.5710000000000004e-01 2.6726228086114237e+00 1.4137611533587489e+01 6.3626920348583642e+00 0 -2 0
+348 2 4 5.2999999999999999e-02 8.1911152060473835e-02 1.4692935765232779e+01 1.8380956100244661e-01 1 -2 -1
+104 1 4 5.2999999999999999e-02 2.9137919554007121e+00 1.4109221864485288e+01 -1.2848082165395347e-03 -2 1 3
+343 2 1 -1.5900000000000000e-01 1.5025941006641419e-01 1.3872586813946324e+01 9.5434790416816107e-01 1 -2 -1
+198 1 5 4.2409999999999998e-01 3.3263561638513188e+00 1.2048317213703360e+01 4.1493225130191487e+00 -1 2 -2
+349 2 4 5.2999999999999999e-02 -4.7533304233178342e-01 1.1743319381729441e+01 1.1379390844809540e+00 1 -2 -1
+381 3 8 5.2999999999999999e-02 -2.5253459769271025e-01 1.5016546350800526e+01 8.8563352367762960e+00 -6 -5 0
+62 1 4 5.2999999999999999e-02 -3.0101575816639070e-01 8.9505133973015845e+00 8.7311617779673369e+00 2 -1 1
+165 1 3 -5.5710000000000004e-01 2.6495621319898675e+00 9.9725814348209738e+00 1.3719978940978105e+01 1 1 -1
+296 2 4 5.2999999999999999e-02 1.3616049035244895e+00 1.2418520845427265e+01 1.1927818173816899e+01 -1 2 1
+57 1 3 -5.5710000000000004e-01 8.0025188914569867e-01 8.2231792347140633e+00 1.0382903917002796e+01 2 -1 1
+94 1 4 5.2999999999999999e-02 3.1134847866002588e+00 9.7191046074117668e+00 1.1282865354000007e+01 1 0 -3
+291 2 3 -5.5710000000000004e-01 5.7746831232943996e-01 1.0502193148917126e+01 1.1931381160382449e+01 -1 2 1
+304 2 4 5.2999999999999999e-02 3.1480866720513800e+00 1.2554444617491869e+01 7.6680859654405946e+00 0 -2 0
+297 2 5 4.2409999999999998e-01 1.2581372902155021e+00 1.0392480540302307e+01 1.2645034320330218e+01 -1 2 1
+63 1 5 4.2409999999999998e-01 6.9962328213572200e-01 9.0038329278533400e+00 1.0950522205481576e+01 2 -1 1
+168 1 4 5.2999999999999999e-02 7.4732895006075384e-01 7.5654030176846749e+00 1.5093830258489049e+01 1 1 -1
+56 1 2 2.7000000000000000e-02 -3.0829835630448443e-01 8.1698186033941287e+00 9.5432386080912188e+00 2 -1 1
+93 1 3 -5.5710000000000004e-01 3.1184068671991230e+00 8.1800617489551524e+00 8.9323958196463522e+00 1 0 -3
+103 1 4 5.2999999999999999e-02 2.0548927400547661e+00 1.3964074878457176e+01 1.4776678767988326e+01 -2 1 2
+99 1 5 4.2409999999999998e-01 2.1923343441361740e+00 8.0584065948694708e+00 9.2971820594261239e+00 1 0 -3
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diff --git a/examples/USER/fep/C7inEthanol/fep10/in.deletion b/examples/USER/fep/C7inEthanol/fep10/in.deletion
new file mode 100644
index 0000000000000000000000000000000000000000..a7f09d09ba12c897da69a0f379e907a044b1687d
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep10/in.deletion
@@ -0,0 +1,57 @@
+# LAMMPS atomistic input script
+
+echo screen
+units real
+atom_style full
+
+pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5
+bond_style class2
+angle_style class2
+dihedral_style class2
+improper_style class2
+pair_modify mix sixthpower tail yes
+special_bonds lj/coul 0 0 1
+
+read_data data.init_conf_with_heptane
+
+pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 1.0
+pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 1.0
+pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0
+pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
+pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0
+
+pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 1.0
+pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 1.0
+pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0
+pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
+pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0
+
+pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
+pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0
+pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 1.0
+pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 1.0
+pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 1.0
+
+timestep 1.0
+kspace_style pppm 1.0e-5
+
+variable lambda equal ramp(1.0,0.0)
+variable q1 equal -0.1590*v_lambda
+variable q2 equal -0.1060*v_lambda
+variable q3 equal 0.0530*v_lambda
+
+fix ADAPT all adapt/fep 10 &
+ pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda &
+ atom charge 6 v_q1 &
+ atom charge 7 v_q2 &
+ atom charge 8 v_q3 &
+ after yes
+
+thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_modify line one
+thermo 100
+
+fix 1 all nvt temp 300 300 100
+run 100000
+
+write_data data.after_heptane_deletion
diff --git a/examples/USER/fep/C7inEthanol/fep10/log.lammps b/examples/USER/fep/C7inEthanol/fep10/log.lammps
new file mode 100644
index 0000000000000000000000000000000000000000..fbd4a49a3e18722a2e7424f47938351fb09e33c8
--- /dev/null
+++ b/examples/USER/fep/C7inEthanol/fep10/log.lammps
@@ -0,0 +1,1125 @@
+LAMMPS (27 Nov 2018)
+# LAMMPS atomistic input script
+
+echo screen
+ orthogonal box = (-0.505141 -0.806203 -0.862753) to (15.7831 15.482 15.4255)
+ 4 by 2 by 2 MPI processor grid
+WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:580)
+ reading atoms ...
