Merge pull request #1898 from akohlmey/next_lammps_version

Update version info for next release candidate

.github/CODEOWNERS

@@ -111,6 +111,7 @@ src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
 
 # tools
 tools/msi2lmp/*       @akohlmey

.github/CONTRIBUTING.md

@@ -68,12 +68,12 @@ How quickly your contribution will be integrated depends largely on how much eff
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
-* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
-* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
 * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 

.gitignore

@@ -26,6 +26,7 @@ vgcore.*
 .vagrant
 \#*#
 .#*
+.vscode
 
 .DS_Store
 .DS_Store?

cmake/CMakeLists.txt

@@ -36,7 +36,6 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
 include(PreventInSourceBuilds)
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
-  #release comes with -O3 by default
   set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@@ -420,7 +419,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
@@ -588,8 +587,9 @@ if(BUILD_TOOLS)
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
   # ninja-build currently does not support fortran. thus we skip building this tool
-  if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
+  if(CMAKE_GENERATOR STREQUAL "Ninja")
     message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
+  else()
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
@@ -681,7 +681,7 @@ endforeach()
 
 get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
 include(FeatureSummary)
-feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
+feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
    Build type       ${CMAKE_BUILD_TYPE}
    Install path     ${CMAKE_INSTALL_PREFIX}
@@ -701,7 +701,7 @@ if (${_index} GREATER -1)
 endif()
 list (FIND LANGUAGES "C" _index)
 if (${_index} GREATER -1)
-  message(STATUS "C Compiler ${CMAKE_C_COMPILER}
+  message(STATUS "C compiler ${CMAKE_C_COMPILER}
      Type     ${CMAKE_C_COMPILER_ID}
      Version  ${CMAKE_C_COMPILER_VERSION}
      C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
@@ -711,22 +711,22 @@ if(CMAKE_EXE_LINKER_FLAGS)
    Executable      ${CMAKE_EXE_LINKER_FLAGS}")
 endif()
 if(BUILD_SHARED_LIBS)
-  message(STATUS "Shared libraries  ${CMAKE_SHARED_LINKER_FLAGS}")
+  message(STATUS "Shared library flags:  ${CMAKE_SHARED_LINKER_FLAGS}")
 else()
-  message(STATUS "Static libraries  ${CMAKE_STATIC_LINKER_FLAGS}")
+  message(STATUS "Static library flags:  ${CMAKE_STATIC_LINKER_FLAGS}")
 endif()
 message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
 if(BUILD_MPI)
-  message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
+  message(STATUS "Using MPI with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
 endif()
 if(PKG_GPU)
-  message(STATUS "GPU Api: ${GPU_API}")
+  message(STATUS "GPU API: ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU Arch: ${GPU_ARCH}")
+    message(STATUS "GPU architecture: ${GPU_ARCH}")
   elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OCL Tune: ${OCL_TUNE}")
+    message(STATUS "OpenCL parameter tuning: ${OCL_TUNE}")
   endif()
-  message(STATUS "GPU Precision: ${GPU_PREC}")
+  message(STATUS "GPU precision: ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
@@ -738,4 +738,20 @@ if(PKG_KSPACE)
   else()
     message(STATUS "Using double precision FFTs")
   endif()
+  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+    message(STATUS "Using threaded FFTs")
+  else()
+    message(STATUS "Using non-threaded FFTs")
+  endif()
+  if(PKG_KOKKOS)
+    if(KOKKOS_ENABLE_CUDA)
+      if (${FFT} STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: cuFFT")
+      endif()
+    else()
+      message(STATUS "Kokkos FFT: ${FFT}")
+    endif()
+  endif()
 endif()

cmake/Modules/FindFFTW3.cmake

@@ -1,20 +1,22 @@
 # - Find fftw3
-# Find the native FFTW3 headers and libraries.
+# Find the native double precision FFTW3 headers and libraries.
 #
-#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
-#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
+#  FFTW3_INCLUDE_DIRS  - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES     - List of libraries when using fftw3.
+#  FFTW3_OMP_LIBRARIES - List of libraries when using fftw3.
+#  FFTW3_FOUND         - True if fftw3 found.
 #
 
 find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3 fftw3)
 find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
-
 find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
+find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
 
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
 set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
+set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
@@ -22,4 +24,4 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY FFTW3_OMP_LIBRARY)

cmake/Modules/FindFFTW3F.cmake

@@ -1,8 +1,8 @@
-# - Find fftw3f
-# Find the native FFTW3F headers and libraries.
+# Find the native single precision FFTW3 headers and libraries.
 #
 #  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
 #  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_OMP_LIBRARIES - List of libraries when using fftw3.
 #  FFTW3F_FOUND        - True if fftw3f found.
 #
 
@@ -10,11 +10,12 @@ find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3F fftw3f)
 find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
-
 find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
 
-set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
 set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
@@ -22,4 +23,4 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY)

cmake/Modules/FindNetCDF.cmake

@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" ""
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

cmake/Modules/FindPNetCDF.cmake

@@ -0,0 +1,55 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" ""
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)

cmake/Modules/FindQE.cmake

@@ -1,29 +0,0 @@
-# - Find quantum-espresso
-# Find the native QE headers and libraries.
-#
-#  QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
-#  QE_LIBRARIES    - List of libraries when using quantum-espresso.
-#  QE_FOUND        - True if quantum-espresso found.
-#
-
-find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
-
-find_library(QECOUPLE_LIBRARY NAMES qecouple)
-find_library(PW_LIBRARY NAMES pw)
-find_library(QEMOD_LIBRARY NAMES qemod)
-find_library(QEFFT_LIBRARY NAMES qefft)
-find_library(QELA_LIBRARY NAMES qela)
-find_library(CLIB_LIBRARY NAMES clib)
-find_library(IOTK_LIBRARY NAMES iotk)
-
-
-set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
-set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
-
-mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)

cmake/Modules/Packages/KIM.cmake

@@ -5,6 +5,16 @@ if(PKG_KIM)
     include_directories(${CURL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
     add_definitions(-DLMP_KIM_CURL)
+    set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+    mark_as_advanced(LMP_DEBUG_CURL)
+    if(LMP_DEBUG_CURL)
+      add_definitions(-DLMP_DEBUG_CURL)
+    endif()
+    set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+    mark_as_advanced(LMP_NO_SSL_CHECK)
+    if(LMP_NO_SSL_CHECK)
+      add_definitions(-DLMP_NO_SSL_CHECK)
+    endif()
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)

cmake/Modules/Packages/KOKKOS.cmake

@@ -10,7 +10,7 @@ if(PKG_KOKKOS)
     set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
     set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
     add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  
+
     set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                             ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                             ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
@@ -39,7 +39,15 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
   if(PKG_KSPACE)
-    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+    if(KOKKOS_ENABLE_CUDA)
+      if(NOT ${FFT} STREQUAL "KISS")
+        add_definitions(-DFFT_CUFFT)
+        list(APPEND LAMMPS_LINK_LIBS cufft)
+      endif()
+    endif()
   endif()
 
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")

cmake/Modules/Packages/KSPACE.cmake

@@ -21,9 +21,27 @@ if(PKG_KSPACE)
     add_definitions(-DFFT_FFTW3)
     include_directories(${${FFTW}_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+      option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
+    else()
+      option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
+    endif()
+
+    if(FFT_FFTW_THREADS)
+      if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+        add_definitions(-DFFT_FFTW_THREADS)
+        list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_OMP_LIBRARIES})
+      else()
+        message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
+      endif()
+    endif()
   elseif(FFT STREQUAL "MKL")
     find_package(MKL REQUIRED)
     add_definitions(-DFFT_MKL)
+    option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
+    if(FFT_MKL_THREADS)
+      add_definitions(-DFFT_MKL_THREADS)
+    endif()
     include_directories(${MKL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
   else()

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,6 +1,24 @@
 if(PKG_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(${NETCDF_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else(NETCDF_FOUND)
+    find_package(PNetCDF REQUIRED)
+  endif(NETCDF_FOUND)
+
+  if(NETCDF_FOUND)
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_NETCDF)
+  endif(NETCDF_FOUND)
+
+  if(PNETCDF_FOUND)
+    include_directories(${PNETCDF_INCLUDES})
+    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_PNETCDF)
+  endif(PNETCDF_FOUND)
+
+  add_definitions(-DNC_64BIT_DATA=0x0020)
 endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
-      URL_MD5 de30d6e7c2dcc0973298e24a6da24286
+      URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
+      URL_MD5 204d2edae58d9b10ba3ad460cad64191
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}

cmake/Modules/Packages/USER-QMMM.cmake

@@ -1,9 +1,13 @@
 if(PKG_USER-QMMM)
-  enable_language(Fortran)
   enable_language(C)
 
-  message(WARNING "Building QMMM with CMake is still experimental")
-  find_package(QE REQUIRED)
-  include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
+  if(NOT BUILD_LIB)
+    message(FATAL_ERROR "Building a QM/MM executable with USER-QMMM requires BUILD_LIB=yes")
+  endif()
+  if(NOT BUILD_SHARED_LIBS)
+    message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
+  endif()
+  add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
+  list(APPEND LAMMPS_LINK_LIBS qmmm)
+  target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
 endif()

doc/.gitignore

@@ -1,6 +1,8 @@
 /old
 /html
+/html-offline
 /latex
+/mathjax
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi

doc/Makefile

@@ -3,8 +3,8 @@
 SHELL         = /bin/bash
 BUILDDIR      = ${CURDIR}
 RSTDIR        = $(BUILDDIR)/src
-TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
+MATHJAX       = $(BUILDDIR)/mathjax
 TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
@@ -28,63 +28,66 @@ HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
-OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
+.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
 
 # ------------------------------------------
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       create HTML doc pages in html dir"
-	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
-	@echo "  epub       create ePUB format manual for e-book readers"
-	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
+	@echo "  html          create HTML doc pages in html dir"
+	@echo "  pdf           create Developer.pdf and Manual.pdf in this dir"
+	@echo "  fetch         fetch HTML and PDF files from LAMMPS web site"
+	@echo "  epub          create ePUB format manual for e-book readers"
+	@echo "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
-	@echo "  clean      remove all intermediate RST files"
-	@echo "  clean-all  reset the entire build environment"
+	@echo "  clean         remove all intermediate RST files"
+	@echo "  clean-all     reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
-	@echo "  spelling   spell-check the manual"
+	@echo "  style_check   check for complete and consistent style lists"
+	@echo "  package_check check for complete and consistent package lists"
+	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax
 
-clean:
+clean: clean-spelling
 	rm -rf html epub latex
-	rm -rf spelling
 
 clean-spelling:
 	rm -rf spelling
 
-rst: clean $(OBJECTS) $(ANCHORCHECK)
-
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK) $(MATHJAX)
 	@(\
 		. $(VENV)/bin/activate ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
+		python utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
-	-rm html/searchindex.js
 	@rm -rf html/_sources
 	@rm -rf html/PDF
 	@rm -rf html/USER
+	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
 	@cp -r src/USER html/USER
+	@mkdir -p html/JPG
+	@cp `grep -A2 '\.\. image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
 	@rm -rf html/USER/.[sg]*
 	@rm -rf html/USER/*/.[sg]*
 	@rm -rf html/USER/*/*.[sg]*
+	@mkdir -p html/_static/mathjax
+	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+spelling: $(VENV) utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
@@ -94,7 +97,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	)
 	@echo "Spell check finished."
 
-epub: $(OBJECTS)
+epub: $(VENV)
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
@@ -113,7 +116,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: $(OBJECTS) $(ANCHORCHECK)
+pdf: $(ANCHORCHECK)
 	@(\
 		cd src/Developer; \
 		pdflatex developer; \
@@ -122,24 +125,28 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                rst_anchor_check src/*.rst ;\
-                echo "############################################" ;\
-                deactivate ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
+		python utils/check-packages.py -s ../src -d src ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
@@ -162,20 +169,26 @@ fetch:
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		rst_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		deactivate ;\
+	)
+
+style_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		deactivate ;\
+	)
+
+package_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
-	@(\
-		mkdir -p $(RSTDIR) ; \
-		. $(VENV)/bin/activate ;\
-		txt2rst -v $< > $@ ;\
-		deactivate ;\
-	)
-
 $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
@@ -186,6 +199,9 @@ $(VENV):
 		deactivate;\
 	)
 
+$(MATHJAX):
+	@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
+
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \

doc/github-development-workflow.md

@@ -104,14 +104,17 @@ Here are some items to check:
   * every new command or style should have documentation. The names of
   source files (c++ and manual) should follow the name of the style.
   (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
-  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.rst`)
   * all new style names should be lower case, the must be no dashes,
   blanks, or underscores separating words, only forward slashes.
   * new style docs should be added to the "overview" files in
-  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
-  and `doc/src/lammps.book`
+  `doc/src/Commands_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
   * check whether manual cleanly translates with `make html` and `make pdf`
+  * if documentation is (still) provided as a .txt file, convert to .rst
+  and remove the .txt file. For files in doc/txt the conversion is automatic.
+  * remove all .txt files in `doc/txt` that are out of sync with their .rst counterparts in `doc/src`
   * check spelling of manual with `make spelling` in doc folder
+  * check style tables and command lists with `make style_check`
   * new source files in packages should be added to `src/.gitignore`
   * removed or renamed files in packages should be added to `src/Purge.list`
   * C++ source files should use C++ style include files for accessing
@@ -136,7 +139,7 @@ Here are some items to check:
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
   * indentation is 2 spaces per level
-  * there should be NO tabs and no trailing whitespace
+  * there should be NO tabs and no trailing whitespace (review the "checkstyle" test on pull requests)
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "20 November 2019" "2019-11-20"
+.TH LAMMPS "27 February 2020" "2020-02-27"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -11,13 +11,18 @@ or
 
 mpirun \-np 2
 .B lmp
-<input file> [OPTIONS] ...
+\-in <input file> [OPTIONS] ...
 
 or
 
 .B lmp
 \-r2data file.restart file.data
 
+or
+
+.B lmp
+\-h
+
 .SH DESCRIPTION
 .B LAMMPS
 is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
@@ -249,7 +254,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2019 Sandia Corporation
+© 2003--2020 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/src/.gitignore

@@ -1,2 +1,3 @@
-Eqs
-JPG
+/Eqs
+/JPG
+/false_positives.txt

doc/src/Build.rst

@@ -21,8 +21,3 @@ as described on the :doc:`Install <Install>` doc page.
    Build_extras
    Build_windows
    Build_development
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_basics.rst

@@ -19,94 +19,115 @@ CMake and make:
 Serial vs parallel build
 -------------------------------------
 
-LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
-library.  Or it can built to run on a single processor (serial)
-without MPI.  It can also be built with support for OpenMP threading
-(see more discussion below).
+LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
+<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
+for distributed memory parallel computation.  You need to have such a
+library installed for building and running LAMMPS in parallel using a
+domain decomposition parallelization.  It is compatible with the MPI
+standard version 2.x and later.  LAMMPS can also be built into a
+"serial" executable for use with a single processor using the bundled
+MPI STUBS library.
 
-**CMake variables**\ :
+Independent of the distributed memory MPI parallelization, parts of
+LAMMPS are also written with support for shared memory parallelization
+using the OpenMP threading standard. A more detailed discussion of that
+is below.
 
+**CMake build**\ :
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
-   -D BUILD_OMP=value        # yes or no (default)
+   -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
    -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
                              # no default value
 
-The executable created by CMake (after running make) is lmp\_name.  If
-the LAMMPS\_MACHINE variable is not specified, the executable is just
-lmp.  Using BUILD\_MPI=no will produce a serial executable.
+The executable created by CMake (after running make) is named *lmp* unless
+the LAMMPS\_MACHINE option is set.  When setting `LAMMPS_MACHINE=name`
+the executable will be named *lmp\_name*\.  Using `BUILD\_MPI=no` will
+enforce building a serial executable using the MPI STUBS library.
 
 **Traditional make**\ :
 
+The build with traditional makefiles has to be done inside the source folder `src`.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   cd lammps/src
    make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
    make serial             # serial build, produces lmp_serial using Makefile/serial
-   make mybox          # uses Makefile.mybox to produce lmp_mybox
-
-Serial build (see src/MAKE/Makefile.serial):
+   make mybox              # uses Makefile.mybox to produce lmp_mybox
 
 
-.. parsed-literal::
+Any "make machine" command will look up the make settings from a file
+Makefile.machine, create a folder Obj\_machine with all objects and
+generated files and an executable called *lmp\_machine*\ .  The standard
+parallel build with `make mpi` assumes a standard MPI installation with
+MPI compiler wrappers where all necessary compiler and linker flags to
+get access and link with the suitable MPI headers and libraries are set
+by the wrapper programs.  For other cases or the serial build, you have
+to adjust the make file variables MPI\_INC, MPI\_PATH, MPI\_LIB as well
+as CC and LINK.  To enable OpenMP threading usually a compiler specific
+flag needs to be added to the compile and link commands.  For the GNU
+compilers, this is *-fopenmp*\ , which can be added to the CC and LINK
+makefile variables.
 
+For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
+
+.. code-block:: make
+
+   CC =            g++
+   LINK =          g++
    MPI_INC =       -I../STUBS
    MPI_PATH =      -L../STUBS
    MPI_LIB =       -lmpi_stubs
 
-For a parallel build, if MPI is installed on your system in the usual
-place (e.g. under /usr/local), you do not need to specify the 3
-variables MPI\_INC, MPI\_PATH, MPI\_LIB.  The MPI wrapper on the compiler
-(e.g. mpicxx, mpiCC) knows where to find the needed include and
-library files.  Failing this, these 3 variables can be used to specify
-where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
-are found, and the name of the library files (MPI\_LIB).
+You also need to build the STUBS library for your platform before making
+LAMMPS itself.  A "make serial" build does this for you automatically,
+otherwise, type "make mpi-stubs" from the src directory, or "make" from
+the src/STUBS dir.  If the build fails, you will need to edit the
+STUBS/Makefile for your platform.  The stubs library does not provide
+MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
+and thus is not compatible with those packages.
 
-For a serial build, you need to specify the 3 variables, as shown
-above.
+.. note::
 
-For a serial LAMMPS build, use the dummy MPI library provided in
-src/STUBS.  You also need to build the STUBS library for your platform
-before making LAMMPS itself.  A "make serial" build does this for.
-Otherwise, type "make mpi-stubs" from the src directory, or "make"
-from the src/STUBS dir.  If the build fails, you will need to edit the
-STUBS/Makefile for your platform.
+   The file STUBS/mpi.c provides a CPU timer function called
+   MPI\_Wtime() that calls gettimeofday() .  If your operating system
+   does not support gettimeofday() , you will need to insert code to
+   call another timer.  Note that the ANSI-standard function clock()
+   rolls over after an hour or so, and is therefore insufficient for
+   timing long LAMMPS simulations.
 
-The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
-that calls gettimeofday() .  If your system doesn't support
-gettimeofday() , you'll need to insert code to call another timer.
-Note that the ANSI-standard function clock() rolls over after an hour
-or so, and is therefore insufficient for timing long LAMMPS
-simulations.
+**MPI and OpenMP support info**\ :
 
-**CMake and make info**\ :
+If you are installing MPI yourself to build a parallel LAMMPS
+executable, we recommend either MPICH or OpenMPI which are regularly
+used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
+downloaded from the `MPICH home page <https://www.mpich.org>`_ and
+OpenMPI can be downloaded correspondingly from the `OpenMPI home page
+<https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
+specific vendor provided and standard compliant MPI library is currently
+known to be incompatible with LAMMPS.  If you are running on a large
+parallel machine, your system admins or the vendor should have already
+installed a version of MPI, which is likely to be faster than a
+self-installed MPICH or OpenMPI, so you should study the provided
+documentation to find out how to build and link with it.
 
-If you are installing MPI yourself, we recommend MPICH2 from Argonne
-National Laboratory or OpenMPI.  MPICH can be downloaded from the
-`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
-OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_.  Other MPI packages should also work.
-If you are running on a large parallel machine, your system admins or
-the vendor should have already installed a version of MPI, which is
-likely to be faster than a self-installed MPICH or OpenMPI, so find
-out how to build and link with it.
-
-The majority of OpenMP (threading) support in LAMMPS is provided by
-the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
-details. The USER-INTEL package also provides OpenMP support (it is
+The majority of OpenMP (threading) support in LAMMPS is provided by the
+USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
+details. The USER-INTEL package also includes OpenMP threading (it is
 compatible with USER-OMP) and adds vectorization support when compiled
-with the Intel compilers on top of that. Also, the KOKKOS package can
-be compiled for using OpenMP threading.
+with compatible compilers, in particular the Intel compilers on top of
+OpenMP. Also, the KOKKOS package can be compiled to include OpenMP
+threading.
 
-However, there are a few commands in LAMMPS that have native OpenMP
-support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
-USER-DPD packages.  In addition some packages support OpenMP threading
-indirectly through the libraries they interface to: e.g. LATTE and
-USER-COLVARS.  See the :doc:`Packages details <Packages_details>` doc
-page for more info on these packages and the doc pages for their
-respective commands for OpenMP threading info.
+In addition, there are a few commands in LAMMPS that have native OpenMP
+support included as well.  These are commands in the MPIIO, SNAP,
+USER-DIFFRACTION, and USER-DPD packages.  In addition some packages
+support OpenMP threading indirectly through the libraries they interface
+to: e.g. LATTE and USER-COLVARS.  See the :doc:`Packages details
+<Packages_details>` doc page for more info on these packages and the doc
+pages for their respective commands for OpenMP threading info.
 
 For CMake, if you use BUILD\_OMP=yes, you can use these packages and
 turn on their native OpenMP support and turn on their native OpenMP
@@ -143,22 +164,37 @@ Choice of compiler and compile/link options
 ---------------------------------------------------------
 
 The choice of compiler and compiler flags can be important for
-performance.  Vendor compilers can produce faster code than
-open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
-trying the `Intel C++ compiler <intel_>`_.
+performance.  Vendor provided compilers for a specific hardware can
+produce faster code than open-source compilers like the GNU compilers.
+On x86 hardware most popular compilers are quite similar in performance
+of C/C++ code at high optimization levels.  When using the USER-INTEL
+package, there is a distinct advantage in using the `Intel C++ compiler
+<intel_>`_ due to much improved vectorization through SSE and AVX
+instructions on compatible hardware as the source code includes changes
+and compiler directives to enable high degrees of vectorization.
 
