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Commit 07cd194e authored by Steven J. Plimpton's avatar Steven J. Plimpton
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tweaks to Manual formatting

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doc/src/Build.txt
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...@@ -24,17 +24,9 @@ as described on the "Install"_Install.html doc page. ...@@ -24,17 +24,9 @@ as described on the "Install"_Install.html doc page.
Build_cmake Build_cmake
Build_make Build_make
Build_link Build_link
.. toctree::
:maxdepth: 1
Build_basics Build_basics
Build_settings Build_settings
Build_package Build_package
.. toctree::
:maxdepth: 1
Build_extras Build_extras
END_RST --> END_RST -->
...@@ -43,12 +35,9 @@ END_RST --> ...@@ -43,12 +35,9 @@ END_RST -->
"Build LAMMPS with CMake"_Build_cmake.html "Build LAMMPS with CMake"_Build_cmake.html
"Build LAMMPS with make"_Build_make.html "Build LAMMPS with make"_Build_make.html
"Link LAMMPS as a library to another code"_Build_link.html :all(b) "Link LAMMPS as a library to another code"_Build_link.html
"Basic build options"_Build_basics.html
Build options: "Optional build settings"_Build_settings.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 "Include packages in build"_Build_package.html
"Packages with extra build options"_Build_extras.html :all(b) "Packages with extra build options"_Build_extras.html :all(b)
......
doc/src/Build_basics.txt
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...@@ -20,7 +20,7 @@ CMake and make: ...@@ -20,7 +20,7 @@ CMake and make:
:line :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 LAMMPS can be built to run in parallel using the ubiquitous "MPI
(message-passing (message-passing
...@@ -118,7 +118,7 @@ please refer to its documentation. ...@@ -118,7 +118,7 @@ please refer to its documentation.
:line :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 The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than performance. Vendor compilers can produce faster code than
...@@ -210,7 +210,7 @@ Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre ...@@ -210,7 +210,7 @@ Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre
:line :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 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 library. The LAMMPS library can be called from another application or
...@@ -271,7 +271,7 @@ should be the file /usr/local/lib/libmpich.so. ...@@ -271,7 +271,7 @@ should be the file /usr/local/lib/libmpich.so.
:line :line
Build the LAMMPS documentation :h3,link(doc) Build the LAMMPS documentation :h4,link(doc)
[CMake variable]: [CMake variable]:
...@@ -294,7 +294,7 @@ lammps/doc dir to see other options. ...@@ -294,7 +294,7 @@ lammps/doc dir to see other options.
:line :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 After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to library, along with other LAMMPS files (library header, doc files) to
......
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. ...@@ -23,7 +23,7 @@ explain how to do this for building both with CMake and make.
:line :line
FFT library :h3,link(fft) FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the When the KSPACE package is included in a LAMMPS build, the
"kspace_style pppm"_kspace_style.html command performs 3d FFTs which "kspace_style pppm"_kspace_style.html command performs 3d FFTs which
...@@ -126,7 +126,7 @@ ARRAY mode. ...@@ -126,7 +126,7 @@ ARRAY mode.
:line :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 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 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. ...@@ -189,7 +189,7 @@ in whichever lib/gpu/Makefile is used must be the same as above.
:line :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 The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command PNG image files. Likewise the "dump movie"_dump_image.html command
...@@ -245,7 +245,7 @@ crash. ...@@ -245,7 +245,7 @@ crash.
:line :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 If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including gzip compression by several LAMMPS commands, including
...@@ -276,7 +276,7 @@ what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables. ...@@ -276,7 +276,7 @@ what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
:line :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 This setting enables the use of the posix_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make malloc() when LAMMPS allocates large chunks or memory. This can make
...@@ -308,7 +308,7 @@ manages its dynamical memory. ...@@ -308,7 +308,7 @@ manages its dynamical memory.
:line :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 If your system or MPI version does not recognize "long long" data
types, the following setting will be needed. It converts "long long" types, the following setting will be needed. It converts "long long"
...@@ -325,7 +325,7 @@ LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre ...@@ -325,7 +325,7 @@ LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
:line :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. This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller. With this option enabled LAMMPS errors do not kill the caller.
......