+ 383 atoms
+ reading velocities ...
+ 383 velocities
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 9 = max dihedrals/atom
+ scanning impropers ...
+ 4 = max impropers/atom
+ reading bonds ...
+ 342 bonds
+ reading angles ...
+ 562 angles
+ reading dihedrals ...
+ 534 dihedrals
+ reading impropers ...
+ 348 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 10 = max # of special neighbors
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.288287
+ grid = 10 10 10
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00279394
+ estimated relative force accuracy = 8.41388e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 1296 90
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.5
+ ghost atom cutoff = 11.5
+ binsize = 5.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair lj/class2/coul/long, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/class2/coul/long/soft, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.61 | 13.92 | 14.89 Mbytes
+Step S/CPU Temp Press Volume TotEng PotEng v_lambda v_q1 v_q2 v_q3
+ 0 0 301.82904 533.3184 4321.3892 -79.144423 -422.82793 1 -0.159 -0.106 0.053
+ 100 799.51858 297.06821 2966.9114 4321.3892 -67.550969 -405.81346 0.999 -0.158841 -0.105894 0.052947
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+ 90700 1049.6449 304.75869 491.81214 4321.3892 -32.483415 -379.50282 0.093 -0.014787 -0.009858 0.004929
+ 90800 1088.5448 312.11022 -92.527225 4321.3892 -14.727062 -370.11743 0.092 -0.014628 -0.009752 0.004876
+ 90900 1169.7241 314.93574 -2223.9697 4321.3892 -3.1788972 -361.7866 0.091 -0.014469 -0.009646 0.004823
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+ 91100 1132.3002 284.14469 -6023.7201 4321.3892 -53.764775 -377.31165 0.089 -0.014151 -0.009434 0.004717
+ 91200 1293.3931 287.66353 6150.766 4321.3892 -43.173588 -370.72726 0.088 -0.013992 -0.009328 0.004664
+ 91300 1336.8356 314.97898 -1327.131 4321.3892 -25.333246 -383.99018 0.087 -0.013833 -0.009222 0.004611
+ 91400 1289.2974 303.31879 3138.2432 4321.3892 -29.501306 -374.88114 0.086 -0.013674 -0.009116 0.004558
+ 91500 1307.7006 282.75736 -1380.4769 4321.3892 -49.448632 -371.41579 0.085 -0.013515 -0.00901 0.004505
+ 91600 1269.0586 283.29722 -1951.6655 4321.3892 -84.343844 -406.92573 0.084 -0.013356 -0.008904 0.004452
+ 91700 1144.9321 289.77029 974.6449 4321.3892 -75.621497 -405.57407 0.083 -0.013197 -0.008798 0.004399
+ 91800 1085.0704 296.98697 -4825.7121 4321.3892 -46.671488 -384.84148 0.082 -0.013038 -0.008692 0.004346
+ 91900 1160.6722 297.70607 323.7418 4321.3892 -37.504047 -376.49285 0.081 -0.012879 -0.008586 0.004293
+ 92000 1168.8859 305.08167 -2096.4485 4321.3892 -43.171767 -390.55894 0.08 -0.01272 -0.00848 0.00424
+ 92100 1228.4777 286.00549 -806.12564 4321.3892 -47.22354 -372.88925 0.079 -0.012561 -0.008374 0.004187
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+ 92500 1298.4844 294.4471 208.34033 4321.3892 -38.759251 -374.03717 0.075 -0.011925 -0.00795 0.003975
+ 92600 1297.8766 288.8217 -3247.9498 4321.3892 -58.775189 -387.64763 0.074 -0.011766 -0.007844 0.003922
+ 92700 1395.0835 284.70355 2129.8976 4321.3892 -49.160932 -373.34416 0.073 -0.011607 -0.007738 0.003869
+ 92800 1216.7991 289.23676 -1741.3631 4321.3892 -33.817002 -363.16207 0.072 -0.011448 -0.007632 0.003816
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+ 93500 1128.6811 309.42525 -2607.9261 4321.3892 -23.331773 -375.66484 0.065 -0.010335 -0.00689 0.003445
+ 93600 1139.317 292.99169 -774.0168 4321.3892 -37.333014 -370.95369 0.064 -0.010176 -0.006784 0.003392
+ 93700 1370.9087 290.86283 1786.595 4321.3892 -45.640938 -376.83756 0.063 -0.010017 -0.006678 0.003339
+ 93800 1277.8603 318.07879 -422.91954 4321.3892 -46.284829 -408.47143 0.062 -0.009858 -0.006572 0.003286
+ 93900 1121.6075 304.32679 5.9451702 4321.3892 -49.580127 -396.10774 0.061 -0.009699 -0.006466 0.003233
+ 94000 1006.7719 283.12544 -733.87123 4321.3892 -46.292757 -368.67904 0.06 -0.00954 -0.00636 0.00318