 .. _intel: https://software.intel.com/en-us/intel-compilers
 
+On parallel clusters or supercomputers which use "environment modules"
+for their compile/link environments, you can often access different
+compilers by simply loading the appropriate module before building
+LAMMPS.
 
+**CMake build**\ :
 
-On parallel clusters or supercomputers which use "modules" for their
-compile/link environments, you can often access different compilers by
-simply loading the appropriate module before building LAMMPS.
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any
+:doc:`accelerator packages <Speed_packages>` you have included in the
+build.
 
-**CMake variables**\ :
+You can tell CMake to look for a specific compiler with these variable
+settings.  Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags.  You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
 
-
-.. parsed-literal::
+.. code-block:: bash
 
    -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
    -D CMAKE_C_COMPILER=name              # name of C compiler
@@ -168,42 +204,42 @@ simply loading the appropriate module before building LAMMPS.
    -D CMAKE_C_FLAGS=string               # flags to use with C compiler
    -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
 
-By default CMake will use a compiler it finds and it will add
-optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
 
-You can tell CMake to look for a specific compiler with these variable
-settings.  Likewise you can specify the FLAGS variables if you want to
-experiment with alternate optimization flags.  You should specify all
-3 compilers, so that the small number of LAMMPS source files written
-in C or Fortran are built with a compiler consistent with the one used
-for all the C++ files:
+A few example command lines are:
 
+.. code-block:: bash
 
-.. parsed-literal::
-
-   Building with GNU Compilers:
+   # Building with GNU Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-   Building with Intel Compilers:
+   # Building with Intel Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
-   Building with LLVM/Clang Compilers:
+   # Building with LLVM/Clang Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
 
+For compiling with the Clang/LLVM compilers a special CMake preset is
+included that can be loaded with `-C ../cmake/presets/clang.cmake`.
+
 .. note::
 
-   When the cmake command completes, it prints info to the screen
-   as to which compilers it is using, and what flags will be used in the
-   compilation.  Note that if the top-level compiler is mpicxx, it is
-   simply a wrapper on a real compiler.  The underlying compiler info is
-   what will be listed in the CMake output.  You should check to insure
-   you are using the compiler and optimization flags are the ones you
-   want.
+   When the cmake command completes, it prints a summary to the screen
+   which compilers it is using and what flags and settings will be used
+   for the  compilation.  Note that if the top-level compiler is mpicxx,
+   it is simply a wrapper on a real compiler.  The underlying compiler
+   info is what CMake will try to determine and report.  You should check
+   to confirm you are using the compiler and optimization flags you want.
 
-**Makefile.machine settings**\ :
+**Makefile.machine settings for traditional make**\ :
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  For a parallel build it is recommended to use
+mpicxx or mpiCC, since these compiler wrappers will include a variety of
+settings appropriate for your MPI installation and thus avoiding the
+guesswork of finding the right flags.
 
 Parallel build (see src/MAKE/Makefile.mpi):
 
-
-.. parsed-literal::
+.. code-block:: bash
 
    CC =            mpicxx
    CCFLAGS =       -g -O3
@@ -212,33 +248,26 @@ Parallel build (see src/MAKE/Makefile.mpi):
 
 Serial build (see src/MAKE/Makefile.serial):
 
-
-.. parsed-literal::
+.. code-block:: make
 
    CC =            g++
    CCFLAGS =       -g -O3
    LINK =          g++
    LINKFLAGS =     -g -O
 
-The "compiler/linker settings" section of a Makefile.machine lists
-compiler and linker settings for your C++ compiler, including
-optimization flags.  You should always use mpicxx or mpiCC for
-a parallel build, since these compiler wrappers will include
-a variety of settings appropriate for your MPI installation.
-
 .. note::
 
-   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
-   optimization flags that are either required or recommended for optimal
-   performance.  You need to include these in the CCFLAGS and LINKFLAGS
-   settings above.  For details, see the individual package doc pages
-   listed on the :doc:`Speed packages <Speed_packages>` doc page.  Or
-   examine these files in the src/MAKE/OPTIONS directory.  They
-   correspond to each of the 5 accelerator packages and their hardware
-   variants:
+   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>`
+   included, there may be specific optimization flags that are either
+   required or recommended to enable required features and to achieve
+   optimal performance.  You need to include these in the CCFLAGS and
+   LINKFLAGS settings above.  For details, see the individual package
+   doc pages listed on the :doc:`Speed packages <Speed_packages>` doc
+   page.  Or examine these files in the src/MAKE/OPTIONS directory.
+   They correspond to each of the 5 accelerator packages and their
+   hardware variants:
 
-
-.. parsed-literal::
+.. code-block:: bash
 
    Makefile.opt                   # OPT package
    Makefile.omp                   # USER-OMP package
@@ -249,10 +278,8 @@ a variety of settings appropriate for your MPI installation.
    Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
    Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
 
-
 ----------
 
-
 .. _exe:
 
 Build LAMMPS as an executable or a library
@@ -265,10 +292,13 @@ page for more info on coupling LAMMPS to other codes.  See the
 :doc:`Python <Python_head>` doc page for more info on wrapping and
 running LAMMPS from Python via its library interface.
 
-**CMake variables**\ :
+**CMake build**\ :
 
+For CMake builds, you can select through setting CMake variables which
+files the compilation produces during the configuration step.  If none
+are set, defaults are applied.
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D BUILD_EXE=value           # yes (default) or no
    -D BUILD_LIB=value           # yes or no (default)
@@ -277,24 +307,32 @@ running LAMMPS from Python via its library interface.
                                 # no default value
 
 Setting BUILD\_EXE=no will not produce an executable.  Setting
-BUILD\_LIB=yes will produce a static library named liblammps.a.
+BUILD\_LIB=yes will produce a static library named *liblammps.a*\ .
 Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
-shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
-libraries will be named liblammps\_name.a or liblammps\_name.so instead.
+shared library named *liblammps.so* instead. If LAMMPS\_LIB\_SUFFIX is
+set to *name* in addition, the name of the generated libraries will be
+changed to either *liblammps\_name.a* or *liblammps\_name.so*\ ,
+respectively.
 
 **Traditional make**\ :
 
+With the traditional makefile based build process, the choice of
+the generated executable or library depends on the "mode" setting.
+Several options are available and "mode=exe" is the default.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   cd lammps/src
    make machine               # build LAMMPS executable lmp_machine
+   mkae mode=exe machine      # same as "make machine"
    make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
    make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so
+   make mode=shexe machine    # same as "mode=exe" but uses objects from "mode=shlib"
 
-The two library builds also create generic soft links, named
-liblammps.a and liblammps.so, which point to the liblammps\_machine
-files.
+The two "exe" builds will generate and executable *lmp\_machine*\ ,
+while the two library builds will create a file *liblammps\_machine.a*
+or *liblammps\_machine.so*\ . They will also create generic soft links,
+named *liblammps.a* and *liblammps.so*\ , which point to the specific
+*liblammps\_machine.a/so* files.
 
 **CMake and make info**\ :
 
@@ -302,32 +340,40 @@ Note that for a shared library to be usable by a calling program, all
 the auxiliary libraries it depends on must also exist as shared
 libraries.  This will be the case for libraries included with LAMMPS,
 such as the dummy MPI library in src/STUBS or any package libraries in
-the lib/packages directory, since they are always built as shared
-libraries using the -fPIC switch.  However, if a library like MPI or
-FFTW does not exist as a shared library, the shared library build will
-generate an error.  This means you will need to install a shared
-library version of the auxiliary library.  The build instructions for
-the library should tell you how to do this.
-
-As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
-Argonne National Lab, as a shared library in the default
-/usr/local/lib location:
-
-.. _mpich: http://www-unix.mcs.anl.gov/mpi
+the lib/packages directory, since they are always built in a shared
+library compatible way using the -fPIC switch.  However, if a library
+like MPI or FFTW does not exist as a shared library, the shared library
+build may generate an error.  This means you will need to install a
+shared library version of the auxiliary library.  The build instructions
+for the library should tell you how to do this.
 
 
+As an example, here is how to build and install the `MPICH library
+<mpich_>`_, a popular open-source version of MPI, as a shared library
+in the default /usr/local/lib location:
 
+.. _mpich: https://www.mpich.org
 
-.. parsed-literal::
+.. code-block:: bash
 
    ./configure --enable-shared
    make
    make install
 
-You may need to use "sudo make install" in place of the last line if
-you do not have write privileges for /usr/local/lib.  The end result
-should be the file /usr/local/lib/libmpich.so.
+You may need to use "sudo make install" in place of the last line if you
+do not have write privileges for /usr/local/lib.  The end result should
+be the file /usr/local/lib/libmpich.so.  On many Linux installations the
+folder "${HOME}/.local" is an alternative to using /usr/local and does
+not require superuser or sudo access.  In that case the configuration
+step becomes:
 
+.. code-block:: bash
+
+  ./configure --enable-shared --prefix=${HOME}/.local
+
+Avoiding using "sudo" for custom software installation (i.e. from source
+and not through a package manager tool provided by the OS) is generally
+recommended to ensure the integrity of the system software installation.
 
 ----------
 
@@ -337,30 +383,39 @@ should be the file /usr/local/lib/libmpich.so.
 Build the LAMMPS documentation
 ----------------------------------------
 
-**CMake variable**\ :
+The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
+can be translated to different output format using the `Sphinx <sphinx_>`_
+document generator tool.  Currently the translation to HTML and PDF (via
+LaTeX) are supported.  For that to work a Python 3 interpreter and
+internet access is required.  For the documentation build a python
+based virtual environment is set up in the folder doc/docenv and various
+python packages are installed into that virtual environment via the pip
+tool.  The actual translation is then done via make commands.
+
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _sphinx: https://sphinx-doc.org
+
+**Documentation make option**\ :
+
+The following make commands can be issued in the doc folder of the
+LAMMPS source distribution.
+
+.. code-block:: bash
+
+  make html          # create HTML doc pages in html directory
+  make pdf           # create Developer.pdf and Manual.pdf in this directory
+  make fetch         # fetch HTML and PDF files from LAMMPS web site
+  make clean         # remove all intermediate files
+  make clean-all     # reset the entire doc build environment
+  make anchor_check  # scan for duplicate anchor labels
+  make style_check   # check for complete and consistent style lists
+  make package_check # check for complete and consistent package lists
+  make spelling      # spell-check the manual
 
 
-.. parsed-literal::
-
-   -D BUILD_DOC=value       # yes or no (default)
-
-This will create the HTML doc pages within the CMake build directory.
-The reason to do this is if you want to "install" LAMMPS on a system
-after the CMake build via "make install", and include the doc pages in
-the install.
-
-**Traditional make**\ :
-
-
-.. parsed-literal::
-
-   cd lammps/doc
-   make html       # html doc pages
-   make pdf        # single Manual.pdf file
-
-This will create a lammps/doc/html dir with the HTML doc pages so that
-you can browse them locally on your system.  Type "make" from the
-lammps/doc dir to see other options.
+Thus "make html" will create a "doc/html" directory with the HTML format
+manual pages so that you can browse them with a web browser locally on
+your system.
 
 .. note::
 
@@ -369,6 +424,19 @@ lammps/doc dir to see other options.
    `download page <http://lammps.sandia.gov/download.html>`_.
 
 
+**CMake build option**\ :
+
+It is also possible to create the HTML version of the manual within
+the :doc:`CMake build directory <Build_cmake>`.  The reason for this
+option is to include the installation of the HTML manual pages into
+the "install" step when installing LAMMPS after the CMake build via
+"make install".
+
+.. code-block:: bash
+
+   -D BUILD_DOC=value       # yes or no (default)
+
+
 ----------
 
 
@@ -380,19 +448,20 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.
 
-**CMake variable**\ :
+**CMake build3**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D BUILD_TOOLS=value       # yes or no (default)
 
-The generated binaries will also become part of the LAMMPS installation (see below)
+The generated binaries will also become part of the LAMMPS installation
+(see below).
 
 **Traditional make**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cd lammps/tools
    make all              # build all binaries of tools
@@ -416,10 +485,10 @@ a globally visible place on your system, for others to access.  Note
 that you may need super-user privileges (e.g. sudo) if the directory
 you want to copy files to is protected.
 
-**CMake variable**\ :
+**CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
    make                        # perform make after CMake command
@@ -430,8 +499,3 @@ you want to copy files to is protected.
 There is no "install" option in the src/Makefile for LAMMPS.  If you
 wish to do this you will need to first build LAMMPS, then manually
 copy the desired LAMMPS files to the appropriate system directories.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_cmake.rst

@@ -20,7 +20,7 @@ make command to build LAMMPS, which uses the created
 Makefile(s). Example:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cd lammps                        # change to the LAMMPS distribution directory
    mkdir build; cd build            # create a new directory (folder) for build
@@ -52,7 +52,7 @@ After compilation, you may optionally install the LAMMPS executable into
 your system with:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make install    # optional, copy LAMMPS executable & library elsewhere
 
@@ -115,7 +115,7 @@ folder, recreate the directory and start over.
 **Command-line version of CMake**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cmake [options ...] /path/to/lammps/cmake  # build from any dir
    cmake [options ...] ../cmake               # build from lammps/build
@@ -127,7 +127,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
    -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
@@ -177,7 +177,7 @@ directory.
 **Curses version (terminal-style menu) of CMake**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    ccmake ../cmake
 
@@ -195,7 +195,7 @@ more information.
 **GUI version of CMake**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cmake-gui ../cmake
 
@@ -216,7 +216,7 @@ for more information.
 Check if your machine already has CMake installed:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    which cmake             # do you have it?
    which cmake3            # version 3 may have this name
@@ -226,10 +226,10 @@ On clusters or supercomputers which use environment modules to manage
 software packages, do this:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   module list            # is a cmake module already loaded?
-   module avail           # is a cmake module available?
+   module list            # is a module for cmake already loaded?
+   module avail           # is a module for cmake available?
    module load cmake3     # load cmake module with appropriate name
 
 Most Linux distributions offer pre-compiled cmake packages through
@@ -238,8 +238,3 @@ enough version, you can download the latest version at
 `https://cmake.org/download/ <https://cmake.org/download/>`_.
 Instructions on how to install it on various platforms can be found
 `on this page <https://cmake.org/install/>`_.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_development.rst

@@ -18,14 +18,14 @@ generated by the CMake build. To enable a more verbose output during
 compilation you can use the following option.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
 
 Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make VERBOSE=1
 
@@ -48,7 +48,7 @@ it. Please note that they come with a performance hit. However, they are
 usually faster than using tools like Valgrind.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
    -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
@@ -72,7 +72,7 @@ developers can run the tests directly on their workstation.
    this is incomplete and only represents a small subset of tests that we run
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
    -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
@@ -81,7 +81,7 @@ developers can run the tests directly on their workstation.
 If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make test
 
@@ -93,14 +93,14 @@ You can also collect code coverage metrics while running the tests by enabling
 coverage support during building.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
 
 This will also add the following targets to generate coverage reports after running the LAMMPS executable:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make test               # run tests first!
    make gen_coverage_html  # generate coverage report in HTML format
@@ -109,12 +109,6 @@ This will also add the following targets to generate coverage reports after runn
 These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    pip install git+https://github.com/gcovr/gcovr.git
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_extras.rst

@@ -5,10 +5,15 @@ When building with some packages, additional steps may be required,
 in addition to:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   -D PKG_NAME=yes    # CMake
-   make yes-name      # make
+   $ cmake -D PKG_NAME=yes
+
+or
+
+.. code-block:: bash
+
+   $ make yes-name
 
 as described on the :doc:`Build\_package <Build_package>` doc page.
 
@@ -20,18 +25,35 @@ You may need to tell LAMMPS where it is found on your system.
 
 This is the list of packages that may require additional steps.
 
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+.. table_from_list::
+   :columns: 6
 
+   * :ref:`COMPRESS <compress>`
+   * :ref:`GPU <gpu>`
+   * :ref:`KIM <kim>`
+   * :ref:`KOKKOS <kokkos>`
+   * :ref:`LATTE <latte>`
+   * :ref:`MESSAGE <message>`
+   * :ref:`MSCG <mscg>`
+   * :ref:`OPT <opt>`
+   * :ref:`POEMS <poems>`
+   * :ref:`PYTHON <python>`
+   * :ref:`VORONOI <voronoi>`
+   * :ref:`USER-ADIOS <user-adios>`
+   * :ref:`USER-ATC <user-atc>`
+   * :ref:`USER-AWPMD <user-awpmd>`
+   * :ref:`USER-COLVARS <user-colvars>`
+   * :ref:`USER-H5MD <user-h5md>`
+   * :ref:`USER-INTEL <user-intel>`
+   * :ref:`USER-MOLFILE <user-molfile>`
+   * :ref:`USER-NETCDF <user-netcdf>`
+   * :ref:`USER-PLUMED <user-plumed>`
+   * :ref:`USER-OMP <user-omp>`
+   * :ref:`USER-QMMM <user-qmmm>`
+   * :ref:`USER-QUIP <user-quip>`
+   * :ref:`USER-SCAFACOS <user-scafacos>`
+   * :ref:`USER-SMD <user-smd>`
+   * :ref:`USER-VTK <user-vtk>`   
 
 ----------
 
@@ -49,15 +71,15 @@ available on your system.
 If CMake cannot find the library, you can set these variables:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
    -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
 
 **Traditional make**\ :
 
-If make cannot find the library, you can edit the
-lib/compress/Makefile.lammps file to specify the paths and library
+If make cannot find the library, you can edit the file
+lib/compress/Makefile.lammps to specify the paths and library
 name.
 
 
@@ -75,7 +97,7 @@ which GPU hardware to build for.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D GPU_API=value          # value = opencl (default) or cuda
    -D GPU_PREC=value         # precision setting
@@ -125,12 +147,12 @@ using a command like these, which simply invoke the lib/gpu/Install.py
 script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-gpu               # print help message
-   make lib-gpu args="-b"     # build GPU library with default Makefile.linux
-   make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
-   make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  $ make lib-gpu               # print help message
+  $ make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+  $ make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+  $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
 
 Note that this procedure starts with a Makefile.machine in lib/gpu, as
 specified by the "-m" switch.  For your convenience, machine makefiles
@@ -177,11 +199,12 @@ KIM package
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>`
+use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+web page to
 learn how to install a pre-build binary of the OpenKIM Repository of Models.
 See the list of all KIM models here: https://openkim.org/browse/models
 
@@ -192,15 +215,35 @@ minutes to hours) to build.  Of course you only need to do that once.)
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
+   -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
+   -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
 
 If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
+*For using OpenKIM web queries in LAMMPS*\ :
+
+If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
+libcurl calls within the KIM web query display a lot of information about
+libcurl operations. You hardly ever want this set in production use, you will
+almost always want this when you debug/report problems.
+
+The libcurl performs peer SSL certificate verification by default. This
+verification is done using a CA certificate store that the SSL library can
+use to make sure the peer's server certificate is valid. If SSL reports an
+error ("certificate verify failed") during the handshake and thus refuses
+further communication with that server, you can set LMP\_NO\_SSL\_CHECK.
+If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection
+succeeds regardless of the names in the certificate. This option is insecure.
+As an alternative, you can specify your own CA cert path by setting the
+environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the
+KIM web query would get this value from the environmental variable.
+
 **Traditional make**\ :
 
 You can download and build the KIM library manually if you prefer;
@@ -209,16 +252,23 @@ step from the lammps/src dir, using a command like these, which simply
 invoke the lib/kim/Install.py script with the specified args.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-kim              # print help message
-   make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-   make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-   make lib-kim args="-b -a everything"     # install KIM API lib with all models
-   make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-   make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
-   make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+  $ make lib-kim              # print help message
+  $ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+  $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+  $ make lib-kim args="-b -a everything"     # install KIM API lib with all models
+  $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+  $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+  $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
 
+Settings for OpenKIM web queries discussed above need to be applied by adding
+them to the LMP\_INC variable through editing the Makefile.machine you are
+using.  For example:
+
+.. code-block:: make
+
+   LMP_INC =       -DLMP_NO_SSL_CHECK
 
 ----------
 
@@ -267,7 +317,7 @@ case-sensitive values, e.g. BDW, not bdw.
 For multicore CPUs using OpenMP, set these 2 variables.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D KOKKOS_ARCH=archCPU         # archCPU = CPU from list above
    -D KOKKOS_ENABLE_OPENMP=yes
@@ -275,7 +325,7 @@ For multicore CPUs using OpenMP, set these 2 variables.
 For Intel KNLs using OpenMP, set these 2 variables:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D KOKKOS_ARCH=KNL
    -D KOKKOS_ENABLE_OPENMP=yes
@@ -283,7 +333,7 @@ For Intel KNLs using OpenMP, set these 2 variables:
 For NVIDIA GPUs using CUDA, set these 4 variables:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU
                                       # archGPU = GPU from list above
@@ -296,7 +346,7 @@ Kokkos library: lib/kokkos/bin/nvcc\_wrapper.  The setting should
 include the full path name to the wrapper, e.g.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper
 
@@ -309,7 +359,7 @@ src/MAKE/OPTIONS/Makefile.kokkos\* files for examples.
 For multicore CPUs using OpenMP:
 
 
-.. parsed-literal::
+.. code-block:: make
 
    KOKKOS_DEVICES = OpenMP
    KOKKOS_ARCH = archCPU      # archCPU = CPU from list above
@@ -317,7 +367,7 @@ For multicore CPUs using OpenMP:
 For Intel KNLs using OpenMP:
 
 
-.. parsed-literal::
+.. code-block:: make
 
    KOKKOS_DEVICES = OpenMP
    KOKKOS_ARCH = KNL
@@ -325,20 +375,22 @@ For Intel KNLs using OpenMP:
 For NVIDIA GPUs using CUDA:
 
 
-.. parsed-literal::
+.. code-block:: make
 
    KOKKOS_DEVICES = Cuda
    KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU
                                     # archGPU = GPU from list above
+   FFT_INC = -DFFT_CUFFT            # enable use of cuFFT (optional)
+   FFT_LIB = -lcufft                # link to cuFFT library
 
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx.  The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
+For GPUs, you also need the following 2 lines in your Makefile.machine
+before the CC line is defined, in this case for use with OpenMPI mpicxx.
+The 2 lines define a nvcc wrapper compiler, which will use nvcc for
 compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
 files.
 
