From dd64c063cf804205bfb5ea90ed1be325243814d9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 22:28:20 -0400
Subject: [PATCH] various fixes for the manual to address breakage from merging
MESSAGE and USER-SCAFACOS packages
---
doc/src/Build_package.txt | 4 ++--
doc/src/Howto_client_server.txt | 2 +-
doc/src/Packages_details.txt | 4 ++--
doc/src/Run_options.txt | 2 +-
doc/src/commands_list.txt | 2 ++
doc/src/fix_client_md.txt | 2 +-
doc/src/fixes.txt | 1 +
doc/src/kspace_modify.txt | 2 +-
doc/src/kspace_style.txt | 4 ++--
doc/src/lammps.book | 1 +
10 files changed, 14 insertions(+), 10 deletions(-)
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 285220e6c6..f1aa4bb671 100644
--- a/doc/src/Build_package.txt
+++ b/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)
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index 714c23f066..061c4efb68 100644
--- a/doc/src/Howto_client_server.txt
+++ b/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
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 443d78922c..b0b72f1f13 100644
--- a/doc/src/Packages_details.txt
+++ b/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:]
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index 27f436ed55..1fc00bc2e3 100644
--- a/doc/src/Run_options.txt
+++ b/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
diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt
index 8fae57a718..db3ef36ddf 100644
--- a/doc/src/commands_list.txt
+++ b/doc/src/commands_list.txt
@@ -89,6 +89,8 @@ Commands :h1
run
run_style
server
+ server_mc
+ server_md
set
shell
special_bonds
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
index 5b62d5617d..77f6b82c5e 100644
--- a/doc/src/fix_client_md.txt
+++ b/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
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 7a45ed8086..f2f257b134 100644
--- a/doc/src/fixes.txt
+++ b/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
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 7e40323664..41973601d7 100644
--- a/doc/src/kspace_modify.txt
+++ b/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
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index ddf4e15703..6d8a289470 100644
--- a/doc/src/kspace_style.txt
+++ b/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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 72a07945e7..828863ae67 100644
--- a/doc/src/lammps.book
+++ b/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
--
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