+ 94100 935.98726 309.35995 -2763.6937 4321.3892 -16.012954 -368.27167 0.059 -0.009381 -0.006254 0.003127
+ 94200 920.27928 321.35685 4355.0455 4321.3892 9.3724178 -356.54681 0.058 -0.009222 -0.006148 0.003074
+ 94300 967.97595 312.78817 2348.5812 4321.3892 -20.00037 -376.1627 0.057 -0.009063 -0.006042 0.003021
+ 94400 1018.827 296.12119 -3374.9334 4321.3892 -32.84738 -370.03153 0.056 -0.008904 -0.005936 0.002968
+ 94500 1021.8044 296.02242 1733.7546 4321.3892 -42.175723 -379.24741 0.055 -0.008745 -0.00583 0.002915
+ 94600 1061.8865 291.58691 -3637.6907 4321.3892 -49.67462 -381.69572 0.054 -0.008586 -0.005724 0.002862
+ 94700 1117.3251 299.85297 3597.4653 4321.3892 -57.409636 -398.84305 0.053 -0.008427 -0.005618 0.002809
+ 94800 1131.5391 283.00102 3677.9322 4321.3892 -51.928185 -374.1728 0.052 -0.008268 -0.005512 0.002756
+ 94900 1237.6831 305.71843 -1190.4296 4321.3892 -21.13139 -369.24363 0.051 -0.008109 -0.005406 0.002703
+ 95000 1323.5844 308.04416 1255.5563 4321.3892 -7.0314362 -357.79191 0.05 -0.00795 -0.0053 0.00265
+ 95100 1298.9324 314.70594 812.32969 4321.3892 -15.803668 -374.1497 0.049 -0.007791 -0.005194 0.002597
+ 95200 1292.7408 299.68997 4369.0866 4321.3892 -48.802563 -390.05037 0.048 -0.007632 -0.005088 0.002544
+ 95300 1313.8364 307.27814 -2352.9934 4321.3892 -54.373095 -404.26132 0.047 -0.007473 -0.004982 0.002491
+ 95400 1201.8365 298.47877 -2718.7005 4321.3892 -45.986629 -385.85528 0.046 -0.007314 -0.004876 0.002438
+ 95500 1103.6045 306.69668 -741.22716 4321.3892 -37.949989 -387.17613 0.045 -0.007155 -0.00477 0.002385
+ 95600 1035.5871 286.79853 -1438.1728 4321.3892 -27.503416 -354.07213 0.044 -0.006996 -0.004664 0.002332
+ 95700 1013.5068 320.48771 -5332.312 4321.3892 1.4199032 -363.50966 0.043 -0.006837 -0.004558 0.002279
+ 95800 962.97959 304.6672 4340.0573 4321.3892 -20.784782 -367.70001 0.042 -0.006678 -0.004452 0.002226
+ 95900 994.9843 299.96049 1484.318 4321.3892 -52.16709 -393.72294 0.041 -0.006519 -0.004346 0.002173
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+ 96100 1088.3112 304.24734 -1088.2219 4321.3892 -36.639733 -383.07688 0.039 -0.006201 -0.004134 0.002067
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+ 96400 1209.7709 301.6218 130.93366 4321.3892 -45.370521 -388.81805 0.036 -0.005724 -0.003816 0.001908
+ 96500 1204.9443 292.54592 -682.29661 4321.3892 -62.29541 -395.4085 0.035 -0.005565 -0.00371 0.001855
+ 96600 1289.3438 300.5615 -174.9403 4321.3892 -57.725164 -399.96536 0.034 -0.005406 -0.003604 0.001802
+ 96700 1338.818 308.2797 -1794.2828 4321.3892 -28.915577 -379.94425 0.033 -0.005247 -0.003498 0.001749
+ 96800 1359.4009 305.91475 1486.7387 4321.3892 -8.4642777 -356.80006 0.032 -0.005088 -0.003392 0.001696
+ 96900 1407.6407 306.58372 544.53377 4321.3892 -25.698784 -374.79629 0.031 -0.004929 -0.003286 0.001643
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+ 97100 1184.017 311.13508 3386.5961 4321.3892 -35.636018 -389.91602 0.029 -0.004611 -0.003074 0.001537
+ 97200 1052.5132 302.83751 -450.40793 4321.3892 -48.013358 -392.84518 0.028 -0.004452 -0.002968 0.001484
+ 97300 936.51847 296.05186 2250.9701 4321.3892 -65.08671 -402.19191 0.027 -0.004293 -0.002862 0.001431
+ 97400 879.09894 281.15562 204.89405 4321.3892 -79.023788 -399.1671 0.026 -0.004134 -0.002756 0.001378
+ 97500 868.33473 269.68695 -3949.5957 4321.3892 -90.496345 -397.58063 0.025 -0.003975 -0.00265 0.001325
+ 97600 915.76128 283.95639 441.03454 4321.3892 -55.42154 -378.754 0.024 -0.003816 -0.002544 0.001272
+ 97700 896.34506 289.78136 -6167.1083 4321.3892 -37.414959 -367.38014 0.023 -0.003657 -0.002438 0.001219
+ 97800 923.57325 298.24796 -2426.5007 4321.3892 -29.79808 -369.40392 0.022 -0.003498 -0.002332 0.001166
+ 97900 939.86442 304.1769 -769.76822 4321.3892 -28.013008 -374.36994 0.021 -0.003339 -0.002226 0.001113
+ 98000 965.49764 315.25564 4166.1952 4321.3892 -55.957081 -414.92904 0.02 -0.00318 -0.00212 0.00106
+ 98100 1078.2676 307.26587 -1181.6991 4321.3892 -78.786952 -428.6612 0.019 -0.003021 -0.002014 0.001007