 
-.. parsed-literal::
+.. code-block:: make
 
    KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
    export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
@@ -359,7 +411,7 @@ library.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
    -D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location)
@@ -379,12 +431,12 @@ simply invokes the lib/latte/Install.py script with the specified
 args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-latte                          # print help message
-   make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
-   make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
-   make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
+  $ make lib-latte                          # print help message
+  $ make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+  $ make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+  $ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
                                            #   copy Makefile.lammps.gfortran to Makefile.lammps
 
 Note that 3 symbolic (soft) links, "includelink" and "liblink" and
@@ -409,7 +461,7 @@ be installed on your system.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
    -D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
@@ -424,11 +476,11 @@ one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/message/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-message               # print help message
-   make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
-   make lib-message args="-s"     # build as serial lib with no ZMQ support
+  $ make lib-message               # print help message
+  $ make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
+  $ make lib-message args="-s"     # build as serial lib with no ZMQ support
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an
@@ -453,7 +505,7 @@ lib/mscg/README and MSCG/Install files for more details.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
    -D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location)
@@ -474,14 +526,14 @@ step from the lammps/src dir, using a command like these, which simply
 invoke the lib/mscg/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-mscg             # print help message
-   make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+  $ make lib-mscg             # print help message
+  $ make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
                                        # with the settings compatible with "make serial"
-   make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+  $ make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
                                        # with the settings compatible with "make mpi"
-   make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
+  $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink", will
 be created in lib/mscg to point to the MS-CG src/installation dir.
@@ -530,12 +582,12 @@ dir, using a command like these, which simply invoke the
 lib/poems/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-poems                   # print help message
-   make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-   make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-   make lib-poems args="-m icc"     # build with Intel icc compiler
+  $ make lib-poems                   # print help message
+  $ make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+  $ make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+  $ make lib-poems args="-m icc"     # build with Intel icc compiler
 
 The build should produce two files: lib/poems/libpoems.a and
 lib/poems/Makefile.lammps.  The latter is copied from an existing
@@ -562,7 +614,7 @@ lib/python/README for more details.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D PYTHON_EXECUTABLE=path   # path to Python executable to use
 
@@ -598,7 +650,7 @@ To build with this package, you must download and build the `Voro++ library <vor
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
    -D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
@@ -620,12 +672,12 @@ simply invoke the lib/voronoi/Install.py script with the specified
 args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-voronoi                          # print help message
-   make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-   make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-   make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+  $ make lib-voronoi                          # print help message
+  $ make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+  $ make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+  $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink", are
 created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
@@ -651,7 +703,7 @@ installation and the instructions below are followed for the respective build sy
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
    -D PKG_USER-ADIOS=yes
@@ -661,16 +713,16 @@ installation and the instructions below are followed for the respective build sy
 Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make yes-user-adios
+  $ make yes-user-adios
 
 otherwise, set ADIOS2\_DIR environment variable when turning on the package:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
+  $ ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
 
 
 ----------
@@ -697,12 +749,12 @@ dir, using a command like these, which simply invoke the
 lib/atc/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-atc                      # print help message
-   make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-   make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-   make lib-atc args="-m icc"        # build with Intel icc compiler
+  $ make lib-atc                      # print help message
+  $ make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+  $ make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+  $ make lib-atc args="-m icc"        # build with Intel icc compiler
 
 The build should produce two files: lib/atc/libatc.a and
 lib/atc/Makefile.lammps.  The latter is copied from an existing
@@ -719,12 +771,12 @@ lib/linalg.  In the latter case you also need to build the library in
 lib/linalg with a command like these:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-linalg                     # print help message
-   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-   make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-   make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+  $ make lib-linalg                     # print help message
+  $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+  $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+  $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
 
 ----------
@@ -748,12 +800,12 @@ dir, using a command like these, which simply invoke the
 lib/awpmd/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-awpmd                   # print help message
-   make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-   make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-   make lib-awpmd args="-m icc"     # build with Intel icc compiler
+  $ make lib-awpmd                   # print help message
+  $ make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+  $ make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+  $ make lib-awpmd args="-m icc"     # build with Intel icc compiler
 
 The build should produce two files: lib/awpmd/libawpmd.a and
 lib/awpmd/Makefile.lammps.  The latter is copied from an existing
@@ -770,12 +822,12 @@ provided in lib/linalg.  In the latter case you also need to build the
 library in lib/linalg with a command like these:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-linalg                     # print help message
-   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-   make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-   make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+  $ make lib-linalg                     # print help message
+  $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+  $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+  $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
 
 ----------
@@ -822,12 +874,12 @@ command like these, which simply invoke the lib/colvars/Install.py script with
 the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-colvars                      # print help message
-   make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-   make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-   make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+  $ make lib-colvars                      # print help message
+  $ make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+  $ make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+  $ make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
 
 The "machine" argument of the "-m" flag is used to find a Makefile.machine to
 use as build recipe.  If it does not already exist in lib/colvars, it will be
@@ -836,8 +888,10 @@ core LAMMPS makefiles.
 
 Optional flags may be specified as environment variables:
 
-COLVARS\_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
-COLVARS\_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+.. code-block:: bash
+
+    $ COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+    $ COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
 
 The build should produce two files: the library lib/colvars/libcolvars.a
 (which also includes Lepton objects if enabled) and the specification file
@@ -858,6 +912,9 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
+The USER-PLUMED package has been tested to work with Plumed versions
+2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
+with a different version of the Plumed kernel.
 
 
 PLUMED can be linked into MD codes in three different modes: static,
@@ -896,7 +953,7 @@ your environment.  There are then two additional commands that control
 the manner in which PLUMED is obtained and linked into LAMMPS.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
    -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime
@@ -932,12 +989,12 @@ Download/compilation/configuration of the plumed library can be done
 from the src folder through the following make args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-plumed                         # print help message
-   make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
-   make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
-   make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+  $ make lib-plumed                         # print help message
+  $ make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+  $ make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+  $ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
                                                    # /usr/local and use shared linkage mode
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink" are
@@ -948,10 +1005,10 @@ mode. After this step is completed, you can install the USER-PLUMED
 package and compile LAMMPS in the usual manner:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make yes-user-plumed
-   make machine
+  $ make yes-user-plumed
+  $ make machine
 
 Once this compilation completes you should be able to run LAMMPS in the
 usual way.  For shared linkage mode, libplumed.so must be found by the
@@ -999,10 +1056,10 @@ dir, using a command like these, which simply invoke the
 lib/h5md/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-h5md                     # print help message
-   make lib-h5md args="-m h5cc"      # build with h5cc compiler
+  $ make lib-h5md                     # print help message
+  $ make lib-h5md args="-m h5cc"      # build with h5cc compiler
 
 The build should produce two files: lib/h5md/libch5md.a and
 lib/h5md/Makefile.lammps.  The latter is copied from an existing
@@ -1030,7 +1087,7 @@ on the :doc:`Speed intel <Speed_intel>` doc page.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D INTEL_ARCH=value     # value = cpu (default) or knl
    -D INTEL_LRT_MODE=value # value = threads, none, or c++11
@@ -1057,7 +1114,7 @@ additional information.
 For CPUs:
 
 
-.. parsed-literal::
+.. code-block:: make
 
    OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
    CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
@@ -1067,7 +1124,7 @@ For CPUs:
 For KNLs:
 
 
-.. parsed-literal::
+.. code-block:: make
 
    OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
    CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
@@ -1086,7 +1143,7 @@ USER-MOLFILE package
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
    -D PKG_USER-MOLFILE=yes
@@ -1166,9 +1223,9 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
 
 .. parsed-literal::
 
-   CCFLAGS: -fopenmp               # for GNU Compilers
+   CCFLAGS: -fopenmp               # for GNU and Clang Compilers 
    CCFLAGS: -qopenmp -restrict     # for Intel compilers on Linux
-   LINKFLAGS: -fopenmp             # for GNU Compilers
+   LINKFLAGS: -fopenmp             # for GNU and Clang Compilers
    LINKFLAGS: -qopenmp             # for Intel compilers on Linux
 
 For other platforms and compilers, please consult the documentation
@@ -1184,25 +1241,40 @@ how to address compatibility :ref:`issues with the 'default(none)' directive <de
 USER-QMMM package
 ---------------------------------
 
-.. note::
-
-   The LAMMPS executable these steps produce is not yet functional
-   for a QM/MM simulation.  You must also build Quantum ESPRESSO and
-   create a new executable (pwqmmm.x) which links LAMMPS and Quantum
-   ESPRESSO together.  These are steps 3 and 4 described in the
-   lib/qmmm/README file.  Unfortunately, the Quantum ESPRESSO developers
-   have been breaking the interface that the QM/MM code in LAMMPS is using,
-   so that currently (Summer 2018) using this feature requires either
-   correcting the library interface feature in recent Quantum ESPRESSO
-   releases, or using an outdated version of QE. The last version of
-   Quantum ESPRESSO known to work with this QM/MM interface was version
-   5.4.1 from 2016.
+For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
+need to build LAMMPS as a library.  A LAMMPS executable with fix qmmm
+included can be built, but will not be able to do a QM/MM simulation
+on as such.  You must also build a QM code - currently only Quantum
+ESPRESSO (QE) is supported - and create a new executable which links
+LAMMPS and the QM code together.  Details are given in the
+lib/qmmm/README file.  It is also recommended to read the instructions
+for :doc:`linking with LAMMPS as a library <Build_link>` for
+background information.  This requires compatible Quantum Espresso
+and LAMMPS versions.  The current interface and makefiles have last
+been verified to work in February 2020 with Quantum Espresso versions
+6.3 to 6.5.
 
 **CMake build**\ :
 
-The CMake build system currently does not support building the full
-QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
-You must use the traditional make build for this package.
+When using CMake, building a LAMMPS library is required and it is
+recommended to build a shared library, since any libraries built from
+the sources in the *lib* folder (including the essential libqmmm.a)
+are not included in the static LAMMPS library and (currently) not
+installed, while their code is included in the shared LAMMPS library.
+Thus a typical command line to configure building LAMMPS for USER-QMMM
+would be:
+
+.. code-block:: bash
+
+    cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
+            -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
+
+After completing the LAMMPS build and also configuring and compiling
+Quantum ESPRESSO with external library support (via "make couple"),
+go back to the lib/qmmm folder and follow the instructions on the
+README file to build the combined LAMMPS/QE QM/MM executable
+(pwqmmm.x) in the lib/qmmm folder.  You need to make certain, that
+
 
 **Traditional make**\ :
 
@@ -1213,12 +1285,12 @@ lammps/src dir, using a command like these, which simply invoke the
 lib/qmmm/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-qmmm                      # print help message
-   make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
-   make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
-   make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+  $ make lib-qmmm                      # print help message
+  $ make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+  $ make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+  $ make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
 
 The build should produce two files: lib/qmmm/libqmmm.a and
 lib/qmmm/Makefile.lammps.  The latter is copied from an existing
@@ -1230,10 +1302,10 @@ a corresponding Makefile.lammps.machine file.
 
 You can then install QMMM package and build LAMMPS in the usual
 manner.  After completing the LAMMPS build and compiling Quantum
-ESPRESSO with external library support, go back to the lib/qmmm folder
-and follow the instructions on the README file to build the combined
-LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder.
-
+ESPRESSO with external library support (via "make couple"), go back to
+the lib/qmmm folder and follow the instructions in the README file to
+build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
+lib/qmmm folder.
 
 ----------
 
@@ -1252,7 +1324,7 @@ lib/quip/README file for details on how to do this.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
@@ -1288,7 +1360,7 @@ To build with this package, you must download and build the `ScaFaCoS Coulomb so
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes
    -D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location)
@@ -1333,7 +1405,7 @@ Eigen3 is a template library, so you do not need to build it.
 **CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
    -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
@@ -1351,11 +1423,11 @@ the lammps/src dir, using a command like these, which simply invoke
 the lib/smd/Install.py script with the specified args:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
-   make lib-smd                         # print help message
-   make lib-smd args="-b"               # download to lib/smd/eigen3
-   make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+  $ make lib-smd                         # print help message
+  $ make lib-smd args="-b"               # download to lib/smd/eigen3
+  $ make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
 
 Note that a symbolic (soft) link named "includelink" is created in
 lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
@@ -1392,8 +1464,3 @@ the settings are not valid for your system, check if one of the other
 lib/vtk/Makefile.lammps.\* files is compatible and copy it to
 Makefile.lammps.  If none of the provided files work, you will need to
 edit the Makefile.lammps file.  See lib/vtk/README for details.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_link.rst

@@ -3,62 +3,228 @@ Link LAMMPS as a library to another code
 
 LAMMPS can be used as a library by another application, including
 Python scripts.  The files src/library.cpp and library.h define the
-C-style API for using LAMMPS as a library.  See the :doc:`Howto library <Howto_library>` doc page for a description of the
-interface and how to extend it for your needs.
+C-style API for using LAMMPS as a library.  See the :doc:`Howto
+library <Howto_library>` doc page for a description of the interface
+and how to extend it for your needs.
 
 The :doc:`Build basics <Build_basics>` doc page explains how to build
 LAMMPS as either a shared or static library.  This results in one of
 these 2 files:
 
-liblammps.so      # shared library
-liblammps.a       # static library
+.. parsed-literal::
 
+   liblammps.so      # shared library
+   liblammps.a       # static library
+
+.. note::
+
+   Care should be taken to use the same MPI library for the calling
+   code and the LAMMPS library.  The library.h file includes mpi.h and
+   uses definitions from it so those need to be available and
+   consistent.  When LAMMPS is compiled with the MPI STUBS library,
+   then its mpi.h file needs to be included.  While it is technically
+   possible to use a full MPI library in the calling code and link to
+   a serial LAMMPS library compiled with MPI STUBS, it is recommended
+   to use the *same* MPI library for both, and then use MPI\_Comm\_split()
+   in the calling code to pass a suitable communicator with a subset
+   of MPI ranks to the function creating the LAMMPS instance.
 
 ----------
 
 
 **Link with LAMMPS as a static library**\ :
 
-The calling application can link to LAMMPS as a static library with a
-link command like this:
+The calling application can link to LAMMPS as a static library with
+compilation and link commands as in the examples shown below.  These
+are examples for a code written in C in the file *caller.c*.
+The benefit of linking to a static library is, that the resulting
+executable is independent of that library since all required
+executable code from the library is copied into the calling executable.
 
-g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+*CMake build*\ :
 
-The -L argument is the path to where the liblammps.a file is.  The
--llammps argument is shorthand for the file liblammps.a.
+This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
+and installed with "make install" and the PKG\_CONFIG\_PATH environment
+variable updated to include the *liblammps.pc* file installed into the
+configured destination folder, if needed.  The commands to compile and
+link the coupled executable are then:
 
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+
+
+*Traditional make*\ :
+
+This assumes that LAMMPS has been compiled in the folder
+"${HOME}/lammps/src" with "make mode=lib mpi". The commands to compile
+and link the coupled executable are then:
+
+.. code-block:: bash
+
+   mpicc -c -O -I${HOME}/lammps/src caller.c
+   mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps
+
+The *-I* argument is the path to the location of the *library.h*
+header file containing the interface to the LAMMPS C-style library
+interface.  The *-L* argument is the path to where the *liblammps.a*
+file is located.  The *-llammps* argument is shorthand for telling the
+compiler to link the file *liblammps.a*\ .
+
+However, it is only as simple as shown above for the case of a plain
+LAMMPS library without any optional packages that depend on libraries
+(bundled or external).  Otherwise, you need to include all flags,
+libraries, and paths for the coupled executable, that are also
+required to link the LAMMPS executable.
+
+*CMake build*\ :
+
+When using CMake, additional libraries with sources in the lib folder
+are built, but not included in liblammps.a and (currently) not
+installed with "make install" and not included in the *pkgconfig*
+configuration file.  They can be found in the top level build folder,
+but you have to determine the necessary link flags manually.  It is
+therefore recommended to either use the traditional make procedure to
+build and link with a static library or build and link with a shared
+library instead.
+
+*Traditional make*\ :
+
+After you have compiled a static LAMMPS library using the conventional
+build system for example with "make mode=lib serial". And you also
+have installed the POEMS package after building its bundled library in
+lib/poems. Then the commands to build and link the coupled executable
+change to:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
+     -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs 
+
+Note, that you need to link with "g++" instead of "gcc", since LAMMPS
+is C++ code.  You can display the currently applied settings for building
+LAMMPS for the "serial" machine target by using the command:
+
+.. code-block:: bash
+
+   make mode=print serial
+
+Which should output something like:
+
+.. code-block:: bash
+
+   # Compiler: 
+   CXX=g++
+   # Linker: 
+   LD=g++
+   # Compilation: 
+   CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS
+   # Linking: 
+   LDFLAGS=-g -O
+   # Libraries: 
+   LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs
+
+From this you can gather the necessary paths and flags.  With
+makefiles for other *machine* configurations you need to do the
+equivalent and replace "serial" with the corresponding *machine* name
+of the makefile.
 
 ----------
 
-
 **Link with LAMMPS as a shared library**\ :
 
-If you wish to link to liblammps.so, the operating system finds shared
-libraries to load at run-time using the environment variable
-LD\_LIBRARY\_PATH.  To enable this you can do one of two things:
+When linking to LAMMPS built as a shared library, the situation
+becomes much simpler, as all dependent libraries and objects are
+included in the shared library, which is - technically speaking -
+effectively a regular LAMMPS executable that is missing the `main()`
+function.  Thus those libraries need not to be specified when linking
+the calling executable.  Only the *-I* flags are needed.  So the
+example case from above of the serial version static LAMMPS library
+with the POEMS package installed becomes:
 
-(1) Copy the liblammps.so file to a location the system can find it,
-such as /usr/local/lib.  I.e. a directory already listed in your
-LD\_LIBRARY\_PATH variable.  You can type
+*CMake build*\ :
 
+The commands with a shared LAMMPS library compiled with the CMake
+build process are the same as for the static library.
 
-.. parsed-literal::
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf --libs)
+
+*Traditional make*\ :
+
+The commands with a shared LAMMPS library compiled with the
+traditional make build using "make mode=shlib serial" becomes:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/src -llammps
+
+*Locating liblammps.so at runtime*\ :
+   
+However, now the `liblammps.so` file is required at runtime and needs
+to be in a folder, where the shared linker program of the operating
+system can find it.  This would be either a folder like "/usr/local/lib64"
+or "${HOME}/.local/lib64" or a folder pointed to by the LD\_LIBRARY\_PATH
+environment variable. You can type
+
+.. code-block:: bash
 
    printenv LD_LIBRARY_PATH
 
 to see what directories are in that list.
 
-(2) Add the LAMMPS src directory (or the directory you perform CMake
-build in) to your LD\_LIBRARY\_PATH, so that the current version of the
-shared library is always available to programs that use it.
+Or you can add the LAMMPS src directory (or the directory you performed
+a CMake style build in) to your LD\_LIBRARY\_PATH, so that the current
+version of the shared library is always available to programs that use it.
 
-For the csh or tcsh shells, you would add something like this to your
-~/.cshrc file:
+For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
+would add something like this to your ~/.profile file:
+
+.. code-block:: bash
+
+   LD_LIBRARY_PATH ${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/lammps/src
+   export LD_LIBRARY_PATH
+
+For the csh or tcsh shells, you would equivalently add something like this
+to your ~/.cshrc file:
 
 
-.. parsed-literal::
+.. code-block:: csh
 
-   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
+
+You can verify whether all required shared libraries are found with the
+`ldd` tool.  Example:
+
+.. code-block:: bash
+
+   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller 
+        linux-vdso.so.1 (0x00007ffe729e0000)
+        liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
+        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
+        libm.so.6 => /lib64/libm.so.6 (0x00007fc91b83e000)
+        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc91b824000)
+        libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
+
+
+If a required library is missing, you would get a 'not found' entry:
+
+.. code-block:: bash
+
+   $  ldd caller 
+        linux-vdso.so.1 (0x00007ffd672fe000)
+        liblammps.so => not found
+        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)
+        libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb7c7d40000)
+        libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fb7c7d26000)
+        libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
 
 
 ----------
@@ -67,25 +233,22 @@ For the csh or tcsh shells, you would add something like this to your
 **Calling the LAMMPS library**\ :
 
 Either flavor of library (static or shared) allows one or more LAMMPS
-objects to be instantiated from the calling program.
+objects to be instantiated from the calling program. When used from a
+C++ program, most of the symbols and functions in LAMMPS are wrapped
+in a LAMMPS\_NS namespace; you can safely use any of its classes and
+methods from within the calling code, as needed, and you will not incur
+conflicts with functions and variables in your code that share the name.
+This, however, does not extend to all additional libraries bundled with
+LAMMPS in the lib folder and some of the low-level code of some packages.
 
-When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
-namespace; you can safely use any of its classes and methods from
-within the calling code, as needed.
-
-When used from a C or Fortran program, the library has a simple
+To be compatible with C, Fortran, Python programs, the library has a simple
 C-style interface, provided in src/library.cpp and src/library.h.
 
 See the :doc:`Python library <Python_library>` doc page for a
 description of the Python interface to LAMMPS, which wraps the C-style
-interface.
+interface from a shared library through the ctypes python module.
 
 See the sample codes in examples/COUPLE/simple for examples of C++ and
 C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the :doc:`Howto couple <Howto_couple>` doc page.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_make.rst

@@ -7,18 +7,33 @@ src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
 below).  It can include various options for customizing your LAMMPS
 build with a number of global compilation options and features.
 
