diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index fc7329aad5846382382bf1e112bece67570c45d6..438ea561a10f9fa87f0e119aedd26bdbd13e89dd 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -8,27 +8,44 @@ Section"_Examples.html :c
:line
-How to discussions :h2
+Howto discussions :h2
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
"glossary"_http://lammps.sandia.gov website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.
-
-The example input scripts included in the examples dir of the LAMMPS
+terminology with links to corresponding LAMMPS manual pages. The
+example input scripts included in the examples dir of the LAMMPS
distribution and highlighted on the "Examples"_Examples.html doc page
also show how to setup and run various kinds of simulations.
+Tutorials howto :h3
+
<!-- RST
.. toctree::
+ :name: tutorials
:maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+General howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: general
:maxdepth: 1
Howto_restart
@@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
Howto_library
Howto_couple
-.. toctree::
- :maxdepth: 1
+END_RST -->
- Howto_output
- Howto_chunk
+<!-- HTML_ONLY -->
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"Run multiple simulations from one input script"_Howto_multiple.html
+"Multi-replica simulations"_Howto_replica.html
+"Library interface to LAMMPS"_Howto_library.html
+"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Settings howto :h3
+
+<!-- RST
.. toctree::
+ :name: settings
:maxdepth: 1
Howto_2d
Howto_triclinic
+ Howto_thermostat
+ Howto_barostat
Howto_walls
Howto_nemd
- Howto_granular
- Howto_spherical
Howto_dispersion
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+
+Analysis howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: analysis
:maxdepth: 1
+ Howto_output
+ Howto_chunk
Howto_temperature
- Howto_thermostat
- Howto_barostat
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+"Calculate temperature"_Howto_temperature.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Force fields howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: force
:maxdepth: 1
Howto_bioFF
@@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
Howto_tip4p
Howto_spc
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Packages howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: packages
:maxdepth: 1
+ Howto_spherical
+ Howto_granular
Howto_body
Howto_polarizable
Howto_coreshell
@@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
END_RST -->
-<!-- HTML_ONLY -->
-
-"Using GitHub with LAMMPS"_Howto_github.html
-"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
-
-"Restart a simulation"_Howto_restart.html
-"Visualize LAMMPS snapshots"_Howto_viz.html
-"Run multiple simulations from one input script"_Howto_multiple.html
-"Multi-replica simulations"_Howto_replica.html
-"Library interface to LAMMPS"_Howto_library.html
-"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
-"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
-"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+<!-- HTML_ONLY -->
-"2d simulations"_Howto_2d.html
-"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
-"Walls"_Howto_walls.html
-"NEMD simulations"_Howto_nemd.html
-"Granular models"_Howto_granular.html
"Finite-size spherical and aspherical particles"_Howto_spherical.html
-"Long-range dispersion settings"_Howto_dispersion.html :all(b)
-
-"Calculate temperature"_Howto_temperature.html
-"Thermostats"_Howto_thermostat.html
-"Barostats"_Howto_barostat.html
-"Calculate elastic constants"_Howto_elastic.html
-"Calculate thermal conductivity"_Howto_kappa.html
-"Calculate viscosity"_Howto_viscosity.html
-"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
-
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
-"TIP3P water model"_Howto_tip3p.html
-"TIP4P water model"_Howto_tip4p.html
-"SPC water model"_Howto_spc.html :all(b)
-
+"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 30e186410657b0770183fd160d2769b44be58d5c..c5e5aff61b1ce5149ee2a2acef906bf31eb6bdd5 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -66,7 +66,7 @@ every LAMMPS command.
.. toctree::
:maxdepth: 2
- :numbered:
+ :numbered: 3
:caption: User Documentation
:name: userdoc
:includehidden:
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 8b4e779cbe869ca7eda71988c841b41ea116f0a3..a9ad5032cec07de0048ba0288733267caaf18f8e 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
reside in that directory. Most of them are larger packages in their
own sub-directories with their own Makefiles and/or README files.