+ 98200 1247.6092 289.07166 202.07604 4321.3892 -73.395206 -402.55228 0.018 -0.002862 -0.001908 0.000954
+ 98300 1200.7015 285.31381 -2299.6769 4321.3892 -45.2464 -370.12452 0.017 -0.002703 -0.001802 0.000901
+ 98400 1085.8992 311.10198 -3232.7903 4321.3892 -33.607942 -387.85026 0.016 -0.002544 -0.001696 0.000848
+ 98500 1091.9796 292.79852 -1965.1408 4321.3892 -38.555567 -371.95629 0.015 -0.002385 -0.00159 0.000795
+ 98600 1144.6557 290.76805 -4137.567 4321.3892 -50.778851 -381.86754 0.014 -0.002226 -0.001484 0.000742
+ 98700 1170.8695 283.83023 2206.1755 4321.3892 -58.562343 -381.75115 0.013 -0.002067 -0.001378 0.000689
+ 98800 1193.8331 287.40594 1967.1514 4321.3892 -74.339987 -401.60034 0.012 -0.001908 -0.001272 0.000636
+ 98900 1230.3623 289.38887 -1622.2824 4321.3892 -78.82881 -408.34707 0.011 -0.001749 -0.001166 0.000583
+ 99000 1266.8669 310.73931 4085.1571 4321.3892 -53.129655 -406.95901 0.01 -0.00159 -0.00106 0.00053
+ 99100 1251.781 306.15188 1860.7013 4321.3892 -29.112509 -377.71829 0.009 -0.001431 -0.000954 0.000477
+ 99200 1152.1594 314.46538 -138.58309 4321.3892 -26.023578 -384.09569 0.008 -0.001272 -0.000848 0.000424
+ 99300 1195.7914 294.0181 2065.5118 4321.3892 -49.077056 -383.86648 0.007 -0.001113 -0.000742 0.000371
+ 99400 1266.2656 287.47157 -2921.4005 4321.3892 -65.534324 -392.86941 0.006 -0.000954 -0.000636 0.000318
+ 99500 1269.4126 292.64019 -2312.8277 4321.3892 -58.326345 -391.54679 0.005 -0.000795 -0.00053 0.000265
+ 99600 1296.8191 302.22068 2864.3077 4321.3892 -44.992409 -389.12186 0.004 -0.000636 -0.000424 0.000212
+ 99700 1410.231 300.25576 552.56231 4321.3892 -32.773166 -374.66523 0.003 -0.000477 -0.000318 0.000159
+ 99800 1435.524 336.9684 -1254.1072 4321.3892 -4.899367 -388.59499 0.002 -0.000318 -0.000212 0.000106
+ 99900 1433.3697 319.25818 3463.0802 4321.3892 8.0883629 -355.44117 0.001 -0.000159 -0.000106 5.3e-05
+ 100000 1318.7622 291.43698 -2961.7602 4321.3892 -27.295831 -359.14621 0 -0 -0 0
+Loop time of 78.283 on 16 procs for 100000 steps with 383 atoms
+
+Performance: 110.369 ns/day, 0.217 hours/ns, 1277.417 timesteps/s
+94.1% CPU use with 16 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 15.43 | 19.194 | 29.637 | 81.5 | 24.52
+Bond | 3.2625 | 3.4917 | 4.0461 | 11.0 | 4.46
+Kspace | 29.911 | 40.821 | 44.717 | 57.6 | 52.14
+Neigh | 0.96168 | 0.96819 | 0.97633 | 0.5 | 1.24
+Comm | 10.348 | 10.581 | 10.846 | 4.3 | 13.52
+Output | 0.030217 | 0.031298 | 0.040418 | 1.3 | 0.04
+Modify | 1.8451 | 1.9233 | 1.9863 | 3.6 | 2.46
+Other | | 1.273 | | | 1.63
+
+Nlocal: 23.9375 ave 37 max 16 min
+Histogram: 3 3 2 2 1 2 0 1 1 1
+Nghost: 2317.44 ave 2369 max 2273 min
+Histogram: 3 3 1 1 0 1 2 1 2 2
+Neighs: 5966.62 ave 8863 max 4086 min
+Histogram: 4 2 2 0 2 1 2 1 0 2
+
+Total # of neighbors = 95466
+Ave neighs/atom = 249.258
+Ave special neighs/atom = 4.72063
+Neighbor list builds = 3058
+Dangerous builds = 0
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.288285
+ grid = 10 10 10
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00277417
+ estimated relative force accuracy = 8.35432e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 1296 90
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11.5
+ ghost atom cutoff = 11.5
+ binsize = 5.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair lj/class2/coul/long, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/class2/coul/long/soft, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Total wall time: 0:01:18
diff --git a/examples/USER/fep/README b/examples/USER/fep/README
index 187c26be80d9f105fe033cfe11ffd5d7a5c5b384..64c46f2b03a385d0a3118487ed50b84b65ca8414 100644
--- a/examples/USER/fep/README
+++ b/examples/USER/fep/README
@@ -9,3 +9,6 @@ compute fep examples
* `CC-CO` -- free energy difference of transforming ethane into
methanol, in water (more complex). FEP, TI and BAR methods.
+
+* 'C7inEthanol' -- insertion / deletion of a hexane molecule in ethanol.