+Those makefiles are written for and tested with GNU make and may not
+be compatible with other make programs.  In most cases, if the "make"
+program is not GNU make, then there will be a GNU make program
+available under the name "gmake".  If GNU make or a compatible make is
+not available, you may have to first install it or switch to building
+with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
+make based build process and the scripts they are calling expect a few
+additional tools to be available and functioning.
+
+  * a Bourne shell compatible "Unix" shell program (often this is bash)
+  * a few shell utilities: ls, mv, ln, rm, grep, sed, tr, cat, touch, diff, dirname
+  * python (optional, required for "make lib-XXX" in the src folder)
+
 To include LAMMPS packages (i.e. optional commands and styles) you
-must install them first, as discussed on the :doc:`Build package <Build_package>` doc page.  If the packages require
-provided or external libraries, you must build those libraries before
-building LAMMPS.  Building :doc:`LAMMPS with CMake <Build_cmake>` can
-automate all of this for many types of machines, especially
-workstations, desktops and laptops, so we suggest you try it first.
+must enable them first, as discussed on the :doc:`Build package
+<Build_package>` doc page.  If a packages requires (provided or
+external) libraries, you must configure and build those libraries
+**before** building LAMMPS itself and especially **before** enabling
+such a package with "make yes-<package>".  Building :doc:`LAMMPS
+with CMake <Build_cmake>` can automate much of this for many types of
+machines, especially workstations, desktops, and laptops, so we suggest
+you try it first when building LAMMPS in those cases.
 
-These commands perform a default LAMMPS build, producing the LAMMPS
-executable lmp\_serial or lmp\_mpi in lammps/src:
+The commands below perform a default LAMMPS build, producing the LAMMPS
+executable lmp\_serial and lmp\_mpi in lammps/src:
 
-
-.. parsed-literal::
+.. code-block:: bash
 
    cd lammps/src
    make serial     # build a serial LAMMPS executable
@@ -42,18 +57,21 @@ re-compiled.
 
 .. note::
 
-   When you build LAMMPS for the first time, a long list of \*.d
-   files will be printed out rapidly.  This is not an error; it is the
-   Makefile doing its normal creation of dependencies.
-
+   Before the actual compilation starts, LAMMPS will perform several
+   steps to collect information from the configuration and setup that
+   is then embedded into the executable.  When you build LAMMPS for
+   the first time, it will also compile a tool to quickly assemble
+   a list of dependencies, that are required for the make program to
+   correctly detect which parts need to be recompiled after changes
+   were made to the sources.
 
 ----------
 
-
-The lammps/src/MAKE tree contains all the Makefile.machine files
-included in the LAMMPS distribution.  Typing "make machine" uses
-Makefile.machine.  Thus the "make serial" or "make mpi" lines above
-use Makefile.serial and Makefile.mpi.  Others are in these dirs:
+The lammps/src/MAKE tree contains the Makefile.machine files included
+in the LAMMPS distribution.  Typing "make machine" uses
+*Makefile.machine*\ .  Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi, respectively.  Other makefiles
+are in these directories:
 
 
 .. parsed-literal::
@@ -64,7 +82,7 @@ use Makefile.serial and Makefile.mpi.  Others are in these dirs:
 
 Typing "make" lists all the available Makefile.machine files.  A file
 with the same name can appear in multiple folders (not a good idea).
-The order the dirs are searched is as follows: src/MAKE/MINE,
+The order the directories are searched is as follows: src/MAKE/MINE,
 src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
 to a customized file you put in src/MAKE/MINE.
 
@@ -76,7 +94,7 @@ compilers, OS configurations, and LAMMPS itself keep changing, their
 settings may become outdated:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make mac             # build serial LAMMPS on a Mac
    make mac_mpi         # build parallel LAMMPS on a Mac
@@ -87,8 +105,3 @@ settings may become outdated:
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_package.rst

@@ -14,10 +14,13 @@ package.  In general there is no need to include a package if you
 never plan to use its features.
 
 If you get a run-time error that a LAMMPS command or style is
-"Unknown", it is often because the command is contained in a package,
-and your build did not include that package.  Running LAMMPS with the
-:doc:`-h command-line switch <Run_options>` will print all the included
-packages and commands for that executable.
+"unknown", it is often because the command is contained in a package,
+and your build did not include that package.  If the command or style
+*is* available in a package included in the LAMMPS distribution,
+the error message will indicate which package would be needed.
+Running LAMMPS with the :doc:`-h command-line switch <Run_options>`
+will print *all* optional commands and packages that were enabled
+when building that executable.
 
 For the majority of packages, if you follow the single step below to
 include it, you can then build LAMMPS exactly the same as you would
@@ -42,17 +45,17 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.
 
-**CMake variables**\ :
+**CMake build**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D PKG_NAME=value          # yes or no (default)
 
 Examples:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D PKG_MANYBODY=yes
    -D PKG_USER-INTEL=yes
@@ -74,7 +77,7 @@ once with CMake.
 **Traditional make**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    cd lammps/src
    make ps                    # check which packages are currently installed
@@ -85,7 +88,7 @@ once with CMake.
 Examples:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make no-rigid
    make yes-user-intel
@@ -119,7 +122,7 @@ are already included.  Likewise, if a package is excluded, other files
 dependent on that package are also excluded.
 
 When you download a LAMMPS tarball or download LAMMPS source files
-from the Git or SVN repositories, no packages are pre-installed in the
+from the git repository, no packages are pre-installed in the
 src directory.
 
 .. note::
@@ -136,9 +139,10 @@ src directory.
 **CMake shortcuts for installing many packages**\ :
 
 Instead of specifying all the CMake options via the command-line,
-CMake allows initializing the variable cache using script files. These
-are regular CMake files which can manipulate and set variables, and
-can also contain control flow constructs.
+CMake allows initializing its settings cache using script files.
+These are regular CMake files which can manipulate and set CMake
+variables (which represent selected options), and can also contain
+control flow constructs for more complex operations.
 
 LAMMPS includes several of these files to define configuration
 "presets", similar to the options that exist for the Make based
@@ -146,25 +150,19 @@ system. Using these files you can enable/disable portions of the
 available packages in LAMMPS. If you need a custom preset you can take
 one of them as a starting point and customize it to your needs.
 
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/all\_on.cmake  [OPTIONS] ../cmake | enable all packages                                       |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages                                      |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  | enable just a few core packages                           |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  | enable most common packages                               |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  | disable packages that do require extra libraries or tools |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  | change settings to use the Clang compilers by default     |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake    | enable all packages compatible with MinGW compilers       |
-+-------------------------------------------------------------+-----------------------------------------------------------+
+.. code-block:: bash
+
+    cmake -C ../cmake/presets/all_on.cmake  [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake  # disable all packages
+    cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most common packages
+    cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/mingw.cmake   [OPTIONS] ../cmake  # enable all packages compatible with MinGW compilers
 
 .. note::
 
-   Running cmake this way manipulates the variable cache in your
+   Running cmake this way manipulates the CMake settings cache in your
    current build directory. You can combine multiple presets and options
    in a single cmake run, or change settings incrementally by running
    cmake with new flags.
@@ -172,7 +170,7 @@ one of them as a starting point and customize it to your needs.
 **Example:**
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    # build LAMMPS with most commonly used packages, but then remove
    # those requiring additional library or tools, but still enable
@@ -200,37 +198,30 @@ Just type "make" in lammps/src to see a one-line summary.
 
 These commands install/un-install sets of packages:
 
-+-----------------------------------+-----------------------------------------------------+
-| make yes-all                      | install all packages                                |
-+-----------------------------------+-----------------------------------------------------+
-| make no-all                       | un-install all packages                             |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-standard or make yes-std | install standard packages                           |
-+-----------------------------------+-----------------------------------------------------+
-| make no-standard or make no-std   | un-install standard packages                        |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-user                     | install user packages                               |
-+-----------------------------------+-----------------------------------------------------+
-| make no-user                      | un-install user packages                            |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-lib                      | install packages that require extra libraries       |
-+-----------------------------------+-----------------------------------------------------+
-| make no-lib                       | un-install packages that require extra libraries    |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-ext                      | install packages that require external libraries    |
-+-----------------------------------+-----------------------------------------------------+
-| make no-ext                       | un-install packages that require external libraries |
-+-----------------------------------+-----------------------------------------------------+
+.. code-block:: bash
+
+    make yes-all                        # install all packages
+    make no-all                         # uninstall all packages
+    make yes-standard or make yes-std   # install standard packages
+    make no-standard or make no-std     # uninstall standard packages
+    make yes-user                       # install user packages
+    make no-user                        # uninstall user packages
+    make yes-lib                        # install packages that require extra libraries
+    make no-lib                         # uninstall packages that require extra libraries
+    make yes-ext                        # install packages that require external libraries
+    make no-ext                         # uninstall packages that require external libraries
 
 which install/un-install various sets of packages.  Typing "make
 package" will list all the these commands.
 
 .. note::
 
-   Installing or un-installing a package works by simply copying
-   files back and forth between the main src directory and
-   sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
-   so that the files are included or excluded when LAMMPS is built.
+   Installing or un-installing a package for the make based build process
+   works by simply copying files back and forth between the main source
+   directory src and the sub-directories with the package name (e.g.
+   src/KSPACE, src/USER-ATC), so that the files are included or excluded
+   when LAMMPS is built.  Only source files in the src folder will be
+   compiled. 
 
 The following make commands help manage files that exist in both the
 src directory and in package sub-directories.  You do not normally
@@ -257,9 +248,4 @@ Type "make package-overwrite" to overwrite files in the package
 sub-directories with src files.
 
 Type "make package-diff" to list all differences between pairs of
-files in both the src dir and a package dir.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+files in both the source directory and the package directory.

doc/src/Build_settings.rst

@@ -4,16 +4,15 @@ Optional build settings
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
-| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
-| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
-| :ref:`Size of LAMMPS data types <size>`
-| :ref:`Read or write compressed files <gzip>`
-| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
-| :ref:`Memory allocation alignment <align>`
-| :ref:`Workaround for long long integers <longlong>`
-| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
-| 
+* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
+* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
+* :ref:`Size of LAMMPS data types <size>`
+* :ref:`Read or write compressed files <gzip>`
+* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
+* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
+* :ref:`Memory allocation alignment <align>`
+* :ref:`Workaround for long long integers <longlong>`
+* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library  
 
 
 ----------
@@ -21,41 +20,18 @@ explain how to do this for building both with CMake and make.
 
 .. _cxx11:
 
-C++11 standard compliance test
+C++11 standard compliance
 ------------------------------------------
 
 The LAMMPS developers plan to transition to make the C++11 standard the
 minimum requirement for compiling LAMMPS.  Currently this only applies to
 some packages like KOKKOS while the rest aims to be compatible with the C++98
 standard.  Most currently used compilers are compatible with C++11; some need
-to set extra flags to switch.  To determine the impact of requiring C++11,
-we have added a simple compliance test to the source code, that will cause
-the compilation to abort, if C++11 compliance is not available or enabled.
-To bypass this check, you need to change a setting in the makefile or
-when calling CMake.
+to set extra flags to enable C++11 compliance.  Example for GNU c++:
 
-**CMake variable**\ :
-
-
-.. parsed-literal::
-
-   -D DISABLE_CXX11_REQUIREMENT=yes
-
-You can set additional C++ compiler flags (beyond those selected by CMake)
-through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
-
-
-.. parsed-literal::
-
-   -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
-
-**Makefile.machine setting**\ :
-
-
-.. parsed-literal::
-
-   LMP_INC = -DLAMMPS_CXX98
+.. code-block:: make
 
+   CCFLAGS = -g -O3 -std=c++11
 
 ----------
 
@@ -66,7 +42,7 @@ FFT library
 ---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
-:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
@@ -74,7 +50,7 @@ LAMMPS can use them if they are available on your system.
 **CMake variables**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
    -D FFT_SINGLE=value       # yes or no (default), no = double precision
@@ -86,56 +62,71 @@ LAMMPS can use them if they are available on your system.
    an exception to the rule that all CMake variables can be specified
    with lower-case values.
 
-Usually these settings are all that is needed.  If CMake cannot find
-the FFT library, you can set these variables:
+Usually these settings are all that is needed.  If FFTW3 is selected,
+then CMake will try to detect, if threaded FFTW libraries are available
+and enable them by default.  This setting is independent of whether
+OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
+used.  If CMake cannot detect the FFT library, you can set these variables
+to assist:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
    -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
    -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
 **Makefile.machine settings**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                                  # default is KISS if not specified
    FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+   FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
    FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
 
 # default is FFT\_PACK\_ARRAY if not specified
 
 
-.. parsed-literal::
+.. code-block:: make
 
    FFT_INC =       -I/usr/local/include
    FFT_PATH =      -L/usr/local/lib
    FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
    FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
 As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
-make can find the FFT header and library files.  You must specify
-FFT\_LIB with the appropriate FFT libraries to include in the link.
+the compiler can find the FFT header and library files in its default search path.
+You must specify FFT\_LIB with the appropriate FFT libraries to include in the link.
 
 **CMake and make info**\ :
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
-distribution.  It is portable across all platforms.  Depending on the
-size of the FFTs and the number of processors used, the other
-libraries listed here can be faster.
+distribution.  It is portable across all platforms.  Depending on the size
+of the FFTs and the number of processors used, the other libraries listed
+here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
 per-timestep CPU cost, FFTs are only a portion of long-range
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
-to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command.  The :doc:`Run output <Run_output>`
-doc page gives more details.
+to the screen at the end of a run when using the
+:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+doc page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
+:doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
 platform and can be faster than the KISS FFT library.  You can
@@ -166,10 +157,10 @@ When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
-library libfftw3f.a
+library libfftw3f.a or libfftw3f.so.
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    make clean
    ./configure --enable-single; make; make install
@@ -197,14 +188,14 @@ adequate.
 **CMake variable**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
 
 **Makefile.machine setting**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
 
@@ -235,7 +226,7 @@ support 8-byte integers.  It allows for:
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
-:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+:doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Thus if you model a molecular system with
 more than 2 billion atoms, you need the "bigbig" setting.
@@ -275,21 +266,21 @@ following settings:
 **CMake variables**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D WITH_JPEG=value      # yes or no
-                             # default = yes if CMake finds JPEG files, else no
+                           # default = yes if CMake finds JPEG files, else no
    -D WITH_PNG=value       # yes or no
-                             # default = yes if CMake finds PNG and ZLIB files, else no
+                           # default = yes if CMake finds PNG and ZLIB files, else no
    -D WITH_FFMPEG=value    # yes or no
-                             # default = yes if CMake can find ffmpeg, else no
+                           # default = yes if CMake can find ffmpeg, else no
 
 Usually these settings are all that is needed.  If CMake cannot find
 the graphics header, library, executable files, you can set these
 variables:
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
    -D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
@@ -302,7 +293,7 @@ variables:
 **Makefile.machine settings**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_JPEG
    LMP_INC = -DLAMMPS_PNG
@@ -316,7 +307,7 @@ As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
 find the graphics header and library files.  You must specify JPG\_LIB
 with a list of graphics libraries to include in the link.  You must
 insure ffmpeg is in a directory where LAMMPS can find it at runtime,
-i.e. a dir in your PATH environment variable.
+that is a directory in your PATH environment variable.
 
 **CMake and make info**\ :
 
@@ -326,7 +317,7 @@ supports the "popen" function in the standard runtime library.
 .. note::
 
    On some clusters with high-speed networks, using the fork()
-   library calls (required by popen()) can interfere with the fast
+   library call (required by popen()) can interfere with the fast
    communication library and lead to simulations using ffmpeg to hang or
    crash.
 
@@ -341,12 +332,12 @@ Read or write compressed files
 
 If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
-:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 **CMake variables**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D WITH_GZIP=value       # yes or no
                             # default is yes if CMake can find gzip, else no
@@ -355,7 +346,7 @@ gzip compression by several LAMMPS commands, including
 **Makefile.machine setting**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_GZIP
 
@@ -368,7 +359,7 @@ found by LAMMPS during a run.
 .. note::
 
    On some clusters with high-speed networks, using the fork()
-   library calls (required by popen()) can interfere with the fast
+   library call (required by popen()) can interfere with the fast
    communication library and lead to simulations using compressed output
    or input to hang or crash. For selected operations, compressed file
    I/O is also available using a compression library instead, which is
@@ -395,7 +386,7 @@ aligned on 64-byte boundaries.
 **CMake variable**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
@@ -407,7 +398,7 @@ and this setting ignored.
 **Makefile.machine setting**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
 
@@ -434,14 +425,14 @@ those systems:
 **CMake variable**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
 
 **Makefile.machine setting**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
 
@@ -455,25 +446,21 @@ Exception handling when using 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 calling code.
 Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python.
+e.g. to Python. Of course the calling code has to be set up to
+*catch* exceptions from within LAMMPS.
 
 **CMake variable**\ :
 
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
 
 **Makefile.machine setting**\ :
 
 
-.. parsed-literal::
+.. code-block:: make
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -17,9 +17,9 @@ General remarks
 
 LAMMPS is developed and tested primarily on Linux machines.  The vast
 majority of HPC clusters and supercomputers today runs on Linux as well.
-Thus portability to other platforms is desired, but not always achieved.
+While portability to other platforms is desired, it is not always achieved.
 The LAMMPS developers strongly rely on LAMMPS users giving feedback and
-providing assistance in resolving portability issues. This particularly
+providing assistance in resolving portability issues. This is particularly
 true for compiling LAMMPS on Windows, since this platform has significant
 differences with some low-level functionality.
 
@@ -31,18 +31,20 @@ Running Linux on Windows
 So before trying to build LAMMPS on Windows, please consider if using
 the pre-compiled Windows binary packages are sufficient for your needs
 (as an aside, those packages themselves are build on a Linux machine
-using cross-compilers).  If it is necessary for your to compile LAMMPS
+using cross-compilers).  If it is necessary for you to compile LAMMPS
 on a Windows machine (e.g. because it is your main desktop), please also
-consider using a virtual machine software and run a Linux virtual machine,
-or - if have a recently updated Windows 10 installation - consider using
-the Windows subsystem for Linux, which allows to run a bash shell from
-Ubuntu and from there on, you can pretty much use that shell like you
-are running on an Ubuntu Linux machine (e.g. installing software via
-apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
+consider using a virtual machine software and compile and run LAMMPS in
+a Linux virtual machine, or - if you have a recently updated Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows and from there on, you can pretty much use that
+shell like you are running on an Ubuntu Linux machine (e.g. installing
+software via apt-get and more). For more details on that, please
+see :doc:`this tutorial <Howto_bash>`
 
 .. _gnu:
 
-Using GNU GCC ported to Windows
+Using a GNU GCC ported to Windows
 -----------------------------------------
 
 One option for compiling LAMMPS on Windows natively, that has been known
@@ -83,13 +85,13 @@ traditional build system, but CMake has also been successfully tested
 using the mingw32-cmake and mingw64-cmake wrappers that are bundled
 with the cross-compiler environment on Fedora machines. A CMake preset
 selecting all packages compatible with this cross-compilation build
-is provided. You likely need to disable the GPU package unless you
+is provided. You will likely need to disable the GPU package unless you
 download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
 into your MinGW64 cross-compiler environment. The cross-compilation
 currently will only produce non-MPI serial binaries.
 
-Please keep in mind, though, that this only applies to compiling LAMMPS.
-Whether the resulting binaries do work correctly is no tested by the
+Please keep in mind, though, that this only applies to **compiling** LAMMPS.
+Whether the resulting binaries do work correctly is not tested by the
 LAMMPS developers.  We instead rely on the feedback of the users
 of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
@@ -104,8 +106,3 @@ Support for the Visual C++ compilers is currently not available. The
 CMake build system is capable of creating suitable a Visual Studio
 style build environment, but the LAMMPS code itself is not fully ported
 to support Visual C++. Volunteers to take on this task are welcome.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands.rst

@@ -27,8 +27,3 @@ commands in it are used to define a LAMMPS simulation.
    :maxdepth: 1
 
    Commands_removed
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -1,59 +1,138 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 General commands
 ================
 
 An alphabetic list of all general LAMMPS commands.
 
