From 06c8a672477b2275cb4bd06723a23e7f9c296bb9 Mon Sep 17 00:00:00 2001
From: Agilio Padua <agilio.padua@gmail.com>
Date: Thu, 24 Jan 2019 17:10:39 +0100
Subject: [PATCH] Updated broken links to pair_fep_soft
---
doc/src/Commands_pair.txt | 21 ++++++++++++---------
doc/src/Packages_details.txt | 2 +-
doc/src/compute_fep.txt | 10 +++++-----
doc/src/fix_adapt_fep.txt | 10 +++++-----
doc/src/pair_style.txt | 19 +++++++++++--------
doc/src/pairs.txt | 2 +-
6 files changed, 35 insertions(+), 29 deletions(-)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 46f4950ad7..8e09284907 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,
@@ -169,7 +172,7 @@ 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,
@@ -229,7 +232,7 @@ 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/Packages_details.txt b/doc/src/Packages_details.txt
index 4768c50ca4..0a7facc22a 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1305,7 +1305,7 @@ 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 772b464d18..9241e5b5a8 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -137,20 +137,20 @@ the meaning of these parameters:
"buck"_pair_buck.html: a,c: type pairs:
"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:
"coul/cut"_pair_coul.html: scale: type pairs:
-"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
-"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
"eam"_pair_eam.html: scale: type pairs:
"gauss"_pair_gauss.html: a: type pairs:
"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:
"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: 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_lj_soft.html: epsilon,sigma,lambda: 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_lj_soft.html: epsilon,sigma,lambda: 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:
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 21cf089a9f..8f94a1a38c 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/doc/src/fix_adapt_fep.txt
@@ -116,20 +116,20 @@ styles and their energy formulas for the meaning of these parameters:
"buck"_pair_buck.html: a,c: type pairs:
"buck/mdf"_pair_mdf.html: aparm,cparm: type pairs:
"coul/cut"_pair_coul.html: scale: type pairs:
-"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
-"coul/long/soft"_pair_lj_soft.html: scale, lambda: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
"eam"_pair_eam.html: scale: type pairs:
"gauss"_pair_gauss.html: a: type pairs:
"lennard/mdf"_pair_mdf.html: aparm,bparm: type pairs:
"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: 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_lj_soft.html: epsilon,sigma,lambda: 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_lj_soft.html: epsilon,sigma,lambda: 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:
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 714ec55d2e..17dd4e375a 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
@@ -294,7 +297,7 @@ 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 2810252402..4ab0c33c16 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_lubricate
pair_lubricateU
pair_mdf
--
GitLab