+ The hexane is described by the lj/class2/coul/long/soft potential.
diff --git a/src/USER-FEP/Install.sh b/src/USER-FEP/Install.sh
index 09c2024ad20038652d9a55399f46ffaac6c04aa1..c6e7a53aa1ab4e8293e81470e77c77112943ae54 100755
--- a/src/USER-FEP/Install.sh
+++ b/src/USER-FEP/Install.sh
@@ -50,4 +50,10 @@ action pair_morse_soft.cpp
action pair_morse_soft.h
action pair_tip4p_long_soft.cpp pppm_tip4p.cpp
action pair_tip4p_long_soft.h pppm_tip4p.cpp
+action pair_lj_class2_soft.cpp
+action pair_lj_class2_soft.h
+action pair_lj_class2_coul_cut_soft.cpp
+action pair_lj_class2_coul_cut_soft.h
+action pair_lj_class2_coul_long_soft.cpp pppm.cpp
+action pair_lj_class2_coul_long_soft.h pppm.cpp
diff --git a/src/USER-FEP/README b/src/USER-FEP/README
index 8c942a90d8d667fbc3e702aece4eb9ca275f3de0..90e58f9e829fd1a5ca187ebffe21c2787aaf5c5c 100644
--- a/src/USER-FEP/README
+++ b/src/USER-FEP/README
@@ -16,3 +16,7 @@ Pair style morse/soft was contributed by Stefan Paquay, s.paquay at tue.nl
Applied Physics/Theory of Polymers and Soft Matter,
Eindhoven University of Technology (TU/e), The Netherlands
Contact him in case of problems with this pair style.
+
+Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at
+Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de)
+Contact him in case of problems with these pair styles.
diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7970097cfec1bb609ebe6fd4d8bb92079426f1d2
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
@@ -0,0 +1,519 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_lj_class2_coul_cut_soft.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2CoulCutSoft::PairLJClass2CoulCutSoft(LAMMPS *lmp) : Pair(lmp)
+{
+ writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2CoulCutSoft::~PairLJClass2CoulCutSoft()
+{
+ if (!copymode) {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut_lj);
+ memory->destroy(cut_ljsq);
+ memory->destroy(cut_coul);
+ memory->destroy(cut_coulsq);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(lambda);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(lj4);
+ memory->destroy(offset);
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+ double rsq,forcecoul,forcelj;
+ double factor_coul,factor_lj;
+ double denc, denlj, r4sig6;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ denc = sqrt(lj4[itype][jtype] + rsq);
+ forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
+ } else forcelj = 0.0;
+
+ fpair = factor_coul*forcecoul + factor_lj*forcelj;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq[itype][jtype])
+ ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
+ else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
+ evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
+ memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
+ memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(lambda,n+1,n+1,"pair:lambda");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(lj4,n+1,n+1,"pair:lj4");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::settings(int narg, char **arg)
+{
+ if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command");
+
+ nlambda = force->numeric(FLERR,arg[0]);
+ alphalj = force->numeric(FLERR,arg[1]);
+ alphac = force->numeric(FLERR,arg[2]);
+
+ cut_lj_global = force->numeric(FLERR,arg[3]);
+ if (narg == 4) cut_coul_global = cut_lj_global;
+ else cut_coul_global = force->numeric(FLERR,arg[4]);
+
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) {
+ cut_lj[i][j] = cut_lj_global;
+ cut_coul[i][j] = cut_coul_global;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::coeff(int narg, char **arg)
+{
+ if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+ double lambda_one = force->numeric(FLERR,arg[4]);
+ if (sigma_one <= 0.0)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ double cut_lj_one = cut_lj_global;
+ double cut_coul_one = cut_coul_global;
+ if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]);
+ if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ cut_lj[i][j] = cut_lj_one;
+ lambda[i][j] = lambda_one;
+ cut_coul[i][j] = cut_coul_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::init_style()
+{
+ if (!atom->q_flag)
+ error->all(FLERR,"Pair style lj/class2/coul/cut/soft requires atom attribute q");
+
+ neighbor->request(this,instance_me);
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLJClass2CoulCutSoft::init_one(int i, int j)
+{
+ // always mix epsilon,sigma via sixthpower rules
+ // mix distance via user-defined rule
+
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
+ sigma[i][j] =
+ pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
+ if (lambda[i][i] != lambda[j][j])
+ error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix");
+ lambda[i][j] = lambda[i][i];
+ cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
+ cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
+ }
+
+ double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
+ cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
+ cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
+
+ lj1[i][j] = pow(lambda[i][j], nlambda);
+ lj2[i][j] = pow(sigma[i][j], 6.0);
+ lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
+ lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
+
+ if (offset_flag && (cut_lj[i][j] > 0.0)) {
+ double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0);
+ offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0));
+ } else offset[i][j] = 0.0;
+
+ epsilon[j][i] = epsilon[i][j];
+ sigma[j][i] = sigma[i][j];
+ lambda[j][i] = lambda[i][j];
+ cut_ljsq[j][i] = cut_ljsq[i][j];
+ cut_coulsq[j][i] = cut_coulsq[i][j];
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ lj4[j][i] = lj4[i][j];
+ offset[j][i] = offset[i][j];
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
+ double sig6 = sig3*sig3;
+ double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
+ double rc6 = rc3*rc3;
+ // the tail and pressure corrections are not exact but approximate
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 2.0*rc3) / rc6;
+ }
+