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`angle\_coeff <angle_coeff>`       | :doc:`angle\_style <angle_style>`       | :doc:`atom\_modify <atom_modify>`       | :doc:`atom\_style <atom_style>`         | :doc:`balance <balance>`                    | :doc:`bond\_coeff <bond_coeff>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`bond\_style <bond_style>`         | :doc:`bond\_write <bond_write>`         | :doc:`boundary <boundary>`              | :doc:`box <box>`                        | :doc:`change\_box <change_box>`             | :doc:`clear <clear>`                    |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`comm\_modify <comm_modify>`       | :doc:`comm\_style <comm_style>`         | :doc:`compute <compute>`                | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>`         | :doc:`create\_bonds <create_bonds>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`create\_box <create_box>`         | :doc:`delete\_atoms <delete_atoms>`     | :doc:`delete\_bonds <delete_bonds>`     | :doc:`dielectric <dielectric>`          | :doc:`dihedral\_coeff <dihedral_coeff>`     | :doc:`dihedral\_style <dihedral_style>` |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dimension <dimension>`            | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>`                      | :doc:`dump adios <dump_adios>`          | :doc:`dump image <dump_image>`              | :doc:`dump movie <dump_image>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dump netcdf <dump_netcdf>`        | :doc:`dump netcdf/mpiio <dump_netcdf>`  | :doc:`dump vtk <dump_vtk>`              | :doc:`dump\_modify <dump_modify>`       | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>`                      |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`fix <fix>`                        | :doc:`fix\_modify <fix_modify>`         | :doc:`group <group>`                    | :doc:`group2ndx <group2ndx>`            | :doc:`hyper <hyper>`                        | :doc:`if <if>`                          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`info <info>`                      | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>`                | :doc:`jump <jump>`                          | :doc:`kim\_init <kim_commands>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>`        | :doc:`kspace\_modify <kspace_modify>`   | :doc:`kspace\_style <kspace_style>`     | :doc:`label <label>`                        | :doc:`lattice <lattice>`                |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`log <log>`                        | :doc:`mass <mass>`                      | :doc:`message <message>`                | :doc:`minimize <minimize>`              | :doc:`min\_modify <min_modify>`             | :doc:`min\_style <min_style>`           |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`min\_style spin <min_spin>`       | :doc:`molecule <molecule>`              | :doc:`ndx2group <group2ndx>`            | :doc:`neb <neb>`                        | :doc:`neb/spin <neb_spin>`                  | :doc:`neigh\_modify <neigh_modify>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`neighbor <neighbor>`              | :doc:`newton <newton>`                  | :doc:`next <next>`                      | :doc:`package <package>`                | :doc:`pair\_coeff <pair_coeff>`             | :doc:`pair\_modify <pair_modify>`       |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`pair\_style <pair_style>`         | :doc:`pair\_write <pair_write>`         | :doc:`partition <partition>`            | :doc:`prd <prd>`                        | :doc:`print <print>`                        | :doc:`processors <processors>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`python <python>`                  | :doc:`quit <quit>`                      | :doc:`read\_data <read_data>`           | :doc:`read\_dump <read_dump>`           | :doc:`read\_restart <read_restart>`         | :doc:`region <region>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`replicate <replicate>`            | :doc:`rerun <rerun>`                    | :doc:`reset\_ids <reset_ids>`           | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>`                    | :doc:`run <run>`                        |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`run\_style <run_style>`           | :doc:`server <server>`                  | :doc:`set <set>`                        | :doc:`shell <shell>`                    | :doc:`special\_bonds <special_bonds>`       | :doc:`suffix <suffix>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`tad <tad>`                        | :doc:`temper <temper>`                  | :doc:`temper/grem <temper_grem>`        | :doc:`temper/npt <temper_npt>`          | :doc:`thermo <thermo>`                      | :doc:`thermo\_modify <thermo_modify>`   |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`thermo\_style <thermo_style>`     | :doc:`third\_order <third_order>`       | :doc:`timer <timer>`                    | :doc:`timestep <timestep>`              | :doc:`uncompute <uncompute>`                | :doc:`undump <undump>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`unfix <unfix>`                    | :doc:`units <units>`                    | :doc:`variable <variable>`              | :doc:`velocity <velocity>`              | :doc:`write\_coeff <write_coeff>`           | :doc:`write\_data <write_data>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`write\_dump <write_dump>`         | :doc:`write\_restart <write_restart>`   |                                         |                                         |                                             |                                         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`angle_coeff <angle_coeff>`
+   * :doc:`angle_style <angle_style>`
+   * :doc:`atom_modify <atom_modify>`
+   * :doc:`atom_style <atom_style>`
+   * :doc:`balance <balance>`
+   * :doc:`bond_coeff <bond_coeff>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
+   * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
+   * :doc:`change_box <change_box>`
+   * :doc:`clear <clear>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
+   * :doc:`compute <compute>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
+   * :doc:`dielectric <dielectric>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`dimension <dimension>`
+   * :doc:`displace_atoms <displace_atoms>`
+   * :doc:`dump <dump>`
+   * :doc:`dump atom/adios <dump_adios>`
+   * :doc:`dump custom/adios <dump_adios>`
+   * :doc:`dump image <dump_image>`
+   * :doc:`dump movie <dump_image>`
+   * :doc:`dump netcdf <dump_netcdf>`
+   * :doc:`dump netcdf/mpiio <dump_netcdf>`
+   * :doc:`dump vtk <dump_vtk>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
+   * :doc:`echo <echo>`
+   * :doc:`fix <fix>`
+   * :doc:`fix_modify <fix_modify>`
+   * :doc:`group <group>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`if <if>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
+   * :doc:`include <include>`
+   * :doc:`info <info>`
+   * :doc:`jump <jump>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
+   * :doc:`label <label>`
+   * :doc:`lattice <lattice>`
+   * :doc:`log <log>`
+   * :doc:`mass <mass>`
+   * :doc:`message <message>`
+   * :doc:`minimize <minimize>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
+   * :doc:`molecule <molecule>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`neigh_modify <neigh_modify>`
+   * :doc:`neighbor <neighbor>`
+   * :doc:`newton <newton>`
+   * :doc:`next <next>`
+   * :doc:`package <package>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
+   * :doc:`partition <partition>`
+   * :doc:`prd <prd>`
+   * :doc:`print <print>`
+   * :doc:`processors <processors>`
+   * :doc:`python <python>`
+   * :doc:`quit <quit>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
+   * :doc:`region <region>`
+   * :doc:`replicate <replicate>`
+   * :doc:`rerun <rerun>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
+   * :doc:`restart <restart>`
+   * :doc:`run <run>`
+   * :doc:`run_style <run_style>`
+   * :doc:`server <server>`
+   * :doc:`set <set>`
+   * :doc:`shell <shell>`
+   * :doc:`special_bonds <special_bonds>`
+   * :doc:`suffix <suffix>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`thermo <thermo>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
+   * :doc:`timer <timer>`
+   * :doc:`timestep <timestep>`
+   * :doc:`uncompute <uncompute>`
+   * :doc:`undump <undump>`
+   * :doc:`unfix <unfix>`
+   * :doc:`units <units>`
+   * :doc:`variable <variable>`
+   * :doc:`velocity <velocity>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`

doc/src/Commands_bond.rst

@@ -1,112 +1,160 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
 .. _bond:
 
-Bond\_style potentials
-=================================
+Bond_style potentials
+=====================
 
-All LAMMPS :doc:`bond\_style <bond_style>` commands.  Some styles have
+All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`none <bond_none>`               | :doc:`zero <bond_zero>`                         | :doc:`hybrid <bond_hybrid>`                             |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-|                                       |                                                 |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`class2 (ko) <bond_class2>`      | :doc:`fene (iko) <bond_fene>`                   | :doc:`fene/expand (o) <bond_fene_expand>`               | :doc:`gromos (o) <bond_gromos>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>`           |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`morse (o) <bond_morse>`         | :doc:`nonlinear (o) <bond_nonlinear>`           | :doc:`oxdna/fene <bond_oxdna>`                          | :doc:`oxdna2/fene <bond_oxdna>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`quartic (o) <bond_quartic>`     | :doc:`table (o) <bond_table>`                   |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-
-
-----------
+.. table_from_list::
+   :columns: 4
 
+   * :doc:`none <bond_none>`
+   * :doc:`zero <bond_zero>`
+   * :doc:`hybrid <bond_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <bond_class2>`
+   * :doc:`fene (iko) <bond_fene>`
+   * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gromos (o) <bond_gromos>`
+   * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
+   * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mm3 <bond_mm3>`
+   * :doc:`morse (o) <bond_morse>`
+   * :doc:`nonlinear (o) <bond_nonlinear>`
+   * :doc:`oxdna/fene <bond_oxdna>`
+   * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
+   * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`table (o) <bond_table>`
 
 .. _angle:
 
-Angle\_style potentials
-===================================
+Angle_style potentials
+======================
 
-All LAMMPS :doc:`angle\_style <angle_style>` commands.  Some styles have
+All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`none <angle_none>`                             | :doc:`zero <angle_zero>`                         | :doc:`hybrid <angle_hybrid>`                       |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-|                                                      |                                                  |                                                    |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`charmm (iko) <angle_charmm>`                   | :doc:`class2 (ko) <angle_class2>`                | :doc:`class2/p6 <angle_class2>`                    | :doc:`cosine (ko) <angle_cosine>`            |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/buck6d <angle_cosine_buck6d>`           | :doc:`cosine/delta (o) <angle_cosine_delta>`     | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>`                         | :doc:`dipole (o) <angle_dipole>`             |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`fourier (o) <angle_fourier>`                   | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>`             | :doc:`mm3 <angle_mm3>`                       |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`quartic (o) <angle_quartic>`                   | :doc:`sdk (o) <angle_sdk>`                       | :doc:`table (o) <angle_table>`                     |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-
-
-----------
+.. table_from_list::
+   :columns: 4
 
+   * :doc:`none <angle_none>`
+   * :doc:`zero <angle_zero>`
+   * :doc:`hybrid <angle_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <angle_charmm>`
+   * :doc:`class2 (ko) <angle_class2>`
+   * :doc:`class2/p6 <angle_class2>`
+   * :doc:`cosine (ko) <angle_cosine>`
+   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
+   * :doc:`cosine/delta (o) <angle_cosine_delta>`
+   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
+   * :doc:`cosine/shift (o) <angle_cosine_shift>`
+   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
+   * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cross <angle_cross>`
+   * :doc:`dipole (o) <angle_dipole>`
+   * :doc:`fourier (o) <angle_fourier>`
+   * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mm3 <angle_mm3>`
+   * :doc:`quartic (o) <angle_quartic>`
+   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
 
-Dihedral\_style potentials
-=========================================
+Dihedral_style potentials
+=========================
 
-All LAMMPS :doc:`dihedral\_style <dihedral_style>` commands.  Some styles
+All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`none <dihedral_none>`               | :doc:`zero <dihedral_zero>`               | :doc:`hybrid <dihedral_hybrid>`           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                           |                                           |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`charmm (iko) <dihedral_charmm>`     | :doc:`charmmfsw <dihedral_charmm>`        | :doc:`class2 (ko) <dihedral_class2>`      | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`fourier (io) <dihedral_fourier>`    | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>`         | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`     |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>`         | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>`                   |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`table (o) <dihedral_table>`         | :doc:`table/cut <dihedral_table_cut>`     |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
 
+.. table_from_list::
+   :columns: 4
 
-----------
-
+   * :doc:`none <dihedral_none>`
+   * :doc:`zero <dihedral_zero>`
+   * :doc:`hybrid <dihedral_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`class2 (ko) <dihedral_class2>`
+   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`fourier (io) <dihedral_fourier>`
+   * :doc:`harmonic (iko) <dihedral_harmonic>`
+   * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`nharmonic (o) <dihedral_nharmonic>`
+   * :doc:`opls (iko) <dihedral_opls>`
+   * :doc:`quadratic (o) <dihedral_quadratic>`
+   * :doc:`spherical <dihedral_spherical>`
+   * :doc:`table (o) <dihedral_table>`
+   * :doc:`table/cut <dihedral_table_cut>`
 
 .. _improper:
 
-Improper\_style potentials
-=========================================
+Improper_style potentials
+=========================
 
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`none <improper_none>`          | :doc:`zero <improper_zero>`             | :doc:`hybrid <improper_hybrid>`           |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                      |                                         |                                           |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>`       | :doc:`cvff (io) <improper_cvff>`          | :doc:`distance <improper_distance>`                     |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`distharm <improper_distharm>`  | :doc:`fourier (o) <improper_fourier>`   | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`ring (o) <improper_ring>`      | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>`   |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`none <improper_none>`
+   * :doc:`zero <improper_zero>`
+   * :doc:`hybrid <improper_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <improper_class2>`
+   * :doc:`cossq (o) <improper_cossq>`
+   * :doc:`cvff (io) <improper_cvff>`
+   * :doc:`distance <improper_distance>`
+   * :doc:`distharm <improper_distharm>`
+   * :doc:`fourier (o) <improper_fourier>`
+   * :doc:`harmonic (iko) <improper_harmonic>`
+   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
+   * :doc:`ring (o) <improper_ring>`
+   * :doc:`sqdistharm <improper_sqdistharm>`
+   * :doc:`umbrella (o) <improper_umbrella>`

doc/src/Commands_category.rst

@@ -7,6 +7,7 @@ alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 
 Initialization:
+------------------------------
 
 * :doc:`newton <newton>`,
 * :doc:`package <package>`,
@@ -15,100 +16,107 @@ Initialization:
 * :doc:`units <units>`
 
 Setup simulation box:
+------------------------------
 
 * :doc:`boundary <boundary>`,
 * :doc:`box <box>`,
-* :doc:`change\_box <change_box>`,
-* :doc:`create\_box <create_box>`,
+* :doc:`change_box <change_box>`,
+* :doc:`create_box <create_box>`,
 * :doc:`dimension <dimension>`,
 * :doc:`lattice <lattice>`,
 * :doc:`region <region>`
 
 Setup atoms:
+------------------------------
 
-* :doc:`atom\_modify <atom_modify>`,
-* :doc:`atom\_style <atom_style>`,
+* :doc:`atom_modify <atom_modify>`,
+* :doc:`atom_style <atom_style>`,
 * :doc:`balance <balance>`,
-* :doc:`create\_atoms <create_atoms>`,
-* :doc:`create\_bonds <create_bonds>`,
-* :doc:`delete\_atoms <delete_atoms>`,
-* :doc:`delete\_bonds <delete_bonds>`,
-* :doc:`displace\_atoms <displace_atoms>`,
+* :doc:`create_atoms <create_atoms>`,
+* :doc:`create_bonds <create_bonds>`,
+* :doc:`delete_atoms <delete_atoms>`,
+* :doc:`delete_bonds <delete_bonds>`,
+* :doc:`displace_atoms <displace_atoms>`,
 * :doc:`group <group>`,
 * :doc:`mass <mass>`,
 * :doc:`molecule <molecule>`,
-* :doc:`read\_data <read_data>`,
-* :doc:`read\_dump <read_dump>`,
-* :doc:`read\_restart <read_restart>`,
+* :doc:`read_data <read_data>`,
+* :doc:`read_dump <read_dump>`,
+* :doc:`read_restart <read_restart>`,
 * :doc:`replicate <replicate>`,
 * :doc:`set <set>`,
 * :doc:`velocity <velocity>`
 
 Force fields:
+------------------------------
 
-* :doc:`angle\_coeff <angle_coeff>`,
-* :doc:`angle\_style <angle_style>`,
-* :doc:`bond\_coeff <bond_coeff>`,
-* :doc:`bond\_style <bond_style>`,
-* :doc:`bond\_write <bond_write>`,
+* :doc:`angle_coeff <angle_coeff>`,
+* :doc:`angle_style <angle_style>`,
+* :doc:`bond_coeff <bond_coeff>`,
+* :doc:`bond_style <bond_style>`,
+* :doc:`bond_write <bond_write>`,
 * :doc:`dielectric <dielectric>`,
-* :doc:`dihedral\_coeff <dihedral_coeff>`,
-* :doc:`dihedral\_style <dihedral_style>`,
-* :doc:`improper\_coeff <improper_coeff>`,
-* :doc:`improper\_style <improper_style>`,
-* :doc:`kspace\_modify <kspace_modify>`,
-* :doc:`kspace\_style <kspace_style>`,
-* :doc:`pair\_coeff <pair_coeff>`,
-* :doc:`pair\_modify <pair_modify>`,
-* :doc:`pair\_style <pair_style>`,
-* :doc:`pair\_write <pair_write>`,
-* :doc:`special\_bonds <special_bonds>`
+* :doc:`dihedral_coeff <dihedral_coeff>`,
+* :doc:`dihedral_style <dihedral_style>`,
+* :doc:`improper_coeff <improper_coeff>`,
+* :doc:`improper_style <improper_style>`,
+* :doc:`kspace_modify <kspace_modify>`,
+* :doc:`kspace_style <kspace_style>`,
+* :doc:`pair_coeff <pair_coeff>`,
+* :doc:`pair_modify <pair_modify>`,
+* :doc:`pair_style <pair_style>`,
+* :doc:`pair_write <pair_write>`,
+* :doc:`special_bonds <special_bonds>`
 
 Settings:
+------------------------------
 
-* :doc:`comm\_modify <comm_modify>`,
-* :doc:`comm\_style <comm_style>`,
+* :doc:`comm_modify <comm_modify>`,
+* :doc:`comm_style <comm_style>`,
 * :doc:`info <info>`,
-* :doc:`min\_modify <min_modify>`,
-* :doc:`min\_style <min_style>`,
-* :doc:`neigh\_modify <neigh_modify>`,
+* :doc:`min_modify <min_modify>`,
+* :doc:`min_style <min_style>`,
+* :doc:`neigh_modify <neigh_modify>`,
 * :doc:`neighbor <neighbor>`,
 * :doc:`partition <partition>`,
-* :doc:`reset\_timestep <reset_timestep>`,
-* :doc:`run\_style <run_style>`,
+* :doc:`reset_timestep <reset_timestep>`,
+* :doc:`run_style <run_style>`,
 * :doc:`timer <timer>`,
 * :doc:`timestep <timestep>`
 
 Operations within timestepping (fixes) and diagnostics (computes):
+------------------------------------------------------------------------------------------
 
 * :doc:`compute <compute>`,
-* :doc:`compute\_modify <compute_modify>`,
+* :doc:`compute_modify <compute_modify>`,
 * :doc:`fix <fix>`,
-* :doc:`fix\_modify <fix_modify>`,
+* :doc:`fix_modify <fix_modify>`,
 * :doc:`uncompute <uncompute>`,
 * :doc:`unfix <unfix>`
 
 Output:
+------------------------------
 
 * :doc:`dump image <dump_image>`,
 * :doc:`dump movie <dump_image>`,
 * :doc:`dump <dump>`,
-* :doc:`dump\_modify <dump_modify>`,
+* :doc:`dump_modify <dump_modify>`,
 * :doc:`restart <restart>`,
 * :doc:`thermo <thermo>`,
-* :doc:`thermo\_modify <thermo_modify>`,
-* :doc:`thermo\_style <thermo_style>`,
+* :doc:`thermo_modify <thermo_modify>`,
+* :doc:`thermo_style <thermo_style>`,
 * :doc:`undump <undump>`,
-* :doc:`write\_coeff <write_coeff>`,
-* :doc:`write\_data <write_data>`,
-* :doc:`write\_dump <write_dump>`,
-* :doc:`write\_restart <write_restart>`
+* :doc:`write_coeff <write_coeff>`,
+* :doc:`write_data <write_data>`,
+* :doc:`write_dump <write_dump>`,
+* :doc:`write_restart <write_restart>`
 
 Actions:
+------------------------------
 
 * :doc:`minimize <minimize>`,
 * :doc:`neb <neb>`,
-* :doc:`neb\_spin <neb_spin>`,
+* :doc:`neb_spin <neb_spin>`,
 * :doc:`prd <prd>`,
 * :doc:`rerun <rerun>`,
 * :doc:`run <run>`,
@@ -116,6 +124,7 @@ Actions:
 * :doc:`temper <temper>`
 
 Input script control:
+------------------------------
 
 * :doc:`clear <clear>`,
 * :doc:`echo <echo>`,
@@ -130,8 +139,3 @@ Input script control:
 * :doc:`quit <quit>`,
 * :doc:`shell <shell>`,
 * :doc:`variable <variable>`
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_compute.rst

