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tweaks to Manual formatting

This commit is contained in:
Steven J. Plimpton 2018-08-15 16:27:39 -06:00
parent ccacf0d4bb
commit 07cd194e27
7 changed files with 27 additions and 63 deletions
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17
doc/src/Build.txt
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@ -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 -->
@ -43,12 +35,9 @@ 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:
"Basic build options: serial/parallel, compilers, executable/library"_Build_basics.html
"Optional build settings"_Build_settings.html :all(b)
"Link LAMMPS as a library to another code"_Build_link.html
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
"Packages with extra build options"_Build_extras.html :all(b)

10
doc/src/Build_basics.txt
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@ -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

14
doc/src/Build_settings.txt
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@ -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.

2
doc/src/Intro_authors.txt
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@ -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

14
doc/src/Modify.txt
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@ -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)

14
doc/src/Python_head.txt
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@ -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 -->

19
doc/src/Speed.txt
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@ -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