+ return cut;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&lambda[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ fwrite(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&lambda[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ fread(&cut_coul[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::write_restart_settings(FILE *fp)
+{
+ fwrite(&nlambda,sizeof(double),1,fp);
+ fwrite(&alphalj,sizeof(double),1,fp);
+ fwrite(&alphac,sizeof(double),1,fp);
+
+ fwrite(&cut_lj_global,sizeof(double),1,fp);
+ fwrite(&cut_coul_global,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::read_restart_settings(FILE *fp)
+{
+ if (comm->me == 0) {
+ fread(&nlambda,sizeof(double),1,fp);
+ fread(&alphalj,sizeof(double),1,fp);
+ fread(&alphac,sizeof(double),1,fp);
+
+ fread(&cut_lj_global,sizeof(double),1,fp);
+ fread(&cut_coul_global,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ }
+ MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
+
+ MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulCutSoft::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
+ lambda[i][j],cut_lj[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJClass2CoulCutSoft::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
+{
+ double forcecoul,forcelj,phicoul,philj;
+ double denc, denlj, r4sig6;
+
+ if (rsq < cut_coulsq[itype][jtype]) {
+ denc = sqrt(lj4[itype][jtype] + rsq);
+ forcecoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
+ (denc*denc*denc);
+ } else forcecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ denlj = lj3[itype][jtype] + rsq*r4sig6;
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
+ } else forcelj = 0.0;
+ fforce = factor_coul*forcecoul + factor_lj*forcelj;
+
+ double eng = 0.0;
+ if (rsq < cut_coulsq[itype][jtype]) {
+ phicoul = force->qqrd2e *lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
+ eng += factor_coul*phicoul;
+ }
+ if (rsq < cut_ljsq[itype][jtype]) {
+ philj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype];
+ eng += factor_lj*philj;
+ }
+
+ return eng;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLJClass2CoulCutSoft::extract(const char *str, int &dim)
+{
+ dim = 0;
+ if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+ dim = 2;
+ if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
+ if (strcmp(str,"sigma") == 0) return (void *) sigma;
+ if (strcmp(str,"lambda") == 0) return (void *) lambda;
+ return NULL;
+}
diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h
new file mode 100644
index 0000000000000000000000000000000000000000..d4d8c264b544090e76d3f87385cf23526a63449c
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h
@@ -0,0 +1,81 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/class2/coul/cut/soft,PairLJClass2CoulCutSoft)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H
+#define LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairLJClass2CoulCutSoft : public Pair {
+ public:
+ PairLJClass2CoulCutSoft(class LAMMPS *);
+ virtual ~PairLJClass2CoulCutSoft();
+ virtual void compute(int, int);
+ virtual void settings(int, char **);
+ void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+ double single(int, int, int, int, double, double, double, double &);
+ void *extract(const char *, int &);
+
+ protected:
+ double cut_lj_global,cut_coul_global;
+ double **cut_lj,**cut_ljsq;
+ double **cut_coul,**cut_coulsq;
+ double **epsilon,**sigma, **lambda;
+ double nlambda, alphalj, alphac;
+ double **lj1,**lj2,**lj3,**lj4,**offset;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style lj/class2/coul/cut/soft requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Pair lj/class2/coul/cut/soft different lambda values in mix
+
+The value of lambda has to be the same for I J pairs.
+
+*/
diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..13096a64c6abd14bdda5a45a3df7baabb3af4417
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
@@ -0,0 +1,543 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_lj_class2_coul_long_soft.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "kspace.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define EWALD_F 1.12837917
+#define EWALD_P 0.3275911
+#define A1 0.254829592
+#define A2 -0.284496736
+#define A3 1.421413741
+#define A4 -1.453152027
+#define A5 1.061405429
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2CoulLongSoft::PairLJClass2CoulLongSoft(LAMMPS *lmp) : Pair(lmp)
+{
+ ewaldflag = pppmflag = 1;
+ writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2CoulLongSoft::~PairLJClass2CoulLongSoft()
+{
+ if (!copymode) {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut_lj);
+ memory->destroy(cut_ljsq);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(lambda);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(lj4);
+ memory->destroy(offset);
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+ double fraction;
+ double rsq,r,forcecoul,forcelj;
+ double grij,expm2,prefactor,t,erfc;
+ double factor_coul,factor_lj;
+ double denc, denlj, r4sig6;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ denc = sqrt(lj4[itype][jtype] + rsq);
+ prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ denlj = lj3[itype][jtype] + rsq*r4sig6;
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
+ } else forcelj = 0.0;
+
+ fpair = forcecoul + factor_lj*forcelj;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
+ ecoul = prefactor*erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ denlj = lj3[itype][jtype] + rsq*r4sig6;
+ evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
+ memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(lambda,n+1,n+1,"pair:lambda");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(lj4,n+1,n+1,"pair:lj4");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::settings(int narg, char **arg)
+{
+ if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command");
+
+ nlambda = force->numeric(FLERR,arg[0]);
+ alphalj = force->numeric(FLERR,arg[1]);
+ alphac = force->numeric(FLERR,arg[2]);
+
+ cut_lj_global = force->numeric(FLERR,arg[3]);
+ if (narg == 4) cut_coul = cut_lj_global;
+ else cut_coul = force->numeric(FLERR,arg[4]);
+
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::coeff(int narg, char **arg)
