diff --git a/doc/src/Build.txt b/doc/src/Build.txt index 218664897f..e62268b84b 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 --> @@ -43,12 +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) 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 --> -"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) 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 --> "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