From 703a795af851366233d700e05463ff9e59761993 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 20 Aug 2018 01:50:16 -0400
Subject: [PATCH] Modify Howto and Tools
- add missing TOCs in Howto section
- limit section numbering to maximum of 3 levels
- add "Tool descriptions" header
---
doc/src/Howto.txt | 156 +++++++++++++++++++++++++++++++--------------
doc/src/Manual.txt | 2 +-
doc/src/Tools.txt | 2 +
3 files changed, 110 insertions(+), 50 deletions(-)
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index bcfae46579..9d385f23a4 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -21,67 +21,44 @@ also show how to setup and run various kinds of simulations.
Tutorials howto :h3
-"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)
+<!-- RST
-General howto :h3
+.. toctree::
+ :name: tutorials
+ :maxdepth: 1
-"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)
+ Howto_github
+ Howto_pylammps
+ Howto_bash
-Settings howto :h3
+END_RST -->
-"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)
+<!-- HTML_ONLY -->
-Analysis howto :h3
+"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)
-"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
-"Use chunks to calculate system properties"_Howto_chunk.html
-"Calculate temperature"_Howto_temperature.html
-"Calculate elastic constants"_Howto_elastic.html
-"Calculate thermal conductivity"_Howto_kappa.html
-"Calculate viscosity"_Howto_viscosity.html
-"Calculate diffusion coefficients"_Howto_diffusion.html :all(b)
+<!-- END_HTML_ONLY -->
-Force fields howto :h3
+General howto :h3
-"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)
+<!-- RST
-Packages howto :h3
+.. toctree::
+ :name: general
+ :maxdepth: 1
-"Finite-size spherical and aspherical particles"_Howto_spherical.html
-"Granular models"_Howto_granular.html
-"Body style particles"_Howto_body.html
-"Polarizable models"_Howto_polarizable.html
-"Adiabatic core/shell model"_Howto_coreshell.html
-"Drude induced dipoles"_Howto_drude.html
-"Drude induced dipoles (extended)"_Howto_drude2.html
-"Manifolds (surfaces)"_Howto_manifold.html
-"Magnetic spins"_Howto_spins.html :all(b)
-
-<!-- HTML_ONLY -->
+ Howto_restart
+ Howto_viz
+ Howto_multiple
+ Howto_replica
+ Howto_library
+ Howto_couple
-External howto :h3
+END_RST -->
-"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)
-
-General howto :h3
+<!-- HTML_ONLY -->
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
@@ -90,8 +67,28 @@ General howto :h3
"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_dispersion
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Thermostats"_Howto_thermostat.html
@@ -100,8 +97,29 @@ Settings howto :h3
"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_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
@@ -110,15 +128,55 @@ Analysis howto :h3
"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
+ Howto_tip3p
+ 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
+ Howto_drude
+ Howto_drude2
+ Howto_manifold
+ Howto_spins
+
+END_RST -->
+
+
+<!-- HTML_ONLY -->
+
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 30e1864106..c5e5aff61b 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 5e02e00715..a9ad5032ce 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -89,6 +89,8 @@ Miscellaneous tools :h3
:line
+Tool descriptions :h3
+
amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
--
GitLab