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Updated broken links to pair_fep_soft

This commit is contained in:
Agilio Padua 2019-01-24 17:10:39 +01:00
parent 0bfb34389b
commit 06c8a67247
6 changed files with 35 additions and 29 deletions
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21
doc/src/Commands_pair.txt
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@ -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,

2
doc/src/Packages_details.txt
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@ -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

10
doc/src/compute_fep.txt
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@ -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:

10
doc/src/fix_adapt_fep.txt
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@ -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:

19
doc/src/pair_style.txt
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@ -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

2
doc/src/pairs.txt
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@ -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