more mis-matches between doc pages and src files

doc/src/Commands_bond.txt

@@ -70,7 +70,7 @@ OPT.
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
 "quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html,
+"sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
 
 :line

doc/src/Commands_fix.txt

@@ -216,7 +216,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
+"wall/gran (o)"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Commands_pair.txt

@@ -26,7 +26,7 @@ OPT.
 
 "none"_pair_none.html,
 "zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
+"hybrid (k)"_pair_hybrid.html,
 "hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
 
 "adp (o)"_pair_adp.html,

doc/src/angle_sdk.txt

@@ -7,6 +7,7 @@
 :line
 
 angle_style sdk command :h3
+angle_style sdk/omp command :h3
 
 [Syntax:]
 
@@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
 The also required {lj/sdk} parameters will be extracted automatically
 from the pair_style.
 
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the

doc/src/fix_property_atom.txt

@@ -7,6 +7,7 @@
 :line
 
 fix property/atom command :h3
+fix property/atom/kk command :h3
 
 [Syntax:]
 
@@ -201,6 +202,7 @@ added classes.
 :line
 
 :link(isotopes)
+
 Example for using per-atom masses with TIP4P water to
 study isotope effects. When setting up simulations with the "TIP4P
 pair styles"_Howto_tip4p.html for water, you have to provide exactly
@@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
 
 :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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the per-atom values it stores to "binary restart

doc/src/fix_surface_global.txt

-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix wall/surface/global command :h3
-
-[Description:]
-
-This feature is not yet implemented.
-
-[Related commands:]
-
-"dump image"_dump_image.html
-
-

doc/src/fix_wall_gran.txt

@@ -7,6 +7,7 @@
 :line
 
 fix wall/gran command :h3
+fix wall/gran/omp command :h3
 
 [Syntax:]
 
@@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
 {vshear} < 0.  In this case, {vshear} is the tangential velocity of
 the wall at whatever {radius} has been defined.
 
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the shear friction state of atoms interacting with the

doc/src/pair_born.txt

@@ -11,19 +11,14 @@ pair_style born command :h3
 pair_style born/omp command :h3
 pair_style born/gpu command :h3
 pair_style born/coul/long command :h3
-pair_style born/coul/long/cs command :h3
-pair_style born/coul/long/cs/gpu command :h3
 pair_style born/coul/long/gpu command :h3
 pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
-pair_style born/coul/wolf/cs command :h3
-pair_style born/coul/wolf/cs/gpu command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3
-pair_style born/coul/dsf/cs command :h3
 
 [Syntax:]
 
@@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
+pair_style born/coul/long 10.0 8.
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
-pair_style born/coul/wolf/cs 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
 The {born/coul/dsf} style computes the Coulomb contribution with the
 damped shifted force model as in the "coul/dsf"_pair_coul.html style.
 
-Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-The same correction is introduced for the {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}.  And likewise for
-{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
-
 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.
 
@@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
 interaction.
 
 The {born/coul/long} pair style supports the
-"pair_modify"_pair_modify.html table option ti tabulate the
+"pair_modify"_pair_modify.html table option to tabulate the
 short-range portion of the long-range Coulombic interaction.
 
 These styles support the pair_modify tail option for adding long-range

doc/src/pair_buck.txt

@@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
 pair_style buck/coul/cut/kk command :h3
 pair_style buck/coul/cut/omp command :h3
 pair_style buck/coul/long command :h3
-pair_style buck/coul/long/cs command :h3
 pair_style buck/coul/long/gpu command :h3
 pair_style buck/coul/long/intel command :h3
 pair_style buck/coul/long/kk command :h3
@@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
 
 pair_style style args :pre
 
-style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
+style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
 args = list of arguments for a particular style :ul
   {buck} args = cutoff
     cutoff = global cutoff for Buckingham interactions (distance units)
   {buck/coul/cut} args = cutoff (cutoff2)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
+  {buck/coul/long} args = cutoff (cutoff2)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {buck/coul/msm} args = cutoff (cutoff2)
@@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
 
 pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
 pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
 
@@ -92,10 +89,6 @@ A,C and Coulombic terms.  If two cutoffs are specified, the first is
 used as the cutoff for the A,C terms, and the second is the cutoff for
 the Coulombic term.
 
-Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-
 Note that these potentials are related to the "Born-Mayer-Huggins
 potential"_pair_born.html.
 
