From ccc9fcda775d1751c9cd64a4d22f2733a9c27918 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 15 Aug 2018 16:22:26 -0600
Subject: [PATCH] tweaks to doc page formatting
---
doc/src/Build.txt | 13 +------------
doc/src/Build_basics.txt | 10 +++++-----
doc/src/Build_settings.txt | 14 +++++++-------
doc/src/Intro_authors.txt | 2 +-
doc/src/Modify.txt | 14 ++------------
doc/src/Python_head.txt | 14 ++------------
doc/src/Speed.txt | 19 +++++++------------
7 files changed, 25 insertions(+), 61 deletions(-)
diff --git a/doc/src/Build.txt b/doc/src/Build.txt
index 218664897f..1deaa1bd36 100644
--- a/doc/src/Build.txt
+++ b/doc/src/Build.txt
@@ -24,17 +24,9 @@ as described on the "Install"_Install.html doc page.
Build_cmake
Build_make
Build_link
-
-.. toctree::
- :maxdepth: 1
-
Build_basics
Build_settings
Build_package
-
-.. toctree::
- :maxdepth: 1
-
Build_extras
END_RST -->
@@ -43,10 +35,7 @@ END_RST -->
"Build LAMMPS with CMake"_Build_cmake.html
"Build LAMMPS with make"_Build_make.html
-"Link LAMMPS as a library to another code"_Build_link.html :all(b)
-
-Build options:
-
+"Link LAMMPS as a library to another code"_Build_link.html
"Basic build options: serial/parallel, compilers, executable/library"_Build_basics.html
"Optional build settings"_Build_settings.html :all(b)
"Include packages in build"_Build_package.html
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index 425266a35f..cee78aced3 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -20,7 +20,7 @@ CMake and make:
:line
-Serial vs parallel build :h3,link(serial)
+Serial vs parallel build :h4,link(serial)
LAMMPS can be built to run in parallel using the ubiquitous "MPI
(message-passing
@@ -118,7 +118,7 @@ please refer to its documentation.
:line
-Choice of compiler and compile/link options :h3,link(compile)
+Choice of compiler and compile/link options :h4,link(compile)
The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than
@@ -210,7 +210,7 @@ Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre
:line
-Build LAMMPS as an executable or a library :h3,link(exe)
+Build LAMMPS as an executable or a library :h4,link(exe)
LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
@@ -271,7 +271,7 @@ should be the file /usr/local/lib/libmpich.so.
:line
-Build the LAMMPS documentation :h3,link(doc)
+Build the LAMMPS documentation :h4,link(doc)
[CMake variable]:
@@ -294,7 +294,7 @@ lammps/doc dir to see other options.
:line
-Install LAMMPS after a build :h3,link(install)
+Install LAMMPS after a build :h4,link(install)
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt
index db281c0857..773217e3a0 100644
--- a/doc/src/Build_settings.txt
+++ b/doc/src/Build_settings.txt
@@ -23,7 +23,7 @@ explain how to do this for building both with CMake and make.
:line
-FFT library :h3,link(fft)
+FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the
"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
@@ -126,7 +126,7 @@ ARRAY mode.
:line
-Size of LAMMPS data types :h3,link(size)
+Size of LAMMPS data types :h4,link(size)
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
@@ -189,7 +189,7 @@ in whichever lib/gpu/Makefile is used must be the same as above.
:line
-Output of JPG, PNG, and movie files :h3,link(graphics)
+Output of JPG, PNG, and movie files :h4,link(graphics)
The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command
@@ -245,7 +245,7 @@ crash.
:line
-Read or write compressed files :h3,link(gzip)
+Read or write compressed files :h4,link(gzip)
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
@@ -276,7 +276,7 @@ what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
:line
-Memory allocation alignment :h3,link(align)
+Memory allocation alignment :h4,link(align)
This setting enables the use of the posix_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make
@@ -308,7 +308,7 @@ manages its dynamical memory.