+{
+ if (narg < 5 || narg > 6)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+ double lambda_one = force->numeric(FLERR,arg[4]);
+ if (sigma_one <= 0.0)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ double cut_lj_one = cut_lj_global;
+ if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ lambda[i][j] = lambda_one;
+ cut_lj[i][j] = cut_lj_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::init_style()
+{
+ if (!atom->q_flag)
+ error->all(FLERR,
+ "Pair style lj/class2/coul/long/soft requires atom attribute q");
+
+ neighbor->request(this,instance_me);
+
+ cut_coulsq = cut_coul * cut_coul;
+
+ // insure use of KSpace long-range solver, set g_ewald
+
+ if (force->kspace == NULL)
+ error->all(FLERR,"Pair style requires a KSpace style");
+ g_ewald = force->kspace->g_ewald;
+
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLJClass2CoulLongSoft::init_one(int i, int j)
+{
+ // always mix epsilon,sigma via sixthpower rules
+ // mix distance via user-defined rule
+
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
+ sigma[i][j] =
+ pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
+ if (lambda[i][i] != lambda[j][j])
+ error->all(FLERR,"Pair lj/class2/coul/long/soft different lambda values in mix");
+ lambda[i][j] = lambda[i][i];
+ cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
+ }
+
+ double cut = MAX(cut_lj[i][j],cut_coul);
+ cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
+
+ lj1[i][j] = pow(lambda[i][j], nlambda);
+ lj2[i][j] = pow(sigma[i][j], 6.0);
+ lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
+ lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
+
+ if (offset_flag && (cut_lj[i][j] > 0.0)) {
+ double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0);
+ offset[i][j] = epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0));
+ } else offset[i][j] = 0.0;
+
+ epsilon[j][i] = epsilon[i][j];
+ sigma[j][i] = sigma[i][j];
+ lambda[j][i] = lambda[i][j];
+ cut_ljsq[j][i] = cut_ljsq[i][j];
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ lj4[j][i] = lj4[i][j];
+ offset[j][i] = offset[i][j];
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
+ double sig6 = sig3*sig3;
+ double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
+ double rc6 = rc3*rc3;
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 2.0*rc3) / rc6;
+ }
+
+ return cut;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&lambda[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&lambda[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::write_restart_settings(FILE *fp)
+{
+ fwrite(&nlambda,sizeof(double),1,fp);
+ fwrite(&alphalj,sizeof(double),1,fp);
+ fwrite(&alphac,sizeof(double),1,fp);
+
+ fwrite(&cut_lj_global,sizeof(double),1,fp);
+ fwrite(&cut_coul,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::read_restart_settings(FILE *fp)
+{
+ if (comm->me == 0) {
+ fread(&nlambda,sizeof(double),1,fp);
+ fread(&alphalj,sizeof(double),1,fp);
+ fread(&alphac,sizeof(double),1,fp);
+
+ fread(&cut_lj_global,sizeof(double),1,fp);
+ fread(&cut_coul,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ }
+ MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
+
+ MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2CoulLongSoft::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
+ lambda[i][j],cut_lj[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJClass2CoulLongSoft::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
+{
+ double denc,r,denlj,r4sig6,grij,expm2,t,erfc,prefactor;
+ double fraction,forcecoul,forcelj,phicoul,philj;
+
+ if (rsq < cut_coulsq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ denc = sqrt(lj4[itype][jtype] + rsq);
+ prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
+ (denc*denc*denc);
+ forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else forcecoul = 0.0;
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ denlj = lj3[itype][jtype] + rsq*r4sig6;
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
+ } else forcelj = 0.0;
+ fforce = forcecoul + factor_lj*forcelj;
+
+ double eng = 0.0;
+ if (rsq < cut_coulsq) {
+ prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
+ phicoul = prefactor*erfc;
+ if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
+ eng += phicoul;
+ }
+ if (rsq < cut_ljsq[itype][jtype]) {
+ philj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype];
+ eng += factor_lj*philj;
+ }
+
+ return eng;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLJClass2CoulLongSoft::extract(const char *str, int &dim)
+{
+ dim = 0;
+ if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+ dim = 2;
+ if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
+ if (strcmp(str,"sigma") == 0) return (void *) sigma;
+ if (strcmp(str,"lambda") == 0) return (void *) lambda;
+ return NULL;
+}
diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.h b/src/USER-FEP/pair_lj_class2_coul_long_soft.h
new file mode 100644
index 0000000000000000000000000000000000000000..c334ef19df49184a7bd27df122f2ac3edd66639e
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.h
@@ -0,0 +1,82 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/class2/coul/long/soft,PairLJClass2CoulLongSoft)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H
+#define LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairLJClass2CoulLongSoft : public Pair {
+ public:
+ PairLJClass2CoulLongSoft(class LAMMPS *);
+ virtual ~PairLJClass2CoulLongSoft();
+ virtual void compute(int, int);
+ virtual void settings(int, char **);
+ void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+ double single(int, int, int, int, double, double, double, double &);
+ void *extract(const char *, int &);
+
+ protected:
+ double cut_lj_global;
+ double **cut_lj,**cut_ljsq;
+ double cut_coul,cut_coulsq;
+ double **epsilon,**sigma, **lambda;
+ double nlambda, alphalj, alphac;
+ double **lj1,**lj2,**lj3,**lj4,**offset;
+ double g_ewald;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style lj/class2/coul/long/soft requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Pair style requires a KSpace style
+
+No kspace style is defined.