-"amber2lmp"_#amber
-"binary2txt"_#binary
-"ch2lmp"_#charmm
-"chain"_#chain
-"colvars"_#colvars
-"createatoms"_#createatoms
-"doxygen"_#doxygen
-"drude"_#drude
-"eam database"_#eamdb
-"eam generate"_#eamgn
-"eff"_#eff
-"emacs"_#emacs
-"fep"_#fep
-"i-pi"_#ipi
-"ipp"_#ipp
-"kate"_#kate
-"lmp2arc"_#arc
-"lmp2cfg"_#cfg
-"matlab"_#matlab
-"micelle2d"_#micelle
-"moltemplate"_#moltemplate
-"msi2lmp"_#msi
-"phonon"_#phonon
-"polybond"_#polybond
-"pymol_asphere"_#pymol
-"python"_#pythontools
-"reax"_#reax_tool
-"smd"_#smd
-"vim"_#vim
-"xmgrace"_#xmgrace :ul
-
-:line
-
-amber2lmp tool :h3,link(amber)
+:line
+
+Pre-processing tools :h3
+
+"amber2lmp"_#amber,
+"ch2lmp"_#charmm,
+"chain"_#chain,
+"createatoms"_#createatoms,
+"drude"_#drude,
+"eam database"_#eamdb,
+"eam generate"_#eamgn,
+"eff"_#eff,
+"ipp"_#ipp,
+"micelle2d"_#micelle,
+"moltemplate"_#moltemplate,
+"msi2lmp"_#msi,
+"polybond"_#polybond :tb(c=6,ea=c,a=l)
+
+Post-processing tools :h3
+
+"amber2lmp"_#amber,
+"binary2txt"_#binary,
+"ch2lmp"_#charmm,
+"colvars"_#colvars,
+"eff"_#eff,
+"fep"_#fep,
+"lmp2arc"_#arc,
+"lmp2cfg"_#cfg,
+"matlab"_#matlab,
+"phonon"_#phonon,
+"pymol_asphere"_#pymol,
+"python"_#pythontools,
+"reax"_#reax_tool,
+"smd"_#smd,
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+
+Miscellaneous tools :h3
+
+"doxygen"_#doxygen,
+"emacs"_#emacs,
+"i-pi"_#ipi,
+"kate"_#kate,
+"vim"_#vim :tb(c=5,ea=c,a=l)
+
+:line
+
+Tool descriptions :h3
+
+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
@@ -91,7 +106,7 @@ 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
@@ -104,7 +119,7 @@ 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.
@@ -129,7 +144,7 @@ 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
@@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.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.
@@ -168,7 +183,7 @@ 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
@@ -181,7 +196,7 @@ 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
@@ -193,7 +208,7 @@ 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
@@ -206,7 +221,7 @@ 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
@@ -222,7 +237,7 @@ 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
@@ -235,7 +250,7 @@ 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
@@ -246,7 +261,7 @@ 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 an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -257,7 +272,7 @@ 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
@@ -270,7 +285,7 @@ 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
@@ -287,7 +302,7 @@ 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
@@ -301,7 +316,7 @@ 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
@@ -312,7 +327,7 @@ 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
@@ -328,7 +343,7 @@ 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
@@ -339,7 +354,7 @@ 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
@@ -357,7 +372,7 @@ 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
@@ -374,7 +389,7 @@ 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
@@ -388,7 +403,7 @@ 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'
@@ -405,7 +420,7 @@ 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
@@ -420,7 +435,7 @@ 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
@@ -434,7 +449,7 @@ 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
@@ -452,7 +467,7 @@ 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:
@@ -468,7 +483,7 @@ 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
@@ -479,7 +494,7 @@ 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
@@ -495,7 +510,7 @@ 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
@@ -506,7 +521,7 @@ 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