various fixes for the manual to address breakage from merging MESSAGE and USER-SCAFACOS packages

doc/src/Build_package.txt

@@ -42,7 +42,7 @@ packages:
 "KOKKOS"_Build_extras.html#kokkos,
 "LATTE"_Build_extras.html#latte,
 "MEAM"_Build_extras.html#meam,
-"MESSAGE"_#Build_extras.html#message,
+"MESSAGE"_Build_extras.html#message,
 "MSCG"_Build_extras.html#mscg,
 "OPT"_Build_extras.html#opt,
 "POEMS"_Build_extras.html#poems,
@@ -59,7 +59,7 @@ packages:
 "USER-OMP"_Build_extras.html#user-omp,
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,
-"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
+"USER-SCAFACOS"_Build_extras.html#user-scafacos,
 "USER-SMD"_Build_extras.html#user-smd,
 "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
 

doc/src/Howto_client_server.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Using LAMMPS in client/server mode
+Using LAMMPS in client/server mode :h3
 
 Client/server coupling of two codes is where one code is the "client"
 and sends request messages to a "server" code.  The server responds to

doc/src/Packages_details.txt

@@ -92,7 +92,7 @@ as contained in the file name.
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
 "USER-REAXC"_#PKG-USER-REAXC,
-"USER-SCAFACOS"_#USER-SCAFACOS,
+"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -1860,7 +1860,7 @@ examples/reax :ul
 
 :line
 
-USER-SCAFACOS package :link(USER-SCAFACOS),h4
+USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
 
 [Contents:]
 

doc/src/Run_options.txt

@@ -176,7 +176,7 @@ Option -plog will override the name of the partition log files file.N.
 
 :line
 
-[-mpicolor] color :link(mpi)
+[-mpicolor] color :link(mpicolor)
 
 If used, this must be the first command-line argument after the LAMMPS
 executable name.  It is only used when LAMMPS is launched by an mpirun

doc/src/commands_list.txt

@@ -89,6 +89,8 @@ Commands :h1
    run
    run_style
    server
+   server_mc
+   server_md
    set
    shell
    special_bonds

doc/src/fix_client_md.txt

@@ -50,7 +50,7 @@ md"_server_md.html doc page.
 
 Note that when using LAMMPS as an MD client, your LAMMPS input script
 should not normally contain force field commands, like a
-"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
+"pair_style"_pair_style.html, "bond_style"_bond_style.html, or
 "kspace_style"_kspace_style.html commmand.  However it is possible for
 a server code to only compute a portion of the full force-field, while
 LAMMPS computes the remaining part.  Your LAMMPS script can also

doc/src/fixes.txt

@@ -26,6 +26,7 @@ Fixes :h1
    fix_bond_swap
    fix_bond_react
    fix_box_relax
+   fix_client_md
    fix_cmap
    fix_colvars
    fix_controller

doc/src/kspace_modify.txt

@@ -133,7 +133,7 @@ the code will stop with an error message. When this option is set to
 For a typical application, using the automatic parameter generation
 will provide simulations that are either inaccurate or slow. Using this
 option is thus not recommended. For guidelines on how to obtain good
-parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+parameters, see the "How-To"_Howto_dispersion.html discussion.
 
 :line
 

doc/src/kspace_style.txt

@@ -383,8 +383,8 @@ dimensions.  The only exception is if the slab option is set with
 must be periodic and the z dimension must be non-periodic.
 
 The scafacos KSpace style will only be enabled if LAMMPS is built with
-the USER-SCAFACOS package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+the USER-SCAFACOS package.  See the "Build package"_Build_package.html
+doc page for more info.
 
 The use of ScaFaCos in LAMMPS does not yet support molecular charged
 systems where the short-range Coulombic interactions between atoms in

doc/src/lammps.book

@@ -67,6 +67,7 @@ Howto_multiple.html
 Howto_replica.html
 Howto_library.html
 Howto_couple.html
+Howto_client_server.html
 Howto_output.html
 Howto_chunk.html
 Howto_2d.html