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 ...@@ -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 code would not be as general-purpose as it is without their expertise
and efforts. 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 Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
......
doc/src/Modify.txt
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...@@ -38,19 +38,11 @@ contribute"_Modify_contribute.html doc page. ...@@ -38,19 +38,11 @@ contribute"_Modify_contribute.html doc page.
Modify_compute Modify_compute
Modify_fix Modify_fix
Modify_command Modify_command
.. toctree::
:maxdepth: 1
Modify_dump Modify_dump
Modify_kspace Modify_kspace
Modify_min Modify_min
Modify_region Modify_region
Modify_body Modify_body
.. toctree::
:maxdepth: 1
Modify_thermo Modify_thermo
Modify_variable Modify_variable
...@@ -66,14 +58,12 @@ END_RST --> ...@@ -66,14 +58,12 @@ END_RST -->
"Bond, angle, dihedral, improper styles"_Modify_bond.html "Bond, angle, dihedral, improper styles"_Modify_bond.html
"Compute styles"_Modify_compute.html "Compute styles"_Modify_compute.html
"Fix styles"_Modify_fix.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 "Dump styles"_Modify_dump.html
"Kspace styles"_Modify_kspace.html "Kspace styles"_Modify_kspace.html
"Minimization styles"_Modify_min.html "Minimization styles"_Modify_min.html
"Region styles"_Modify_region.html "Region styles"_Modify_region.html
"Body styles"_Modify_body.html :all(b) "Body styles"_Modify_body.html
"Thermodynamic output options"_Modify_thermo.html "Thermodynamic output options"_Modify_thermo.html
"Variable options"_Modify_variable.html :all(b) "Variable options"_Modify_variable.html :all(b)
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doc/src/Python_head.txt
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...@@ -19,10 +19,6 @@ used together. ...@@ -19,10 +19,6 @@ used together.
:maxdepth: 1 :maxdepth: 1
Python_overview Python_overview
.. toctree::
:maxdepth: 1
Python_run Python_run
Python_shlib Python_shlib
Python_install Python_install
...@@ -31,18 +27,13 @@ used together. ...@@ -31,18 +27,13 @@ used together.
Python_library Python_library
Python_pylammps Python_pylammps
Python_examples Python_examples
.. toctree::
:maxdepth: 1
Python_call Python_call
END_RST --> END_RST -->
<!-- HTML_ONLY --> <!-- 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 "Run LAMMPS from Python"_Python_run.html
"Build LAMMPS as a shared library"_Python_shlib.html "Build LAMMPS as a shared library"_Python_shlib.html
"Install LAMMPS in Python"_Python_install.html "Install LAMMPS in Python"_Python_install.html
...@@ -50,8 +41,7 @@ END_RST --> ...@@ -50,8 +41,7 @@ END_RST -->
"Test the Python/LAMMPS interface"_Python_test.html "Test the Python/LAMMPS interface"_Python_test.html
"Python library interface"_Python_library.html "Python library interface"_Python_library.html
"PyLammps interface"_Python_pylammps.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) "Call Python from a LAMMPS input script"_Python_call.html :all(b)
<!-- END_HTML_ONLY --> <!-- END_HTML_ONLY -->
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doc/src/Speed.txt
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...@@ -35,16 +35,13 @@ hardware platforms. ...@@ -35,16 +35,13 @@ hardware platforms.
Speed_bench Speed_bench
Speed_measure Speed_measure
.. toctree::
:maxdepth: 1
Speed_tips Speed_tips
.. toctree::
:maxdepth: 1
Speed_packages Speed_packages
Speed_gpu
Speed_intel
Speed_kokkos
Speed_omp
Speed_opt
Speed_compare Speed_compare
END_RST --> END_RST -->
...@@ -52,10 +49,8 @@ END_RST --> ...@@ -52,10 +49,8 @@ END_RST -->
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
"Benchmarks"_Speed_bench.html "Benchmarks"_Speed_bench.html
"Measuring performance"_Speed_measure.html :all(b) "Measuring performance"_Speed_measure.html
"General tips"_Speed_tips.html
"General tips"_Speed_tips.html :all(b)
"Accelerator packages"_Speed_packages.html "Accelerator packages"_Speed_packages.html
"GPU package"_Speed_gpu.html "GPU package"_Speed_gpu.html
"USER-INTEL package"_Speed_intel.html "USER-INTEL package"_Speed_intel.html
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