link changes for new Tools.html

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

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

doc/src/Section_modify.txt

- "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)

doc/src/Section_perf.txt

-"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)

doc/src/dump.txt

- "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