diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index e69797d9ec09551cc6592a7a791c8ea7459825fa..d6d46570c1c6ca906beff19eacc2f2a2a71bc0cb 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -116,7 +116,7 @@ it gives quick access to documentation for all LAMMPS commands.
Section_howto
Section_example
Section_perf
- Section_tools
+ Tools
Section_modify
Section_python
Section_errors
@@ -210,7 +210,7 @@ END_RST -->
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
-"Additional tools"_Section_tools.html :l
+"Auxiliary tools"_Tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
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/Section_tools.txt b/doc/src/Tools.txt
similarity index 89%
rename from doc/src/Section_tools.txt
rename to doc/src/Tools.txt
index 7cc07cbec55a5e7c4f3545c623875be8cc6919cc..0674e3cfcc01b2d2d48129be704efad8cdaa0616 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Tools.txt
@@ -2,39 +2,46 @@
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_modify.html :c
+<!-- future sequence of sections:
+"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Modify.html :c
+-->
+
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
-9. Additional tools :h2
+Auxiliary tools :h3
LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing
-steps are often necessary to setup and analyze a simulation. A
-list of such tools can be found on the LAMMPS home page
-at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html
+steps are often necessary to setup and analyze a simulation. A list
+of such tools can be found on the "LAMMPS webpage"_lws at these links:
-A few additional tools are provided with the LAMMPS distribution
-and are described in this section.
+"Pre/Post processing"_http://lammps.sandia.gov/prepost.html
+"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html
+"Pizza.py toolkit"_pizza :ul
-Our group has also written and released a separate toolkit called
-"Pizza.py"_pizza which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations. Pizza.py is
-written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza.
+The last link for "Pizza.py"_pizza is a Python-based tool developed at
+Sandia which provides tools for doing setup, analysis, plotting, and
+visualization for LAMMPS simulations.
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+:link(pizza,http://pizza.sandia.gov)
:link(python,http://www.python.org)
+Additional tools included in the LAMMPS distribution are described on
+this page.
+
Note that many users write their own setup or analysis tools or use
other existing codes and convert their output to a LAMMPS input format
or vice versa. The tools listed here are included in the LAMMPS
distribution as examples of auxiliary tools. Some of them are not
-actively supported by Sandia, as they were contributed by LAMMPS
-users. If you have problems using them, we can direct you to the
-authors.
+actively supported by the LAMMPS developers, as they were contributed
+by LAMMPS users. If you have problems using them, we can direct you
+to the authors.
The source code for each of these codes is in the tools sub-directory
of the LAMMPS distribution. There is a Makefile (which you may need
@@ -71,11 +78,12 @@ own sub-directories with their own Makefiles and/or README files.
"reax"_#reax_tool
"smd"_#smd
"vim"_#vim
-"xmgrace"_#xmgrace
+"xmgrace"_#xmgrace :ul
+:line
:line
-amber2lmp tool :h3,link(amber)
+amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@@ -90,7 +98,7 @@ necessary modifications yourself.
:line
-binary2txt tool :h3,link(binary)
+binary2txt tool :h4,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@@ -103,7 +111,7 @@ since binary files are not compatible across all platforms.
:line
-ch2lmp tool :h3,link(charmm)
+ch2lmp tool :h4,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@@ -128,7 +136,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
-chain tool :h3,link(chain)
+chain tool :h4,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@@ -145,7 +153,7 @@ system for the "chain benchmark"_Section_perf.html.
:line
-colvars tools :h3,link(colvars)
+colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@@ -167,7 +175,7 @@ gmail.com) at ICTP, Italy.
:line
-createatoms tool :h3,link(createatoms)
+createatoms tool :h4,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@@ -180,7 +188,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
-doxygen tool :h3,link(doxygen)
+doxygen tool :h4,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@@ -192,7 +200,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
-drude tool :h3,link(drude)
+drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@@ -205,7 +213,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
-eam database tool :h3,link(eamdb)
+eam database tool :h4,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@@ -221,7 +229,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
-eam generate tool :h3,link(eamgn)
+eam generate tool :h4,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@@ -234,7 +242,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
-eff tool :h3,link(eff)
+eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@@ -245,7 +253,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
-emacs tool :h3,link(emacs)
+emacs tool :h4,link(emacs)
The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
@@ -256,7 +264,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
-fep tool :h3,link(fep)
+fep tool :h4,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@@ -269,7 +277,7 @@ See README file in the tools/fep directory.
:line
-i-pi tool :h3,link(ipi)
+i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@@ -286,7 +294,7 @@ calculations with LAMMPS.
:line
-ipp tool :h3,link(ipp)
+ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@@ -300,7 +308,7 @@ tools/createatoms tool's input file.
:line
-kate tool :h3,link(kate)
+kate tool :h4,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -311,7 +319,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
-lmp2arc tool :h3,link(arc)
+lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@@ -327,7 +335,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
-lmp2cfg tool :h3,link(cfg)
+lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@@ -338,7 +346,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
-matlab tool :h3,link(matlab)
+matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@@ -356,7 +364,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
-micelle2d tool :h3,link(micelle)
+micelle2d tool :h4,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@@ -373,7 +381,7 @@ definition file. This tool was used to create the system for the
:line
-moltemplate tool :h3,link(moltemplate)
+moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@@ -387,7 +395,7 @@ supports it. It has its own WWW page at
:line
-msi2lmp tool :h3,link(msi)
+msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -404,7 +412,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
-phonon tool :h3,link(phonon)
+phonon tool :h4,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -419,7 +427,7 @@ University.
:line
-polybond tool :h3,link(polybond)
+polybond tool :h4,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@@ -433,7 +441,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
-pymol_asphere tool :h3,link(pymol)
+pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@@ -451,7 +459,7 @@ This tool was written by Mike Brown at Sandia.
:line
-python tool :h3,link(pythontools)
+python tool :h4,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@@ -467,7 +475,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
-reax tool :h3,link(reax_tool)
+reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -478,7 +486,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
-smd tool :h3,link(smd)
+smd tool :h4,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@@ -494,7 +502,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
-vim tool :h3,link(vim)
+vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@@ -505,7 +513,7 @@ ziegenhain.com)
:line
-xmgrace tool :h3,link(xmgrace)
+xmgrace tool :h4,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
@@ -517,4 +525,3 @@ simulation.
See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)
-
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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 06f4bf371853b4f4ccdba35c94bba57022fff9fa..fe8eb13161eff4f6d256fb85e17f821136d8111c 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -14,7 +14,7 @@ accelerate_opt.html
Section_howto.html
Section_example.html
Section_perf.html
-Section_tools.html
+Tools.html
Section_modify.html
Section_python.html
Section_errors.html