@@ -184,8 +177,7 @@ respa"_run_style.html command.  They do not support the {inner},
 
 [Restrictions:]
 
-The {buck/coul/long} style is part of the KSPACE package.  The
-{buck/coul/long/cs} style is part of the CORESHELL package.  They are
+The {buck/coul/long} style is 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.
 

doc/src/pair_charmm.txt

@@ -8,12 +8,15 @@
 
 pair_style lj/charmm/coul/charmm command :h3
 pair_style lj/charmm/coul/charmm/intel command :h3
+pair_style lj/charmm/coul/charmm/kk command :h3
 pair_style lj/charmm/coul/charmm/omp command :h3
 pair_style lj/charmm/coul/charmm/implicit command :h3
+pair_style lj/charmm/coul/charmm/implicit/kk command :h3
 pair_style lj/charmm/coul/charmm/implicit/omp command :h3
 pair_style lj/charmm/coul/long command :h3
 pair_style lj/charmm/coul/long/gpu command :h3
 pair_style lj/charmm/coul/long/intel command :h3
+pair_style lj/charmm/coul/long/kk command :h3
 pair_style lj/charmm/coul/long/opt command :h3
 pair_style lj/charmm/coul/long/omp command :h3
 pair_style lj/charmm/coul/msm command :h3

doc/src/pair_cs.txt

@@ -7,9 +7,11 @@
 :line
 
 pair_style born/coul/long/cs command :h3
+pair_style born/coul/long/cs/gpu command :h3
 pair_style buck/coul/long/cs command :h3
 pair_style born/coul/dsf/cs command :h3
 pair_style born/coul/wolf/cs command :h3
+pair_style born/coul/wolf/cs/gpu command :h3
 
 [Syntax:]
 
@@ -97,6 +99,38 @@ a long-range solver, thus the only correction is the addition of a
 minimal distance to avoid the possible r = 0.0 case for a
 core/shell pair.
 
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+See the corresponding doc pages for pair styles without the "cs"
+suffix to see how mixing, shifting, tabulation, tail correction,
+restarting, and rRESPA are handled by theses pair styles.
+
+:line
+
 [Restrictions:]
 
 These pair styles are part of the CORESHELL package.  They are only

doc/src/pair_dipole.txt

@@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
 pair_style lj/sf/dipole/sf/gpu command :h3
 pair_style lj/sf/dipole/sf/omp command :h3
 pair_style lj/cut/dipole/long command :h3
+pair_style lj/cut/dipole/long/gpu command :h3
 pair_style lj/long/dipole/long command :h3
 
 [Syntax:]

doc/src/pair_edip.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style edip command :h3
+pair_style edip/omp command :h3
 pair_style edip/multi command :h3
 
 [Syntax:]

doc/src/pair_gran.txt

@@ -7,7 +7,7 @@
 :line
 
 pair_style gran/hooke command :h3
-pair_style gran/omp command :h3
+pair_style gran/hooke/omp command :h3
 pair_style gran/hooke/history command :h3
 pair_style gran/hooke/history/omp command :h3
 pair_style gran/hertz/history command :h3

doc/src/pair_gromacs.txt

@@ -8,8 +8,10 @@
 
 pair_style lj/gromacs command :h3
 pair_style lj/gromacs/gpu command :h3
+pair_style lj/gromacs/kk command :h3
 pair_style lj/gromacs/omp command :h3
 pair_style lj/gromacs/coul/gromacs command :h3
+pair_style lj/gromacs/coul/gromacs/kk command :h3
 pair_style lj/gromacs/coul/gromacs/omp command :h3
 
 [Syntax:]

doc/src/pair_hybrid.txt

@@ -7,9 +7,8 @@
 :line
 
 pair_style hybrid command :h3
-pair_style hybrid/omp command :h3
+pair_style hybrid/kk command :h3
 pair_style hybrid/overlay command :h3
-pair_style hybrid/overlay/omp command :h3
 pair_style hybrid/overlay/kk command :h3
 
 [Syntax:]

doc/src/pair_lj.txt

@@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3
 pair_style lj/cut/omp command :h3
 pair_style lj/cut/coul/cut command :h3
 pair_style lj/cut/coul/cut/gpu command :h3
+pair_style lj/cut/coul/cut/kk command :h3
 pair_style lj/cut/coul/cut/omp command :h3
 pair_style lj/cut/coul/debye command :h3
 pair_style lj/cut/coul/debye/gpu command :h3
@@ -26,6 +27,7 @@ pair_style lj/cut/coul/dsf/omp command :h3
 pair_style lj/cut/coul/long command :h3
 pair_style lj/cut/coul/long/cs command :h3
 pair_style lj/cut/coul/long/gpu command :h3
+pair_style lj/cut/coul/long/kk command :h3
 pair_style lj/cut/coul/long/intel command :h3
 pair_style lj/cut/coul/long/opt command :h3
 pair_style lj/cut/coul/long/omp command :h3

doc/src/pair_lj_expand.txt

@@ -8,6 +8,7 @@
 
 pair_style lj/expand command :h3
 pair_style lj/expand/gpu command :h3
+pair_style lj/expand/kk command :h3
 pair_style lj/expand/omp command :h3
 pair_style lj/expand/coul/long command :h3
 pair_style lj/expand/coul/long/gpu command :h3

doc/src/pair_lj_long.txt

@@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3
 pair_style lj/long/coul/long/omp command :h3
 pair_style lj/long/coul/long/opt command :h3
 pair_style lj/long/tip4p/long command :h3
+pair_style lj/long/tip4p/long/omp command :h3
 
 [Syntax:]
 

doc/src/pair_meam_sw_spline.txt

@@ -7,7 +7,6 @@
 :line
 
 pair_style meam/sw/spline command :h3
-pair_style meam/sw/spline/omp command :h3
 
 [Syntax:]