+
+*/
diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b7f21fc59c67dc602264f891a2eb61dd71f1ded2
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_soft.cpp
@@ -0,0 +1,438 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_lj_class2_soft.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp)
+{
+ writedata = 1;
+ allocated = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLJClass2Soft::~PairLJClass2Soft()
+{
+ if (!copymode) {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(lambda);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(offset);
+ allocated=0;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJClass2Soft::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,forcelj,factor_lj;
+ double denlj, r4sig6;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
+ fpair = factor_lj*forcelj;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
+ evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
+ offset[itype][jtype];
+ evdwl *= factor_lj;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(cut,n+1,n+1,"pair:cut");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(lambda,n+1,n+1,"pair:lambda");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::settings(int narg, char **arg)
+{
+ if (narg != 3) error->all(FLERR,"Illegal pair_style command");
+
+ nlambda = force->numeric(FLERR,arg[0]);
+ alphalj = force->numeric(FLERR,arg[1]);
+
+ cut_global = force->numeric(FLERR,arg[2]);
+
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut[i][j] = cut_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::coeff(int narg, char **arg)
+{
+ if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+ double lambda_one = force->numeric(FLERR,arg[4]);
+ if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients");
+
+ double cut_one = cut_global;
+ if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ lambda[i][j] = lambda_one;
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLJClass2Soft::init_one(int i, int j)
+{
+ // always mix epsilon,sigma via sixthpower rules
+ // mix distance via user-defined rule
+
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
+ pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
+ (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
+ sigma[i][j] =
+ pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
+ if (lambda[i][i] != lambda[j][j])
+ error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix");
+ lambda[i][j] = lambda[i][i];
+ cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
+ }
+
+ lj1[i][j] = pow(lambda[i][j], nlambda);
+ lj2[i][j] = pow(sigma[i][j], 6.0);
+ lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
+
+ if (offset_flag && (cut[i][j] > 0.0)) {
+ double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0);
+ offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj);
+ } else offset[i][j] = 0.0;
+
+ epsilon[j][i] = epsilon[i][j];
+ sigma[j][i] = sigma[i][j];
+ lambda[j][i] = lambda[i][j];
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ offset[j][i] = offset[i][j];
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
+ double sig6 = sig3*sig3;
+ double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
+ double rc6 = rc3*rc3;
+ // check the following expressions for etail_lj & ptail_ij they are not correct !
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
+ sig6 * (sig3 - 2.0*rc3) / rc6;
+ }
+
+ return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&lambda[i][j],sizeof(double),1,fp);
+ fwrite(&cut[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&lambda[i][j],sizeof(double),1,fp);
+ fread(&cut[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::write_restart_settings(FILE *fp)
+{
+ fwrite(&nlambda,sizeof(double),1,fp);
+ fwrite(&alphalj,sizeof(double),1,fp);
+ fwrite(&cut_global,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::read_restart_settings(FILE *fp)
+{
+ int me = comm->me;
+ if (me == 0) {
+ fread(&nlambda,sizeof(double),1,fp);
+ fread(&alphalj,sizeof(double),1,fp);
+ fread(&cut_global,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ }
+ MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+}
+
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJClass2Soft::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
+ lambda[i][j],cut[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJClass2Soft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
+ double &fforce)
+{
+ double forcelj,philj;
+ double r4sig6, denlj;
+
+ if (rsq < cutsq[itype][jtype]) {
+ r4sig6 = rsq*rsq / lj2[itype][jtype];
+ denlj = lj3[itype][jtype] + rsq*r4sig6;
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
+ } else forcelj = 0.0;
+ fforce = factor_lj*forcelj;
+
+ if (rsq < cutsq[itype][jtype]) {
+ denlj = lj3[itype][jtype] + rsq*rsq*rsq / lj2[itype][jtype];
+ philj = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
+ offset[itype][jtype];
+ } else philj = 0.0;
+
+ return factor_lj*philj;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLJClass2Soft::extract(const char *str, int &dim)
+{
+ dim = 2;
+ if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
+ if (strcmp(str,"sigma") == 0) return (void *) sigma;
+ if (strcmp(str,"lambda") == 0) return (void *) lambda;
+ return NULL;
+}
diff --git a/src/USER-FEP/pair_lj_class2_soft.h b/src/USER-FEP/pair_lj_class2_soft.h
new file mode 100644
index 0000000000000000000000000000000000000000..ef031a1911a2d7ebbfd33a831d4e8a57671f6fec
--- /dev/null
+++ b/src/USER-FEP/pair_lj_class2_soft.h
@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/class2/soft,PairLJClass2Soft)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CLASS2_SOFT_H
+#define LMP_PAIR_LJ_CLASS2_SOFT_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairLJClass2Soft : public Pair {
+ public:
+ PairLJClass2Soft(class LAMMPS *);
+ virtual ~PairLJClass2Soft();
+ virtual void compute(int, int);
+ virtual void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ virtual void write_restart_settings(FILE *);
+ virtual void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+ virtual double single(int, int, int, int, double, double, double, double &);
+ void *extract(const char *, int &);
+
+ protected:
+ double cut_global;
+ double **cut;
+ double **epsilon, **sigma, **lambda;
+ double nlambda, alphalj;
+ double **lj1,**lj2,**lj3,**offset;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+E: Illegal ... command
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+Self-explanatory. Check the input script or data file.
+
+E: Pair lj/cut/soft different lambda values in mix
+The value of lambda has to be the same for I J pairs.
+
+*/
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index 61d32892fcf7b5282a3c4bdb475dde78e14e3afc..38de1c7c50a9b44532176393b665ab6f6b881e16 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -427,7 +427,7 @@ double PairBuckMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
void *PairBuckMDF::extract(const char *str, int &dim)
{
dim = 2;
- if (strcmp(str,"aparm") == 0) return (void *) a;
- if (strcmp(str,"cparm") == 0) return (void *) c;
+ if (strcmp(str,"a") == 0) return (void *) a;
+ if (strcmp(str,"c") == 0) return (void *) c;
return NULL;
}
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index 45d0da4d83e03d2bea53c7ab2ca62f57ede9c802..4bc2da23f8060285b3e7f5be0cfae03e766c9ed7 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -389,7 +389,7 @@ double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
void *PairLJ_AB_MDF::extract(const char *str, int &dim)
{
dim = 2;
- if (strcmp(str,"aparm") == 0) return (void *) aparm;
- if (strcmp(str,"bparm") == 0) return (void *) bparm;
+ if (strcmp(str,"a") == 0) return (void *) aparm;
+ if (strcmp(str,"b") == 0) return (void *) bparm;
return NULL;
}