@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 Compute commands
 ================
@@ -14,57 +19,147 @@ Some styles have accelerated versions.  This is indicated by
 additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`ackland/atom <compute_ackland_atom>`                 | :doc:`adf <compute_adf>`                               | :doc:`aggregate/atom <compute_cluster_atom>`                     | :doc:`angle <compute_angle>`                                 | :doc:`angle/local <compute_angle_local>`                 | :doc:`angmom/chunk <compute_angmom_chunk>`                   |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`basal/atom <compute_basal_atom>`                     | :doc:`body/local <compute_body_local>`                 | :doc:`bond <compute_bond>`                                       | :doc:`bond/local <compute_bond_local>`                       | :doc:`centro/atom <compute_centro_atom>`                 | :doc:`centroid/stress/atom <compute_stress_atom>`            |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`chunk/atom <compute_chunk_atom>`                     | :doc:`chunk/spread/atom <compute_chunk_spread_atom>`   | :doc:`cluster/atom <compute_cluster_atom>`                       | :doc:`cna/atom <compute_cna_atom>`                           | :doc:`cnp/atom <compute_cnp_atom>`                       | :doc:`com <compute_com>`                                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`com/chunk <compute_com_chunk>`                       | :doc:`contact/atom <compute_contact_atom>`             | :doc:`coord/atom <compute_coord_atom>`                           | :doc:`damage/atom <compute_damage_atom>`                     | :doc:`dihedral <compute_dihedral>`                       | :doc:`dihedral/local <compute_dihedral_local>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`dilatation/atom <compute_dilatation_atom>`           | :doc:`dipole/chunk <compute_dipole_chunk>`             | :doc:`displace/atom <compute_displace_atom>`                     | :doc:`dpd <compute_dpd>`                                     | :doc:`dpd/atom <compute_dpd_atom>`                       | :doc:`edpd/temp/atom <compute_edpd_temp_atom>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`entropy/atom <compute_entropy_atom>`                 | :doc:`erotate/asphere <compute_erotate_asphere>`       | :doc:`erotate/rigid <compute_erotate_rigid>`                     | :doc:`erotate/sphere <compute_erotate_sphere>`               | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`fep <compute_fep>`                                   | :doc:`force/tally <compute_tally>`                     | :doc:`fragment/atom <compute_cluster_atom>`                      | :doc:`global/atom <compute_global_atom>`                     | :doc:`group/group <compute_group_group>`                 | :doc:`gyration <compute_gyration>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`gyration/chunk <compute_gyration_chunk>`             | :doc:`gyration/shape <compute_gyration_shape>`         | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`       | :doc:`heat/flux <compute_heat_flux>`                         | :doc:`heat/flux/tally <compute_tally>`                   | :doc:`hexorder/atom <compute_hexorder_atom>`                 |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`hma <compute_hma>`                                   | :doc:`improper <compute_improper>`                     | :doc:`improper/local <compute_improper_local>`                   | :doc:`inertia/chunk <compute_inertia_chunk>`                 | :doc:`ke <compute_ke>`                                   | :doc:`ke/atom <compute_ke_atom>`                             |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`ke/atom/eff <compute_ke_atom_eff>`                   | :doc:`ke/eff <compute_ke_eff>`                         | :doc:`ke/rigid <compute_ke_rigid>`                               | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`             | :doc:`meso/t/atom <compute_meso_t_atom>`                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`momentum <compute_momentum>`                         | :doc:`msd <compute_msd>`                               | :doc:`msd/chunk <compute_msd_chunk>`                             | :doc:`msd/nongauss <compute_msd_nongauss>`                   | :doc:`omega/chunk <compute_omega_chunk>`                 | :doc:`orientorder/atom <compute_orientorder_atom>`           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`pair <compute_pair>`                                 | :doc:`pair/local <compute_pair_local>`                 | :doc:`pe <compute_pe>`                                           | :doc:`pe/atom <compute_pe_atom>`                             | :doc:`pe/mol/tally <compute_tally>`                      | :doc:`pe/tally <compute_tally>`                              |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`plasticity/atom <compute_plasticity_atom>`           | :doc:`pressure <compute_pressure>`                     | :doc:`pressure/cylinder <compute_pressure_cylinder>`             | :doc:`pressure/uef <compute_pressure_uef>`                   | :doc:`property/atom <compute_property_atom>`             | :doc:`property/chunk <compute_property_chunk>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`property/local <compute_property_local>`             | :doc:`ptm/atom <compute_ptm_atom>`                     | :doc:`rdf <compute_rdf>`                                         | :doc:`reduce <compute_reduce>`                               | :doc:`reduce/chunk <compute_reduce_chunk>`               | :doc:`reduce/region <compute_reduce>`                        |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`rigid/local <compute_rigid_local>`                   | :doc:`saed <compute_saed>`                             | :doc:`slice <compute_slice>`                                     | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`                   | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/internal/energy <compute_smd_internal_energy>`   | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`     | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                   |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`       | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`sna/atom <compute_sna_atom>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`snad/atom <compute_sna_atom>`                        | :doc:`snav/atom <compute_sna_atom>`                    | :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`                   | :doc:`stress/mop/profile <compute_stress_mop>`               |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`stress/tally <compute_tally>`                        | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             | :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`                       |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/com <compute_temp_com>`                         | :doc:`temp/cs <compute_temp_cs>`                       | :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`                   | :doc:`temp/eff <compute_temp_eff>`                           |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/partial <compute_temp_partial>`                 | :doc:`temp/profile <compute_temp_profile>`             | :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`         | :doc:`temp/rotate <compute_temp_rotate>`                     |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`temp/sphere <compute_temp_sphere>`                   | :doc:`temp/uef <compute_temp_uef>`                     | :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                               | :doc:`vcm/chunk <compute_vcm_chunk>`                         |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
-| :doc:`voronoi/atom <compute_voronoi_atom>`                 | :doc:`xrd <compute_xrd>`                               |                                                                  |                                                              |                                                          |                                                              |
-+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`ackland/atom <compute_ackland_atom>`
+   * :doc:`adf <compute_adf>`
+   * :doc:`aggregate/atom <compute_cluster_atom>`
+   * :doc:`angle <compute_angle>`
+   * :doc:`angle/local <compute_angle_local>`
+   * :doc:`angmom/chunk <compute_angmom_chunk>`
+   * :doc:`basal/atom <compute_basal_atom>`
+   * :doc:`body/local <compute_body_local>`
+   * :doc:`bond <compute_bond>`
+   * :doc:`bond/local <compute_bond_local>`
+   * :doc:`centro/atom <compute_centro_atom>`
+   * :doc:`centroid/stress/atom <compute_stress_atom>`
+   * :doc:`chunk/atom <compute_chunk_atom>`
+   * :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
+   * :doc:`cluster/atom <compute_cluster_atom>`
+   * :doc:`cna/atom <compute_cna_atom>`
+   * :doc:`cnp/atom <compute_cnp_atom>`
+   * :doc:`com <compute_com>`
+   * :doc:`com/chunk <compute_com_chunk>`
+   * :doc:`contact/atom <compute_contact_atom>`
+   * :doc:`coord/atom <compute_coord_atom>`
+   * :doc:`damage/atom <compute_damage_atom>`
+   * :doc:`dihedral <compute_dihedral>`
+   * :doc:`dihedral/local <compute_dihedral_local>`
+   * :doc:`dilatation/atom <compute_dilatation_atom>`
+   * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`displace/atom <compute_displace_atom>`
+   * :doc:`dpd <compute_dpd>`
+   * :doc:`dpd/atom <compute_dpd_atom>`
+   * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
+   * :doc:`entropy/atom <compute_entropy_atom>`
+   * :doc:`erotate/asphere <compute_erotate_asphere>`
+   * :doc:`erotate/rigid <compute_erotate_rigid>`
+   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
+   * :doc:`event/displace <compute_event_displace>`
+   * :doc:`fep <compute_fep>`
+   * :doc:`force/tally <compute_tally>`
+   * :doc:`fragment/atom <compute_cluster_atom>`
+   * :doc:`global/atom <compute_global_atom>`
+   * :doc:`group/group <compute_group_group>`
+   * :doc:`gyration <compute_gyration>`
+   * :doc:`gyration/chunk <compute_gyration_chunk>`
+   * :doc:`gyration/shape <compute_gyration_shape>`
+   * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
+   * :doc:`heat/flux <compute_heat_flux>`
+   * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`hexorder/atom <compute_hexorder_atom>`
+   * :doc:`hma <compute_hma>`
+   * :doc:`improper <compute_improper>`
+   * :doc:`improper/local <compute_improper_local>`
+   * :doc:`inertia/chunk <compute_inertia_chunk>`
+   * :doc:`ke <compute_ke>`
+   * :doc:`ke/atom <compute_ke_atom>`
+   * :doc:`ke/atom/eff <compute_ke_atom_eff>`
+   * :doc:`ke/eff <compute_ke_eff>`
+   * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`meso/e/atom <compute_meso_e_atom>`
+   * :doc:`meso/rho/atom <compute_meso_rho_atom>`
+   * :doc:`meso/t/atom <compute_meso_t_atom>`
+   * :doc:`momentum <compute_momentum>`
+   * :doc:`msd <compute_msd>`
+   * :doc:`msd/chunk <compute_msd_chunk>`
+   * :doc:`msd/nongauss <compute_msd_nongauss>`
+   * :doc:`omega/chunk <compute_omega_chunk>`
+   * :doc:`orientorder/atom <compute_orientorder_atom>`
+   * :doc:`pair <compute_pair>`
+   * :doc:`pair/local <compute_pair_local>`
+   * :doc:`pe <compute_pe>`
+   * :doc:`pe/atom <compute_pe_atom>`
+   * :doc:`pe/mol/tally <compute_tally>`
+   * :doc:`pe/tally <compute_tally>`
+   * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/cylinder <compute_pressure_cylinder>`
+   * :doc:`pressure/uef <compute_pressure_uef>`
+   * :doc:`property/atom <compute_property_atom>`
+   * :doc:`property/chunk <compute_property_chunk>`
+   * :doc:`property/local <compute_property_local>`
+   * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rdf <compute_rdf>`
+   * :doc:`reduce <compute_reduce>`
+   * :doc:`reduce/chunk <compute_reduce_chunk>`
+   * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rigid/local <compute_rigid_local>`
+   * :doc:`saed <compute_saed>`
+   * :doc:`slice <compute_slice>`
+   * :doc:`smd/contact/radius <compute_smd_contact_radius>`
+   * :doc:`smd/damage <compute_smd_damage>`
+   * :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
+   * :doc:`smd/internal/energy <compute_smd_internal_energy>`
+   * :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
+   * :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
+   * :doc:`smd/rho <compute_smd_rho>`
+   * :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
+   * :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
+   * :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
+   * :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
+   * :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
+   * :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
+   * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
+   * :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
+   * :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
+   * :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
+   * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
+   * :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
+   * :doc:`smd/vol <compute_smd_vol>`
+   * :doc:`snap <compute_sna_atom>`
+   * :doc:`sna/atom <compute_sna_atom>`
+   * :doc:`snad/atom <compute_sna_atom>`
+   * :doc:`snav/atom <compute_sna_atom>`
+   * :doc:`spin <compute_spin>`
+   * :doc:`stress/atom <compute_stress_atom>`
+   * :doc:`stress/mop <compute_stress_mop>`
+   * :doc:`stress/mop/profile <compute_stress_mop>`
+   * :doc:`stress/tally <compute_tally>`
+   * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
+   * :doc:`temp (k) <compute_temp>`
+   * :doc:`temp/asphere <compute_temp_asphere>`
+   * :doc:`temp/body <compute_temp_body>`
+   * :doc:`temp/chunk <compute_temp_chunk>`
+   * :doc:`temp/com <compute_temp_com>`
+   * :doc:`temp/cs <compute_temp_cs>`
+   * :doc:`temp/deform <compute_temp_deform>`
+   * :doc:`temp/deform/eff <compute_temp_deform_eff>`
+   * :doc:`temp/drude <compute_temp_drude>`
+   * :doc:`temp/eff <compute_temp_eff>`
+   * :doc:`temp/partial <compute_temp_partial>`
+   * :doc:`temp/profile <compute_temp_profile>`
+   * :doc:`temp/ramp <compute_temp_ramp>`
+   * :doc:`temp/region <compute_temp_region>`
+   * :doc:`temp/region/eff <compute_temp_region_eff>`
+   * :doc:`temp/rotate <compute_temp_rotate>`
+   * :doc:`temp/sphere <compute_temp_sphere>`
+   * :doc:`temp/uef <compute_temp_uef>`
+   * :doc:`ti <compute_ti>`
+   * :doc:`torque/chunk <compute_torque_chunk>`
+   * :doc:`vacf <compute_vacf>`
+   * :doc:`vcm/chunk <compute_vcm_chunk>`
+   * :doc:`voronoi/atom <compute_voronoi_atom>`
+   * :doc:`xrd <compute_xrd>`

doc/src/Commands_fix.rst

@@ -1,10 +1,15 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 Fix commands
 ============
@@ -14,81 +19,224 @@ have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`adapt <fix_adapt>`                         | :doc:`adapt/fep <fix_adapt_fep>`                       | :doc:`addforce <fix_addforce>`                        | :doc:`addtorque <fix_addtorque>`                       | :doc:`append/atoms <fix_append_atoms>`                         | :doc:`atc <fix_atc>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`atom/swap <fix_atom_swap>`                 | :doc:`ave/atom <fix_ave_atom>`                         | :doc:`ave/chunk <fix_ave_chunk>`                      | :doc:`ave/correlate <fix_ave_correlate>`               | :doc:`ave/correlate/long <fix_ave_correlate_long>`             | :doc:`ave/histo <fix_ave_histo>`               |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ave/histo/weight <fix_ave_histo>`          | :doc:`ave/time <fix_ave_time>`                         | :doc:`aveforce <fix_aveforce>`                        | :doc:`balance <fix_balance>`                           | :doc:`bocs <fix_bocs>`                                         | :doc:`bond/break <fix_bond_break>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`bond/create <fix_bond_create>`             | :doc:`bond/react <fix_bond_react>`                     | :doc:`bond/swap <fix_bond_swap>`                      | :doc:`box/relax <fix_box_relax>`                       | :doc:`client/md <fix_client_md>`                               | :doc:`cmap <fix_cmap>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`colvars <fix_colvars>`                     | :doc:`controller <fix_controller>`                     | :doc:`deform (k) <fix_deform>`                        | :doc:`deposit <fix_deposit>`                           | :doc:`dpd/energy (k) <fix_dpd_energy>`                         | :doc:`drag <fix_drag>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`drude <fix_drude>`                         | :doc:`drude/transform/direct <fix_drude_transform>`    | :doc:`drude/transform/inverse <fix_drude_transform>`  | :doc:`dt/reset <fix_dt_reset>`                         | :doc:`edpd/source <fix_dpd_source>`                            | :doc:`efield <fix_efield>`                     |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ehex <fix_ehex>`                           | :doc:`electron/stopping <fix_electron_stopping>`       | :doc:`enforce2d (k) <fix_enforce2d>`                  | :doc:`eos/cv <fix_eos_cv>`                             | :doc:`eos/table <fix_eos_table>`                               | :doc:`eos/table/rx (k) <fix_eos_table_rx>`     |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`evaporate <fix_evaporate>`                 | :doc:`external <fix_external>`                         | :doc:`ffl <fix_ffl>`                                  | :doc:`filter/corotate <fix_filter_corotate>`           | :doc:`flow/gauss <fix_flow_gauss>`                             | :doc:`freeze (k) <fix_freeze>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`gcmc <fix_gcmc>`                           | :doc:`gld <fix_gld>`                                   | :doc:`gle <fix_gle>`                                  | :doc:`gravity (ko) <fix_gravity>`                      | :doc:`grem <fix_grem>`                                         | :doc:`halt <fix_halt>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`heat <fix_heat>`                           | :doc:`hyper/global <fix_hyper_global>`                 | :doc:`hyper/local <fix_hyper_local>`                  | :doc:`imd <fix_imd>`                                   | :doc:`indent <fix_indent>`                                     | :doc:`ipi <fix_ipi>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`langevin (k) <fix_langevin>`               | :doc:`langevin/drude <fix_langevin_drude>`             | :doc:`langevin/eff <fix_langevin_eff>`                | :doc:`langevin/spin <fix_langevin_spin>`               | :doc:`latte <fix_latte>`                                       | :doc:`lb/fluid <fix_lb_fluid>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`lb/momentum <fix_lb_momentum>`             | :doc:`lb/pc <fix_lb_pc>`                               | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`    | :doc:`lb/viscous <fix_lb_viscous>`                     | :doc:`lineforce <fix_lineforce>`                               | :doc:`manifoldforce <fix_manifoldforce>`       |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`meso <fix_meso>`                           | :doc:`meso/move <fix_meso_move>`                       | :doc:`meso/stationary <fix_meso_stationary>`          | :doc:`momentum (k) <fix_momentum>`                     | :doc:`move <fix_move>`                                         | :doc:`mscg <fix_mscg>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`msst <fix_msst>`                           | :doc:`mvv/dpd <fix_mvv_dpd>`                           | :doc:`mvv/edpd <fix_mvv_dpd>`                         | :doc:`mvv/tdpd <fix_mvv_dpd>`                          | :doc:`neb <fix_neb>`                                           | :doc:`neb\_spin <fix_neb_spin>`                |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nph (ko) <fix_nh>`                         | :doc:`nph/asphere (o) <fix_nph_asphere>`               | :doc:`nph/body <fix_nph_body>`                        | :doc:`nph/eff <fix_nh_eff>`                            | :doc:`nph/sphere (o) <fix_nph_sphere>`                         | :doc:`nphug (o) <fix_nphug>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`npt (iko) <fix_nh>`                        | :doc:`npt/asphere (o) <fix_npt_asphere>`               | :doc:`npt/body <fix_npt_body>`                        | :doc:`npt/eff <fix_nh_eff>`                            | :doc:`npt/sphere (o) <fix_npt_sphere>`                         | :doc:`npt/uef <fix_nh_uef>`                    |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve (iko) <fix_nve>`                       | :doc:`nve/asphere (i) <fix_nve_asphere>`               | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`  | :doc:`nve/awpmd <fix_nve_awpmd>`                       | :doc:`nve/body <fix_nve_body>`                                 | :doc:`nve/dot <fix_nve_dot>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` | :doc:`nve/eff <fix_nve_eff>`                           | :doc:`nve/limit <fix_nve_limit>`                      | :doc:`nve/line <fix_nve_line>`                         | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`           | :doc:`nve/noforce <fix_nve_noforce>`           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nve/sphere (ko) <fix_nve_sphere>`          | :doc:`nve/spin <fix_nve_spin>`                         | :doc:`nve/tri <fix_nve_tri>`                          | :doc:`nvk <fix_nvk>`                                   | :doc:`nvt (iko) <fix_nh>`                                      | :doc:`nvt/asphere (o) <fix_nvt_asphere>`       |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nvt/body <fix_nvt_body>`                   | :doc:`nvt/eff <fix_nh_eff>`                            | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`  | :doc:`nvt/sllod (io) <fix_nvt_sllod>`                  | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`                       | :doc:`nvt/sphere (o) <fix_nvt_sphere>`         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`nvt/uef <fix_nh_uef>`                      | :doc:`oneway <fix_oneway>`                             | :doc:`orient/bcc <fix_orient>`                        | :doc:`orient/fcc <fix_orient>`                         | :doc:`phonon <fix_phonon>`                                     | :doc:`pimd <fix_pimd>`                         |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`planeforce <fix_planeforce>`               | :doc:`plumed <fix_plumed>`                             | :doc:`poems <fix_poems>`                              | :doc:`pour <fix_pour>`                                 | :doc:`precession/spin <fix_precession_spin>`                   | :doc:`press/berendsen <fix_press_berendsen>`   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`print <fix_print>`                         | :doc:`property/atom (k) <fix_property_atom>`           | :doc:`python/invoke <fix_python_invoke>`              | :doc:`python/move <fix_python_move>`                   | :doc:`qbmsst <fix_qbmsst>`                                     | :doc:`qeq/comb (o) <fix_qeq_comb>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`qeq/dynamic <fix_qeq>`                     | :doc:`qeq/fire <fix_qeq>`                              | :doc:`qeq/point <fix_qeq>`                            | :doc:`qeq/reax (ko) <fix_qeq_reax>`                    | :doc:`qeq/shielded <fix_qeq>`                                  | :doc:`qeq/slater <fix_qeq>`                    |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`qmmm <fix_qmmm>`                           | :doc:`qtb <fix_qtb>`                                   | :doc:`rattle <fix_shake>`                             | :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`              | :doc:`reax/c/species (k) <fix_reaxc_species>`                  | :doc:`recenter <fix_recenter>`                 |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`restrain <fix_restrain>`                   | :doc:`rhok <fix_rhok>`                                 | :doc:`rigid (o) <fix_rigid>`                          | :doc:`rigid/meso <fix_rigid_meso>`                     | :doc:`rigid/nph (o) <fix_rigid>`                               | :doc:`rigid/nph/small <fix_rigid>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`rigid/npt (o) <fix_rigid>`                 | :doc:`rigid/npt/small <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`                      | :doc:`rigid/nve/small <fix_rigid>`                     | :doc:`rigid/nvt (o) <fix_rigid>`                               | :doc:`rigid/nvt/small <fix_rigid>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`rigid/small (o) <fix_rigid>`               | :doc:`rx (k) <fix_rx>`                                 | :doc:`saed/vtk <fix_saed_vtk>`                        | :doc:`setforce (k) <fix_setforce>`                     | :doc:`shake <fix_shake>`                                       | :doc:`shardlow (k) <fix_shardlow>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`smd <fix_smd>`                             | :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`              | :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`  | :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>`             |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`smd/wall\_surface <fix_smd_wall_surface>`  | :doc:`spring <fix_spring>`                             | :doc:`spring/chunk <fix_spring_chunk>`                | :doc:`spring/rg <fix_spring_rg>`                       | :doc:`spring/self <fix_spring_self>`                           | :doc:`srd <fix_srd>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`store/force <fix_store_force>`             | :doc:`store/state <fix_store_state>`                   | :doc:`tdpd/source <fix_dpd_source>`                   | :doc:`temp/berendsen <fix_temp_berendsen>`             | :doc:`temp/csld <fix_temp_csvr>`                               | :doc:`temp/csvr <fix_temp_csvr>`               |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`temp/rescale <fix_temp_rescale>`           | :doc:`temp/rescale/eff <fix_temp_rescale_eff>`         | :doc:`tfmc <fix_tfmc>`                                | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`ti/spring <fix_ti_spring>`                               | :doc:`tmd <fix_tmd>`                           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`ttm <fix_ttm>`                             | :doc:`ttm/mod <fix_ttm>`                               | :doc:`tune/kspace <fix_tune_kspace>`                  | :doc:`vector <fix_vector>`                             | :doc:`viscosity <fix_viscosity>`                               | :doc:`viscous <fix_viscous>`                   |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/body/polygon <fix_wall_body_polygon>` | :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` | :doc:`wall/colloid <fix_wall>`                        | :doc:`wall/ees <fix_wall_ees>`                         | :doc:`wall/gran <fix_wall_gran>`                               | :doc:`wall/gran/region <fix_wall_gran_region>` |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/harmonic <fix_wall>`                  | :doc:`wall/lj1043 <fix_wall>`                          | :doc:`wall/lj126 <fix_wall>`                          | :doc:`wall/lj93 (k) <fix_wall>`                        | :doc:`wall/morse <fix_wall>`                                   | :doc:`wall/piston <fix_wall_piston>`           |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
-| :doc:`wall/reflect (k) <fix_wall_reflect>`       | :doc:`wall/region <fix_wall_region>`                   | :doc:`wall/region/ees <fix_wall_ees>`                 | :doc:`wall/srd <fix_wall_srd>`                         |                                                                |                                                |
-+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+.. table_from_list::
+   :columns: 6
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`adapt <fix_adapt>`
+   * :doc:`adapt/fep <fix_adapt_fep>`
+   * :doc:`addforce <fix_addforce>`
+   * :doc:`addtorque <fix_addtorque>`
+   * :doc:`append/atoms <fix_append_atoms>`
+   * :doc:`atc <fix_atc>`
+   * :doc:`atom/swap <fix_atom_swap>`
+   * :doc:`ave/atom <fix_ave_atom>`
+   * :doc:`ave/chunk <fix_ave_chunk>`
+   * :doc:`ave/correlate <fix_ave_correlate>`
+   * :doc:`ave/correlate/long <fix_ave_correlate_long>`
+   * :doc:`ave/histo <fix_ave_histo>`
+   * :doc:`ave/histo/weight <fix_ave_histo>`
+   * :doc:`ave/time <fix_ave_time>`
+   * :doc:`aveforce <fix_aveforce>`
+   * :doc:`balance <fix_balance>`
+   * :doc:`bocs <fix_bocs>`
+   * :doc:`bond/break <fix_bond_break>`
+   * :doc:`bond/create <fix_bond_create>`
+   * :doc:`bond/react <fix_bond_react>`
+   * :doc:`bond/swap <fix_bond_swap>`
+   * :doc:`box/relax <fix_box_relax>`
+   * :doc:`client/md <fix_client_md>`
+   * :doc:`cmap <fix_cmap>`
+   * :doc:`colvars <fix_colvars>`
+   * :doc:`controller <fix_controller>`
+   * :doc:`deform (k) <fix_deform>`
+   * :doc:`deposit <fix_deposit>`
+   * :doc:`dpd/energy (k) <fix_dpd_energy>`
+   * :doc:`drag <fix_drag>`
+   * :doc:`drude <fix_drude>`
+   * :doc:`drude/transform/direct <fix_drude_transform>`
+   * :doc:`drude/transform/inverse <fix_drude_transform>`
+   * :doc:`dt/reset <fix_dt_reset>`
+   * :doc:`edpd/source <fix_dpd_source>`
+   * :doc:`efield <fix_efield>`
+   * :doc:`ehex <fix_ehex>`
+   * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`enforce2d (k) <fix_enforce2d>`
+   * :doc:`eos/cv <fix_eos_cv>`
+   * :doc:`eos/table <fix_eos_table>`
+   * :doc:`eos/table/rx (k) <fix_eos_table_rx>`
+   * :doc:`evaporate <fix_evaporate>`
+   * :doc:`external <fix_external>`
+   * :doc:`ffl <fix_ffl>`
+   * :doc:`filter/corotate <fix_filter_corotate>`
+   * :doc:`flow/gauss <fix_flow_gauss>`
+   * :doc:`freeze (k) <fix_freeze>`
+   * :doc:`gcmc <fix_gcmc>`
+   * :doc:`gld <fix_gld>`
+   * :doc:`gle <fix_gle>`
+   * :doc:`gravity (ko) <fix_gravity>`
+   * :doc:`grem <fix_grem>`
+   * :doc:`halt <fix_halt>`
+   * :doc:`heat <fix_heat>`
+   * :doc:`hyper/global <fix_hyper_global>`
+   * :doc:`hyper/local <fix_hyper_local>`
+   * :doc:`imd <fix_imd>`
+   * :doc:`indent <fix_indent>`
+   * :doc:`ipi <fix_ipi>`
+   * :doc:`langevin (k) <fix_langevin>`
+   * :doc:`langevin/drude <fix_langevin_drude>`
+   * :doc:`langevin/eff <fix_langevin_eff>`
+   * :doc:`langevin/spin <fix_langevin_spin>`
+   * :doc:`latte <fix_latte>`
+   * :doc:`lb/fluid <fix_lb_fluid>`
+   * :doc:`lb/momentum <fix_lb_momentum>`
+   * :doc:`lb/pc <fix_lb_pc>`
+   * :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
+   * :doc:`lb/viscous <fix_lb_viscous>`
+   * :doc:`lineforce <fix_lineforce>`
+   * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`meso <fix_meso>`
+   * :doc:`meso/move <fix_meso_move>`
+   * :doc:`meso/stationary <fix_meso_stationary>`
+   * :doc:`momentum (k) <fix_momentum>`
+   * :doc:`move <fix_move>`
+   * :doc:`mscg <fix_mscg>`
+   * :doc:`msst <fix_msst>`
+   * :doc:`mvv/dpd <fix_mvv_dpd>`
+   * :doc:`mvv/edpd <fix_mvv_dpd>`
+   * :doc:`mvv/tdpd <fix_mvv_dpd>`
+   * :doc:`neb <fix_neb>`
+   * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nph (ko) <fix_nh>`
+   * :doc:`nph/asphere (o) <fix_nph_asphere>`
+   * :doc:`nph/body <fix_nph_body>`
+   * :doc:`nph/eff <fix_nh_eff>`
+   * :doc:`nph/sphere (o) <fix_nph_sphere>`
+   * :doc:`nphug <fix_nphug>`
+   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt/asphere (o) <fix_npt_asphere>`
+   * :doc:`npt/body <fix_npt_body>`
+   * :doc:`npt/cauchy <fix_npt_cauchy>`
+   * :doc:`npt/eff <fix_nh_eff>`
+   * :doc:`npt/sphere (o) <fix_npt_sphere>`
+   * :doc:`npt/uef <fix_nh_uef>`
+   * :doc:`nve (iko) <fix_nve>`
+   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
+   * :doc:`nve/awpmd <fix_nve_awpmd>`
+   * :doc:`nve/body <fix_nve_body>`
+   * :doc:`nve/dot <fix_nve_dot>`
+   * :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
+   * :doc:`nve/eff <fix_nve_eff>`
+   * :doc:`nve/limit <fix_nve_limit>`
+   * :doc:`nve/line <fix_nve_line>`
+   * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
+   * :doc:`nve/noforce <fix_nve_noforce>`
+   * :doc:`nve/sphere (ko) <fix_nve_sphere>`
+   * :doc:`nve/spin <fix_nve_spin>`
+   * :doc:`nve/tri <fix_nve_tri>`
+   * :doc:`nvk <fix_nvk>`
+   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
+   * :doc:`nvt/body <fix_nvt_body>`
+   * :doc:`nvt/eff <fix_nh_eff>`
+   * :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+   * :doc:`nvt/sllod (io) <fix_nvt_sllod>`
+   * :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
+   * :doc:`nvt/sphere (o) <fix_nvt_sphere>`
+   * :doc:`nvt/uef <fix_nh_uef>`
+   * :doc:`oneway <fix_oneway>`
+   * :doc:`orient/bcc <fix_orient>`
+   * :doc:`orient/fcc <fix_orient>`
+   * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd <fix_pimd>`
+   * :doc:`planeforce <fix_planeforce>`
+   * :doc:`plumed <fix_plumed>`
+   * :doc:`poems <fix_poems>`
+   * :doc:`pour <fix_pour>`
+   * :doc:`precession/spin <fix_precession_spin>`
+   * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`print <fix_print>`
+   * :doc:`propel/self <fix_propel_self>`
+   * :doc:`property/atom (k) <fix_property_atom>`
+   * :doc:`python/invoke <fix_python_invoke>`
+   * :doc:`python/move <fix_python_move>`
+   * :doc:`qbmsst <fix_qbmsst>`
+   * :doc:`qeq/comb (o) <fix_qeq_comb>`
+   * :doc:`qeq/dynamic <fix_qeq>`
+   * :doc:`qeq/fire <fix_qeq>`
+   * :doc:`qeq/point <fix_qeq>`
+   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/shielded <fix_qeq>`
+   * :doc:`qeq/slater <fix_qeq>`
+   * :doc:`qmmm <fix_qmmm>`
+   * :doc:`qtb <fix_qtb>`
+   * :doc:`rattle <fix_shake>`
+   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
+   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`recenter <fix_recenter>`
+   * :doc:`restrain <fix_restrain>`
+   * :doc:`rhok <fix_rhok>`
+   * :doc:`rigid (o) <fix_rigid>`
+   * :doc:`rigid/meso <fix_rigid_meso>`
+   * :doc:`rigid/nph (o) <fix_rigid>`
+   * :doc:`rigid/nph/small <fix_rigid>`
+   * :doc:`rigid/npt (o) <fix_rigid>`
+   * :doc:`rigid/npt/small <fix_rigid>`
+   * :doc:`rigid/nve (o) <fix_rigid>`
+   * :doc:`rigid/nve/small <fix_rigid>`
+   * :doc:`rigid/nvt (o) <fix_rigid>`
+   * :doc:`rigid/nvt/small <fix_rigid>`
+   * :doc:`rigid/small (o) <fix_rigid>`
+   * :doc:`rx (k) <fix_rx>`
+   * :doc:`saed/vtk <fix_saed_vtk>`
+   * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <fix_setforce>`
+   * :doc:`shake <fix_shake>`
+   * :doc:`shardlow (k) <fix_shardlow>`
+   * :doc:`smd <fix_smd>`
+   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/setvel <fix_smd_setvel>`
+   * :doc:`smd/wall_surface <fix_smd_wall_surface>`
+   * :doc:`spring <fix_spring>`
+   * :doc:`spring/chunk <fix_spring_chunk>`
+   * :doc:`spring/rg <fix_spring_rg>`
+   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`srd <fix_srd>`
+   * :doc:`store/force <fix_store_force>`
+   * :doc:`store/state <fix_store_state>`
+   * :doc:`tdpd/source <fix_dpd_source>`
+   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/csld <fix_temp_csvr>`
+   * :doc:`temp/csvr <fix_temp_csvr>`
+   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
+   * :doc:`tfmc <fix_tfmc>`
+   * :doc:`thermal/conductivity <fix_thermal_conductivity>`
+   * :doc:`ti/spring <fix_ti_spring>`
+   * :doc:`tmd <fix_tmd>`
+   * :doc:`ttm <fix_ttm>`
+   * :doc:`ttm/mod <fix_ttm>`
+   * :doc:`tune/kspace <fix_tune_kspace>`
+   * :doc:`vector <fix_vector>`
+   * :doc:`viscosity <fix_viscosity>`
+   * :doc:`viscous <fix_viscous>`
+   * :doc:`wall/body/polygon <fix_wall_body_polygon>`
+   * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
+   * :doc:`wall/colloid <fix_wall>`
+   * :doc:`wall/ees <fix_wall_ees>`
+   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran/region <fix_wall_gran_region>`
+   * :doc:`wall/harmonic <fix_wall>`
+   * :doc:`wall/lj1043 <fix_wall>`
+   * :doc:`wall/lj126 <fix_wall>`
+   * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/morse <fix_wall>`
+   * :doc:`wall/piston <fix_wall_piston>`
+   * :doc:`wall/reflect (k) <fix_wall_reflect>`
+   * :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
+   * :doc:`wall/region <fix_wall_region>`
+   * :doc:`wall/region/ees <fix_wall_ees>`
+   * :doc:`wall/srd <fix_wall_srd>`