:line
-Workaround for long long integers :h3,link(longlong)
+Workaround for long long integers :h4,link(longlong)
If your system or MPI version does not recognize "long long" data
types, the following setting will be needed. It converts "long long"
@@ -325,7 +325,7 @@ LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
:line
-Exception handling when using LAMMPS as a library :h3,link(exceptions)
+Exception handling when using LAMMPS as a library :h4,link(exceptions)
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller.
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
index 06c86f6e3c..3e9c163eb2 100644
--- a/doc/src/Intro_authors.txt
+++ b/doc/src/Intro_authors.txt
@@ -30,7 +30,7 @@ the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages
+Richard Berger (Temple U), GitHub site and Sphinx doc pages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt
index 666aaba8a7..38fbf17dd9 100644
--- a/doc/src/Modify.txt
+++ b/doc/src/Modify.txt
@@ -38,19 +38,11 @@ contribute"_Modify_contribute.html doc page.
Modify_compute
Modify_fix
Modify_command
-
-.. toctree::
- :maxdepth: 1
-
Modify_dump
Modify_kspace
Modify_min
Modify_region
Modify_body
-
-.. toctree::
- :maxdepth: 1
-
Modify_thermo
Modify_variable
@@ -66,14 +58,12 @@ END_RST -->
"Bond, angle, dihedral, improper styles"_Modify_bond.html
"Compute styles"_Modify_compute.html
"Fix styles"_Modify_fix.html
-"Input script command styles"_Modify_command.html :all(b)
-
+"Input script command styles"_Modify_command.html
"Dump styles"_Modify_dump.html
"Kspace styles"_Modify_kspace.html
"Minimization styles"_Modify_min.html
"Region styles"_Modify_region.html
-"Body styles"_Modify_body.html :all(b)
-
+"Body styles"_Modify_body.html
"Thermodynamic output options"_Modify_thermo.html
"Variable options"_Modify_variable.html :all(b)
diff --git a/doc/src/Python_head.txt b/doc/src/Python_head.txt
index b5d33c5daa..1f02368429 100644
--- a/doc/src/Python_head.txt
+++ b/doc/src/Python_head.txt
@@ -19,10 +19,6 @@ used together.
:maxdepth: 1
Python_overview
-
-.. toctree::
- :maxdepth: 1
-
Python_run
Python_shlib
Python_install
@@ -31,18 +27,13 @@ used together.
Python_library
Python_pylammps
Python_examples
-
-.. toctree::
- :maxdepth: 1
-
Python_call
END_RST -->
<!-- HTML_ONLY -->
-"Overview of Python and LAMMPS"_Python_overview.html :all(b)
-
+"Overview of Python and LAMMPS"_Python_overview.html
"Run LAMMPS from Python"_Python_run.html
"Build LAMMPS as a shared library"_Python_shlib.html
"Install LAMMPS in Python"_Python_install.html
@@ -50,8 +41,7 @@ END_RST -->
"Test the Python/LAMMPS interface"_Python_test.html
"Python library interface"_Python_library.html
"PyLammps interface"_Python_pylammps.html
-"Example Python scripts that use LAMMPS"_Python_examples.html :all(b)
-
+"Example Python scripts that use LAMMPS"_Python_examples.html
"Call Python from a LAMMPS input script"_Python_call.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
index 7eac11ffa5..17d44e8365 100644
--- a/doc/src/Speed.txt
+++ b/doc/src/Speed.txt
@@ -35,16 +35,13 @@ hardware platforms.
Speed_bench
Speed_measure
-
-.. toctree::
- :maxdepth: 1
-
Speed_tips
-
-.. toctree::
- :maxdepth: 1
-
Speed_packages
+ Speed_gpu
+ Speed_intel
+ Speed_kokkos
+ Speed_omp
+ Speed_opt
Speed_compare
END_RST -->
@@ -52,10 +49,8 @@ END_RST -->
<!-- HTML_ONLY -->
"Benchmarks"_Speed_bench.html
-"Measuring performance"_Speed_measure.html :all(b)
-
-"General tips"_Speed_tips.html :all(b)
-
+"Measuring performance"_Speed_measure.html
+"General tips"_Speed_tips.html
"Accelerator packages"_Speed_packages.html
"GPU package"_Speed_gpu.html
"USER-INTEL package"_Speed_intel.html
--
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