diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 2784858f020dc3db8fccea6c4f04d4dc020b6080..a46b29c73b9583cfc9a204adbbc44d217c1d987b 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -188,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html
-for additional tools that can use CHARMM or AMBER to assign force
-field coefficients and convert their output into LAMMPS input.
+"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
+additional tools that can use CHARMM or AMBER to assign force field
+coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
@@ -762,12 +762,12 @@ simulations can be visualized (and analyzed) in a variety of ways.
LAMMPS snapshots are created by the "dump"_dump.html command which can
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
-by several popular visualization tools. The "dump image"_dump_image.html
-and "dump movie"_dump_image.html styles can output internally rendered
-images and convert a sequence of them to a movie during the MD run.
-Several programs included with LAMMPS as auxiliary tools can convert
-between LAMMPS format files and other formats.
-See the "Section 9"_Section_tools.html doc page for details.
+by several popular visualization tools. The "dump
+image"_dump_image.html and "dump movie"_dump_image.html styles can
+output internally rendered images and convert a sequence of them to a
+movie during the MD run. Several programs included with LAMMPS as
+auxiliary tools can convert between LAMMPS format files and other
+formats. See the "Tools"_Tools.html doc page for details.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index 67293b2ee3363b422cdb3f2f58bd0da9a037d9ab..fd1d702d0b8852758e6f88a2015ec10633117b56 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -234,8 +234,8 @@ Multi-replica models :h4
Pre- and post-processing :h4
-Various pre- and post-processing serial tools are packaged
-with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
+Various pre- and post-processing serial tools are packaged with
+LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
@@ -296,9 +296,9 @@ visualize your MD simulation
plot your output data :ul
A few tools for pre- and post-processing tasks are provided as part of
-the LAMMPS package; they are described in "this
-section"_Section_tools.html. However, many people use other codes or
-write their own tools for these tasks.
+the LAMMPS package; they are described on the "Tools"_Tools.html doc
+page. However, many people use other codes or write their own tools
+for these tasks.
As noted above, our group has also written and released a separate
toolkit called "Pizza.py"_pizza which addresses some of the listed
@@ -327,8 +327,8 @@ topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
such problems and dump its information to a file. You can then
-reformat the file as LAMMPS input. Some of the tools in "this
-section"_Section_tools.html can assist in this process.
+reformat the file as LAMMPS input. Some of the tools described on the
+"Tools"_Tools.html doc page can assist in this process.
Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
@@ -442,8 +442,8 @@ directory. :l
The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
-details are given in "Section 9"_Section_tools.html. If you write
-a new tool that users will find useful, it can be added to the LAMMPS
+details are given on the "Tools"_Tools.html doc page. If you write a
+new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
LAMMPS is designed to be easy to extend with new code for features
diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index f1d55758c8b0b498710d2f9c2e83eb9834817481..6948ac062a713729e4c5fc5b89148679d3ae43e3 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -1,5 +1,5 @@
- "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+ "Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_python.html :c
:link(lws,http://lammps.sandia.gov)
diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt
index 9998cb0d9a1371fdcca7c6e927c49925bb6f81d2..56b1d7dd046eda9f1f2d0c56b2405d8e577220e2 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Section_perf.txt
@@ -1,4 +1,6 @@
-"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c
+"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Tools.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 438ff1d4e074779f22217e851799a81f1f7ff857..d130846519207d7250576caa570dbcd96cbb3055 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -1,4 +1,4 @@
- "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@@ -184,10 +184,10 @@ file and in what format. Settings made via the
individual values and the file itself.
The {atom}, {local}, and {custom} styles create files in a simple text
-format that is self-explanatory when viewing a dump file. Many of the
-LAMMPS "post-processing tools"_Section_tools.html, including
-"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this
-format, as does the "rerun"_rerun.html command.
+format that is self-explanatory when viewing a dump file. Some of the
+LAMMPS post-processing tools described on the "Tools"_Tools.html doc
+page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html,
+work with this format, as does the "rerun"_rerun.html command.
For post-processing purposes the {atom}, {local}, and {custom} text
files are self-describing in the following sense.
@@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or
will be about the same size as a text version, but will typically
write out much faster. Of course, when post-processing, you will need
to convert it back to text format (see the "binary2txt
-tool"_Section_tools.html#binary) or write your own code to read the
-binary file. The format of the binary file can be understood by
-looking at the tools/binary2txt.cpp file. This option is only
-available for the {atom} and {custom} styles.
+tool"_Tools.html#binary) or write your own code to read the binary
+file. The format of the binary file can be understood by looking at
+the tools/binary2txt.cpp file. This option is only available for the
+{atom} and {custom} styles.
If the filename ends with ".gz", the dump file (or files, if "*" or "%"
is also used) is written in gzipped format. A gzipped dump file will