doc/src/Commands_input.rst

@@ -45,7 +45,7 @@ belong to the group.
 (3) Sometimes command B will use values that can be set by command A.
 This means command A must precede command B in the input script if it
 is to have the desired effect.  For example, the
-:doc:`read\_data <read_data>` command initializes the system by setting
+:doc:`read_data <read_data>` command initializes the system by setting
 up the simulation box and assigning atoms to processors.  If default
 values are not desired, the :doc:`processors <processors>` and
 :doc:`boundary <boundary>` commands need to be used before read\_data to
@@ -55,8 +55,3 @@ Many input script errors are detected by LAMMPS and an ERROR or
 WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_kspace.rst

@@ -1,28 +1,39 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 KSpace solvers
 ==============
 
-All LAMMPS :doc:`kspace\_style <kspace_style>` solvers.  Some styles have
+All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`ewald (o) <kspace_style>`    | :doc:`ewald/disp <kspace_style>`     | :doc:`msm (o) <kspace_style>`       | :doc:`msm/cg (o) <kspace_style>`      |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`pppm (gok) <kspace_style>`   | :doc:`pppm/cg (o) <kspace_style>`    | :doc:`pppm/disp (i) <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
-| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | :doc:`scafacos <kspace_style>`      |                                       |
-+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`ewald (o) <kspace_style>`
+   * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
+   * :doc:`msm (o) <kspace_style>`
+   * :doc:`msm/cg (o) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
+   * :doc:`pppm/cg (o) <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/stagger <kspace_style>`
+   * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`scafacos <kspace_style>`

doc/src/Commands_pair.rst

@@ -1,136 +1,259 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
-+----------------------------------------+------------------------------------+------------------------------------------+
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
+   :columns: 3
 
-Pair\_style potentials
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
+Pair_style potentials
 ======================
 
-All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have
+All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`none <pair_none>`                                      | :doc:`zero <pair_zero>`                                           | :doc:`hybrid (k) <pair_hybrid>`                     | :doc:`hybrid/overlay (k) <pair_hybrid>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-|                                                              |                                                                   |                                                     |                                                             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`adp (o) <pair_adp>`                                    | :doc:`agni (o) <pair_agni>`                                       | :doc:`airebo (io) <pair_airebo>`                    | :doc:`airebo/morse (io) <pair_airebo>`                      |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`atm <pair_atm>`                                        | :doc:`awpmd/cut <pair_awpmd>`                                     | :doc:`beck (go) <pair_beck>`                        | :doc:`body/nparticle <pair_body_nparticle>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`body/rounded/polygon <pair_body_rounded_polygon>`      | :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`     | :doc:`bop <pair_bop>`                               | :doc:`born (go) <pair_born>`                                |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`born/coul/dsf <pair_born>`                             | :doc:`born/coul/dsf/cs <pair_cs>`                                 | :doc:`born/coul/long (go) <pair_born>`              | :doc:`born/coul/long/cs (g) <pair_cs>`                      |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`born/coul/msm (o) <pair_born>`                         | :doc:`born/coul/wolf (go) <pair_born>`                            | :doc:`born/coul/wolf/cs (g) <pair_cs>`              | :doc:`brownian (o) <pair_brownian>`                         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`brownian/poly (o) <pair_brownian>`                     | :doc:`buck (giko) <pair_buck>`                                    | :doc:`buck/coul/cut (giko) <pair_buck>`             | :doc:`buck/coul/long (giko) <pair_buck>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`buck/coul/long/cs <pair_cs>`                           | :doc:`buck/coul/msm (o) <pair_buck>`                              | :doc:`buck/long/coul/long (o) <pair_buck_long>`     | :doc:`buck/mdf <pair_mdf>`                                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`        | :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`            | :doc:`colloid (go) <pair_colloid>`                  | :doc:`comb (o) <pair_comb>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`comb3 <pair_comb>`                                     | :doc:`cosine/squared <pair_cosine_squared>`                       | :doc:`coul/cut (gko) <pair_coul>`                   | :doc:`coul/cut/soft (o) <pair_fep_soft>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/debye (gko) <pair_coul>`                          | :doc:`coul/diel (o) <pair_coul_diel>`                             | :doc:`coul/dsf (gko) <pair_coul>`                   | :doc:`coul/long (gko) <pair_coul>`                          |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/long/cs (g) <pair_cs>`                            | :doc:`coul/long/soft (o) <pair_fep_soft>`                         | :doc:`coul/msm (o) <pair_coul>`                     | :doc:`coul/shield <pair_coul_shield>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`coul/streitz <pair_coul>`                              | :doc:`coul/wolf (ko) <pair_coul>`                                 | :doc:`coul/wolf/cs <pair_cs>`                       | :doc:`dpd (gio) <pair_dpd>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`dpd/fdt <pair_dpd_fdt>`                                | :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`                          | :doc:`dpd/tstat (go) <pair_dpd>`                    | :doc:`dsmc <pair_dsmc>`                                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`e3b <pair_e3b>`                                        | :doc:`drip <pair_drip>`                                           | :doc:`eam (gikot) <pair_eam>`                       | :doc:`eam/alloy (gikot) <pair_eam>`                         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`eam/cd (o) <pair_eam>`                                 | :doc:`eam/cd/old (o) <pair_eam>`                                  | :doc:`eam/fs (gikot) <pair_eam>`                    | :doc:`edip (o) <pair_edip>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`edip/multi <pair_edip>`                                | :doc:`edpd <pair_meso>`                                           | :doc:`eff/cut <pair_eff>`                           | :doc:`eim (o) <pair_eim>`                                   |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`exp6/rx (k) <pair_exp6_rx>`                            | :doc:`extep <pair_extep>`                                         | :doc:`gauss (go) <pair_gauss>`                      | :doc:`gauss/cut (o) <pair_gauss>`                           |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`gayberne (gio) <pair_gayberne>`                        | :doc:`gran/hertz/history (o) <pair_gran>`                         | :doc:`gran/hooke (o) <pair_gran>`                   | :doc:`gran/hooke/history (ko) <pair_gran>`                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`granular <pair_granular>`                              | :doc:`gw <pair_gw>`                                               | :doc:`gw/zbl <pair_gw>`                             | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`          |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`        | :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`                   | :doc:`kim <pair_kim>`                               | :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`        | :doc:`lcbop <pair_lcbop>`                                         | :doc:`lebedeva/z <pair_lebedeva_z>`                 | :doc:`lennard/mdf <pair_mdf>`                               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`line/lj <pair_line_lj>`                                | :doc:`list <pair_list>`                                           | :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`    | :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`             | :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`               | :doc:`lj/charmm/coul/msm (o) <pair_charmm>`         | :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/charmmfsw/coul/long <pair_charmm>`                  | :doc:`lj/class2 (gko) <pair_class2>`                              | :doc:`lj/class2/coul/cut (ko) <pair_class2>`        | :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`              |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/class2/coul/long (gko) <pair_class2>`               | :doc:`lj/class2/coul/long/soft <pair_fep_soft>`                   | :doc:`lj/class2/soft <pair_fep_soft>`               | :doc:`lj/cubic (go) <pair_lj_cubic>`                        |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut (gikot) <pair_lj>`                              | :doc:`lj/cut/coul/cut (gko) <pair_lj>`                            | :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`     | :doc:`lj/cut/coul/debye (gko) <pair_lj>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/coul/dsf (gko) <pair_lj>`                       | :doc:`lj/cut/coul/long (gikot) <pair_lj>`                         | :doc:`lj/cut/coul/long/cs <pair_cs>`                | :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/coul/msm (go) <pair_lj>`                        | :doc:`lj/cut/coul/wolf (o) <pair_lj>`                             | :doc:`lj/cut/dipole/cut (go) <pair_dipole>`         | :doc:`lj/cut/dipole/long (g) <pair_dipole>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/dipole/sf (go) <pair_dipole>`                   | :doc:`lj/cut/soft (o) <pair_fep_soft>`                            | :doc:`lj/cut/thole/long (o) <pair_thole>`           | :doc:`lj/cut/tip4p/cut (o) <pair_lj>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/cut/tip4p/long (ot) <pair_lj>`                      | :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`                 | :doc:`lj/expand (gko) <pair_lj_expand>`             | :doc:`lj/expand/coul/long (g) <pair_lj_expand>`             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/gromacs (gko) <pair_gromacs>`                       | :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`                | :doc:`lj/long/coul/long (iot) <pair_lj_long>`       | :doc:`lj/long/dipole/long <pair_dipole>`                    |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/long/tip4p/long (o) <pair_lj_long>`                 | :doc:`lj/mdf <pair_mdf>`                                          | :doc:`lj/sdk (gko) <pair_sdk>`                      | :doc:`lj/sdk/coul/long (go) <pair_sdk>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/sdk/coul/msm (o) <pair_sdk>`                        | :doc:`lj/sf/dipole/sf (go) <pair_dipole>`                         | :doc:`lj/smooth (o) <pair_lj_smooth>`               | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`         |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>` | :doc:`lj96/cut (go) <pair_lj96>`                                  | :doc:`local/density <pair_local_density>`           | :doc:`lubricate (o) <pair_lubricate>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`lubricate/poly (o) <pair_lubricate>`                   | :doc:`lubricateU <pair_lubricateU>`                               | :doc:`lubricateU/poly <pair_lubricateU>`            | :doc:`mdpd <pair_meso>`                                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`mdpd/rhosum <pair_meso>`                               | :doc:`meam/c <pair_meamc>`                                        | :doc:`meam/spline (o) <pair_meam_spline>`           | :doc:`meam/sw/spline <pair_meam_sw_spline>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`mgpt <pair_mgpt>`                                      | :doc:`mie/cut (g) <pair_mie>`                                     | :doc:`momb <pair_momb>`                             | :doc:`morse (gkot) <pair_morse>`                            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`morse/smooth/linear (o) <pair_morse>`                  | :doc:`morse/soft <pair_fep_soft>`                                 | :doc:`multi/lucy <pair_multi_lucy>`                 | :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`nb3b/harmonic <pair_nb3b_harmonic>`                    | :doc:`nm/cut (o) <pair_nm>`                                       | :doc:`nm/cut/coul/cut (o) <pair_nm>`                | :doc:`nm/cut/coul/long (o) <pair_nm>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna/coaxstk <pair_oxdna>`                            | :doc:`oxdna/excv <pair_oxdna>`                                    | :doc:`oxdna/hbond <pair_oxdna>`                     | :doc:`oxdna/stk <pair_oxdna>`                               |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna/xstk <pair_oxdna>`                               | :doc:`oxdna2/coaxstk <pair_oxdna2>`                               | :doc:`oxdna2/dh <pair_oxdna2>`                      | :doc:`oxdna2/excv <pair_oxdna2>`                            |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`oxdna2/hbond <pair_oxdna2>`                            | :doc:`oxdna2/stk <pair_oxdna2>`                                   | :doc:`oxdna2/xstk <pair_oxdna2>`                    | :doc:`peri/eps <pair_peri>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`peri/lps (o) <pair_peri>`                              | :doc:`peri/pmb (o) <pair_peri>`                                   | :doc:`peri/ves <pair_peri>`                         | :doc:`polymorphic <pair_polymorphic>`                       |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`python <pair_python>`                                  | :doc:`quip <pair_quip>`                                           | :doc:`reax/c (ko) <pair_reaxc>`                     | :doc:`rebo (io) <pair_airebo>`                              |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`resquared (go) <pair_resquared>`                       | :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | :doc:`smd/hertz <pair_smd_hertz>`                   | :doc:`smd/tlsph <pair_smd_tlsph>`                           |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`      | :doc:`smd/ulsph <pair_smd_ulsph>`                                 | :doc:`smtbq <pair_smtbq>`                           | :doc:`snap (k) <pair_snap>`                                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`snap (k) <pair_snap>`                                  | :doc:`soft (go) <pair_soft>`                                      | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>`                     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`sph/lj <pair_sph_lj>`                                  | :doc:`sph/rhosum <pair_sph_rhosum>`                               | :doc:`sph/taitwater <pair_sph_taitwater>`           | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`     |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`spin/dipole/cut <pair_spin_dipole>`                    | :doc:`spin/dipole/long <pair_spin_dipole>`                        | :doc:`spin/dmi <pair_spin_dmi>`                     | :doc:`spin/exchange <pair_spin_exchange>`                   |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`spin/magelec <pair_spin_magelec>`                      | :doc:`spin/neel <pair_spin_neel>`                                 | :doc:`srp <pair_srp>`                               | :doc:`sw (giko) <pair_sw>`                                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`table (gko) <pair_table>`                              | :doc:`table/rx (k) <pair_table_rx>`                               | :doc:`tdpd <pair_meso>`                             | :doc:`tersoff (giko) <pair_tersoff>`                        |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`tersoff/mod (gko) <pair_tersoff_mod>`                  | :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`                       | :doc:`tersoff/table (o) <pair_tersoff>`             | :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`thole <pair_thole>`                                    | :doc:`tip4p/cut (o) <pair_coul>`                                  | :doc:`tip4p/long (o) <pair_coul>`                   | :doc:`tip4p/long/soft (o) <pair_fep_soft>`                  |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`tri/lj <pair_tri_lj>`                                  | :doc:`ufm (got) <pair_ufm>`                                       | :doc:`vashishta (gko) <pair_vashishta>`             | :doc:`vashishta/table (o) <pair_vashishta>`                 |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
-| :doc:`yukawa (gko) <pair_yukawa>`                            | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`                  | :doc:`zbl (gko) <pair_zbl>`                         |                                                             |
-+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+.. table_from_list::
+   :columns: 4
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+   * :doc:`none <pair_none>`
+   * :doc:`zero <pair_zero>`
+   * :doc:`hybrid (k) <pair_hybrid>`
+   * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   *
+   *
+   *
+   *
+   * :doc:`adp (o) <pair_adp>`
+   * :doc:`agni (o) <pair_agni>`
+   * :doc:`airebo (io) <pair_airebo>`
+   * :doc:`airebo/morse (io) <pair_airebo>`
+   * :doc:`atm <pair_atm>`
+   * :doc:`awpmd/cut <pair_awpmd>`
+   * :doc:`beck (go) <pair_beck>`
+   * :doc:`body/nparticle <pair_body_nparticle>`
+   * :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
+   * :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
+   * :doc:`bop <pair_bop>`
+   * :doc:`born (go) <pair_born>`
+   * :doc:`born/coul/dsf <pair_born>`
+   * :doc:`born/coul/dsf/cs <pair_cs>`
+   * :doc:`born/coul/long (go) <pair_born>`
+   * :doc:`born/coul/long/cs (g) <pair_cs>`
+   * :doc:`born/coul/msm (o) <pair_born>`
+   * :doc:`born/coul/wolf (go) <pair_born>`
+   * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian/poly (o) <pair_brownian>`
+   * :doc:`buck (giko) <pair_buck>`
+   * :doc:`buck/coul/cut (giko) <pair_buck>`
+   * :doc:`buck/coul/long (giko) <pair_buck>`
+   * :doc:`buck/coul/long/cs <pair_cs>`
+   * :doc:`buck/coul/msm (o) <pair_buck>`
+   * :doc:`buck/long/coul/long (o) <pair_buck_long>`
+   * :doc:`buck/mdf <pair_mdf>`
+   * :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
+   * :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
+   * :doc:`colloid (go) <pair_colloid>`
+   * :doc:`comb (o) <pair_comb>`
+   * :doc:`comb3 <pair_comb>`
+   * :doc:`cosine/squared <pair_cosine_squared>`
+   * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`coul/debye (gko) <pair_coul>`
+   * :doc:`coul/diel (o) <pair_coul_diel>`
+   * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/long (gko) <pair_coul>`
+   * :doc:`coul/long/cs (g) <pair_cs>`
+   * :doc:`coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`coul/msm (o) <pair_coul>`
+   * :doc:`coul/shield <pair_coul_shield>`
+   * :doc:`coul/streitz <pair_coul>`
+   * :doc:`coul/wolf (ko) <pair_coul>`
+   * :doc:`coul/wolf/cs <pair_cs>`
+   * :doc:`dpd (gio) <pair_dpd>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
+   * :doc:`dpd/tstat (go) <pair_dpd>`
+   * :doc:`dsmc <pair_dsmc>`
+   * :doc:`e3b <pair_e3b>`
+   * :doc:`drip <pair_drip>`
+   * :doc:`eam (gikot) <pair_eam>`
+   * :doc:`eam/alloy (gikot) <pair_eam>`
+   * :doc:`eam/cd (o) <pair_eam>`
+   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`edip (o) <pair_edip>`
+   * :doc:`edip/multi <pair_edip>`
+   * :doc:`edpd <pair_meso>`
+   * :doc:`eff/cut <pair_eff>`
+   * :doc:`eim (o) <pair_eim>`
+   * :doc:`exp6/rx (k) <pair_exp6_rx>`
+   * :doc:`extep <pair_extep>`
+   * :doc:`gauss (go) <pair_gauss>`
+   * :doc:`gauss/cut (o) <pair_gauss>`
+   * :doc:`gayberne (gio) <pair_gayberne>`
+   * :doc:`gran/hertz/history (o) <pair_gran>`
+   * :doc:`gran/hooke (o) <pair_gran>`
+   * :doc:`gran/hooke/history (ko) <pair_gran>`
+   * :doc:`granular <pair_granular>`
+   * :doc:`gw <pair_gw>`
+   * :doc:`gw/zbl <pair_gw>`
+   * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
+   * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
+   * :doc:`kim <pair_kim>`
+   * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
+   * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
+   * :doc:`lcbop <pair_lcbop>`
+   * :doc:`lebedeva/z <pair_lebedeva_z>`
+   * :doc:`lennard/mdf <pair_mdf>`
+   * :doc:`line/lj <pair_line_lj>`
+   * :doc:`list <pair_list>`
+   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
+   * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/class2 (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
+   * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
+   * :doc:`lj/class2/coul/long (gko) <pair_class2>`
+   * :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
+   * :doc:`lj/class2/soft <pair_fep_soft>`
+   * :doc:`lj/cubic (go) <pair_lj_cubic>`
+   * :doc:`lj/cut (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/long/cs <pair_cs>`
+   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/msm (go) <pair_lj>`
+   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`
+   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
+   * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
+   * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/thole/long (o) <pair_thole>`
+   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/expand (gko) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
+   * :doc:`lj/gromacs (gko) <pair_gromacs>`
+   * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
+   * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/dipole/long <pair_dipole>`
+   * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
+   * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
+   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
+   * :doc:`lj96/cut (go) <pair_lj96>`
+   * :doc:`local/density <pair_local_density>`
+   * :doc:`lubricate (o) <pair_lubricate>`
+   * :doc:`lubricate/poly (o) <pair_lubricate>`
+   * :doc:`lubricateU <pair_lubricateU>`
+   * :doc:`lubricateU/poly <pair_lubricateU>`
+   * :doc:`mdpd <pair_meso>`
+   * :doc:`mdpd/rhosum <pair_meso>`
+   * :doc:`meam/c <pair_meamc>`
+   * :doc:`meam/spline (o) <pair_meam_spline>`
+   * :doc:`meam/sw/spline <pair_meam_sw_spline>`
+   * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mgpt <pair_mgpt>`
+   * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`momb <pair_momb>`
+   * :doc:`morse (gkot) <pair_morse>`
+   * :doc:`morse/smooth/linear (o) <pair_morse>`
+   * :doc:`morse/soft <pair_fep_soft>`
+   * :doc:`multi/lucy <pair_multi_lucy>`
+   * :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
+   * :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
+   * :doc:`nm/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/cut (o) <pair_nm>`
+   * :doc:`nm/cut/coul/long (o) <pair_nm>`
+   * :doc:`oxdna/coaxstk <pair_oxdna>`
+   * :doc:`oxdna/excv <pair_oxdna>`
+   * :doc:`oxdna/hbond <pair_oxdna>`
+   * :doc:`oxdna/stk <pair_oxdna>`
+   * :doc:`oxdna/xstk <pair_oxdna>`
+   * :doc:`oxdna2/coaxstk <pair_oxdna2>`
+   * :doc:`oxdna2/dh <pair_oxdna2>`
+   * :doc:`oxdna2/excv <pair_oxdna2>`
+   * :doc:`oxdna2/hbond <pair_oxdna2>`
+   * :doc:`oxdna2/stk <pair_oxdna2>`
+   * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`peri/eps <pair_peri>`
+   * :doc:`peri/lps (o) <pair_peri>`
+   * :doc:`peri/pmb (o) <pair_peri>`
+   * :doc:`peri/ves <pair_peri>`
+   * :doc:`polymorphic <pair_polymorphic>`
+   * :doc:`python <pair_python>`
+   * :doc:`quip <pair_quip>`
+   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`rebo (io) <pair_airebo>`
+   * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
+   * :doc:`smd/hertz <pair_smd_hertz>`
+   * :doc:`smd/tlsph <pair_smd_tlsph>`
+   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/ulsph <pair_smd_ulsph>`
+   * :doc:`smtbq <pair_smtbq>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`snap (k) <pair_snap>`
+   * :doc:`soft (go) <pair_soft>`
+   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`sph/idealgas <pair_sph_idealgas>`
+   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/rhosum <pair_sph_rhosum>`
+   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
+   * :doc:`spin/dipole/cut <pair_spin_dipole>`
+   * :doc:`spin/dipole/long <pair_spin_dipole>`
+   * :doc:`spin/dmi <pair_spin_dmi>`
+   * :doc:`spin/exchange <pair_spin_exchange>`
+   * :doc:`spin/magelec <pair_spin_magelec>`
+   * :doc:`spin/neel <pair_spin_neel>`
+   * :doc:`srp <pair_srp>`
+   * :doc:`sw (giko) <pair_sw>`
+   * :doc:`table (gko) <pair_table>`
+   * :doc:`table/rx (k) <pair_table_rx>`
+   * :doc:`tdpd <pair_meso>`
+   * :doc:`tersoff (giko) <pair_tersoff>`
+   * :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
+   * :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
+   * :doc:`tersoff/table (o) <pair_tersoff>`
+   * :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
+   * :doc:`thole <pair_thole>`
+   * :doc:`tip4p/cut (o) <pair_coul>`
+   * :doc:`tip4p/long (o) <pair_coul>`
+   * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
+   * :doc:`tri/lj <pair_tri_lj>`
+   * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`vashishta (gko) <pair_vashishta>`
+   * :doc:`vashishta/table (o) <pair_vashishta>`
+   * :doc:`yukawa (gko) <pair_yukawa>`
+   * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
+   * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_parse.rst

@@ -9,134 +9,151 @@ file names or user-chosen ID strings.
 Here are 6 rules for how each line in the input script is parsed by
 LAMMPS:
 
-(1) If the last printable character on the line is a "&" character,
-the command is assumed to continue on the next line.  The next line is
-concatenated to the previous line by removing the "&" character and
-line break.  This allows long commands to be continued across two or
-more lines.  See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
+.. _one:
 
-(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
+1. If the last printable character on the line is a "&" character, the
+   command is assumed to continue on the next line.  The next line is
+   concatenated to the previous line by removing the "&" character and
+   line break.  This allows long commands to be continued across two or
+   more lines.  See the discussion of triple quotes in :ref:`6 <six>`
+   for how to continue a command across multiple line without using "&"
+   characters.
 
-.. code-block:: LAMMPS
+.. _two:
 
-   # this is a comment
+2. All characters from the first "#" character onward are treated as
+   comment and discarded.  The exception to this rule is described in
+   :ref:`6 <six>`. Note that a comment after a trailing "&" character
+   will prevent the command from continuing on the next line.  Also note
+   that for multi-line commands a single leading "#" will comment out
+   the entire command.
 
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).
+   .. code-block:: LAMMPS
 
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus ${myTemp} and $x refer to variable names "myTemp" and
-"x".
+      # this is a comment
+      timestep  1.0   # this is also a comment
 
-How the variable is converted to a text string depends on what style
-of variable it is; see the :doc:`variable <variable>` doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
+.. _three:
 
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an :doc:`equal-style variable <variable>`.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
+3. The line is searched repeatedly for $ characters, which indicate
+   variables that are replaced with a text string.  The exception to
+   this rule is described in :ref:`6 <six>`.
+
+   If the $ is followed by text in curly brackets '{}', then the
+   variable name is the text inside the curly brackets.  If no curly
+   brackets follow the $, then the variable name is the single character
+   immediately following the $.  Thus ${myTemp} and $x refer to variables
+   named "myTemp" and "x", while "$xx" will be interpreted as a variable
+   named "x" followed by an "x" character.
+
+   How the variable is converted to a text string depends on what style
+   of variable it is; see the :doc:`variable <variable>` doc page for
+   details.  It can be a variable that stores multiple text strings, and
+   return one of them.  The returned text string can be multiple "words"
+   (space separated) which will then be interpreted as multiple
+   arguments in the input command.  The variable can also store a
+   numeric formula which will be evaluated and its numeric result
+   returned as a string.
+
+   As a special case, if the $ is followed by parenthesis "()", then the
+   text inside the parenthesis is treated as an "immediate" variable and
+   evaluated as an :doc:`equal-style variable <variable>`.  This is a
+   way to use numeric formulas in an input script without having to
+   assign them to variable names.  For example, these 3 input script
+   lines:
+
+   .. code-block:: LAMMPS
+
+      variable X equal (xlo+xhi)/2+sqrt(v_area)
+      region 1 block $X 2 INF INF EDGE EDGE
+      variable X delete
+
+   can be replaced by:
+
+   .. code-block:: LAMMPS
+
+      region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+
+   so that you do not have to define (or discard) a temporary variable,
+   "X" in this case.
+
+   Additionally, the "immediate" variable expression may be followed by
+   a colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+   The format string must be appropriate for a double-precision
+   floating-point value.  The format string is used to output the result
+   of the variable expression evaluation.  If a format string is not
+   specified a high-precision "%.20g" is used as the default.
+
+   This can be useful for formatting print output to a desired precision:
 
 
-.. code-block:: LAMMPS
+   .. code-block:: LAMMPS
 
-   variable X equal (xlo+xhi)/2+sqrt(v_area)
-   region 1 block $X 2 INF INF EDGE EDGE
-   variable X delete
+      print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
 
-can be replaced by
+   Note that neither the curly-bracket or immediate form of variables
+   can contain nested $ characters for other variables to substitute
+   for.  Thus you may **NOT** do this:
 
+   .. code-block:: LAMMPS
 
-.. code-block:: LAMMPS
+      variable        a equal 2
+      variable        b2 equal 4
+      print           "B2 = ${b$a}"
 
-   region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+   Nor can you specify an expression like "$($x-1.0)" for an immediate
+   variable, but you could use $(v\_x-1.0), since the latter is valid
+   syntax for an :doc:`equal-style variable <variable>`.
 
-so that you do not have to define (or discard) a temporary variable X.
+   See the :doc:`variable <variable>` command for more details of how
+   strings are assigned to variables and evaluated, and how they can
+   be used in input script commands.
 
-Additionally, the "immediate" variable expression may be followed by a
-colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-The format string must be appropriate for a double-precision
-floating-point value.  The format string is used to output the result
-of the variable expression evaluation.  If a format string is not
-specified a high-precision "%.20g" is used as the default.
+.. _four:
 
-This can be useful for formatting print output to a desired precision:
+4. The line is broken into "words" separated by white-space (tabs,
+   spaces).  Note that words can thus contain letters, digits,
+   underscores, or punctuation characters.
 
+.. _five:
+   
+5. The first word is the command name.  All successive words in the line
+   are arguments.
 
-.. code-block:: LAMMPS
+.. _six:
 
-   print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
+6. If you want text with spaces to be treated as a single argument, it
+   can be enclosed in either single or double or triple quotes.  A long
+   single argument enclosed in single or double quotes can span multiple
+   lines if the "&" character is used, as described above.  When the
+   lines are concatenated together (and the "&" characters and line
+   breaks removed), the text will become a single line.  If you want
+   multiple lines of an argument to retain their line breaks, the text
+   can be enclosed in triple quotes, in which case "&" characters are
+   not needed.  For example:
 
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
+   .. code-block:: LAMMPS
 
-
-.. code-block:: LAMMPS
-
-   variable        a equal 2
-   variable        b2 equal 4
-   print           "B2 = ${b$a}"
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v\_x-1.0), since the latter is valid syntax for an
-:doc:`equal-style variable <variable>`.
-
-See the :doc:`variable <variable>` command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by white-space (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name.  All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either single or double or triple quotes.  A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above.  When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line.  If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed.  For example:
-
-
-.. code-block:: LAMMPS
-
-   print "Volume = $v"
-   print 'Volume = $v'
-   if "${steps} > 1000" then quit
-   variable a string "red green blue &
+      print "Volume = $v"
+      print 'Volume = $v'
+      if "${steps} > 1000" then quit
+      variable a string "red green blue &
                       purple orange cyan"
-   print """
-   System volume = $v
-   System temperature = $t
-   """
+      print """
+      System volume = $v
+      System temperature = $t
+      """
 
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
+   In each case, the single, double, or triple quotes are removed when
+   the single argument they enclose is stored internally.
 
-See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
-:doc:`if <if>`, and :doc:`python <python>` commands for examples.
+   See the :doc:`dump modify format <dump_modify>`, :doc:`print
+   <print>`, :doc:`if <if>`, and :doc:`python <python>` commands for
+   examples.
 
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
+   A "#" or "$" character that is between quotes will not be treated as
+   a comment indicator in :ref:`2 <two>` or substituted for as a
+   variable in :ref:`3 <three>`.
 
 .. note::
 
@@ -146,8 +163,3 @@ comment indicator in (2) or substituted for as a variable in (3).
    triple quotes can be nested in the usual manner.  See the doc pages
    for those commands for examples.  Only one of level of nesting is
    allowed, but that should be sufficient for most use cases.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_removed.rst

@@ -57,11 +57,6 @@ restart2data tool
 
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read\_restart <read_restart>` and
-:doc:`write\_data <write_data>` can be used to the same effect.  For added
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For added
 convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_structure.rst

@@ -8,17 +8,20 @@ page.
 
 A LAMMPS input script typically has 4 parts:
 
-1. Initialization
-2. Atom definition
-3. Settings
-4. Run a simulation
+1. :ref:`Initialization <init>`
+2. :ref:`System definition <system>` 
+3. :ref:`Simulation settings <settings>`
+4. :ref:`Run a simulation <run>`
 
 The last 2 parts can be repeated as many times as desired.  I.e. run a
 simulation, change some settings, run some more, etc.  Each of the 4
 parts is now described in more detail.  Remember that almost all
 commands need only be used if a non-default value is desired.
 
-(1) Initialization
+.. _init:
+
+Initialization
+------------------------------
 
 Set parameters that need to be defined before atoms are created or
 read-in from a file.
@@ -26,66 +29,74 @@ read-in from a file.
 The relevant commands are :doc:`units <units>`,
 :doc:`dimension <dimension>`, :doc:`newton <newton>`,
 :doc:`processors <processors>`, :doc:`boundary <boundary>`,
-:doc:`atom\_style <atom_style>`, :doc:`atom\_modify <atom_modify>`.
+:doc:`atom_style <atom_style>`, :doc:`atom_modify <atom_modify>`.
 
 If force-field parameters appear in the files that will be read, these
 commands tell LAMMPS what kinds of force fields are being used:
-:doc:`pair\_style <pair_style>`, :doc:`bond\_style <bond_style>`,
-:doc:`angle\_style <angle_style>`, :doc:`dihedral\_style <dihedral_style>`,
-:doc:`improper\_style <improper_style>`.
+:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`,
+:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
+:doc:`improper_style <improper_style>`.
 
-(2) Atom definition
+.. _system:
 
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the :doc:`read\_data <read_data>` or
-:doc:`read\_restart <read_restart>` commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: :doc:`lattice <lattice>`,
-:doc:`region <region>`, :doc:`create\_box <create_box>`,
-:doc:`create\_atoms <create_atoms>`.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-:doc:`replicate <replicate>` command.
+System definition
+------------------------------
 
-(3) Settings
+There are 3 ways to define the simulation cell and reserve space for
+force field info and fill it with atoms in LAMMPS.  Read them in from
+(1) a data file or (2) a restart file via the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands,
+respectively.  These files can also contain molecular topology
+information.  Or (3) create a simulation cell and fill it with atoms on
+a lattice (with no molecular topology), using these commands:
+:doc:`lattice <lattice>`, :doc:`region <region>`, :doc:`create_box
+<create_box>`, :doc:`create_atoms <create_atoms>` or
+:doc:`read_dump <read_dump>`.
+
+The entire set of atoms can be duplicated to make a larger simulation
+using the :doc:`replicate <replicate>` command.
+
+.. _settings:
+
+Simulation settings
+------------------------------
 
 Once atoms and molecular topology are defined, a variety of settings
 can be specified: force field coefficients, simulation parameters,
-output options, etc.
+output options, and more.
 
 Force field coefficients are set by these commands (they can also be
-set in the read-in files): :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_coeff <bond_coeff>`, :doc:`angle\_coeff <angle_coeff>`,
-:doc:`dihedral\_coeff <dihedral_coeff>`,
-:doc:`improper\_coeff <improper_coeff>`,
-:doc:`kspace\_style <kspace_style>`, :doc:`dielectric <dielectric>`,
-:doc:`special\_bonds <special_bonds>`.
+set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
+:doc:`bond_coeff <bond_coeff>`, :doc:`angle_coeff <angle_coeff>`,
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`improper_coeff <improper_coeff>`,
+:doc:`kspace_style <kspace_style>`, :doc:`dielectric <dielectric>`,
+:doc:`special_bonds <special_bonds>`.
 
 Various simulation parameters are set by these commands:
-:doc:`neighbor <neighbor>`, :doc:`neigh\_modify <neigh_modify>`,
+:doc:`neighbor <neighbor>`, :doc:`neigh_modify <neigh_modify>`,
 :doc:`group <group>`, :doc:`timestep <timestep>`,
-:doc:`reset\_timestep <reset_timestep>`, :doc:`run\_style <run_style>`,
-:doc:`min\_style <min_style>`, :doc:`min\_modify <min_modify>`.
+:doc:`reset_timestep <reset_timestep>`, :doc:`run_style <run_style>`,
+:doc:`min_style <min_style>`, :doc:`min_modify <min_modify>`.
 
 Fixes impose a variety of boundary conditions, time integration, and
 diagnostic options.  The :doc:`fix <fix>` command comes in many flavors.
 
 Various computations can be specified for execution during a
 simulation using the :doc:`compute <compute>`,
-:doc:`compute\_modify <compute_modify>`, and :doc:`variable <variable>`
+:doc:`compute_modify <compute_modify>`, and :doc:`variable <variable>`
 commands.
 
 Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
 and :doc:`restart <restart>` commands.
 
-(4) Run a simulation
+.. _run:
+
+Run a simulation
+------------------------------
 
 A molecular dynamics simulation is run using the :doc:`run <run>`
 command.  Energy minimization (molecular statics) is performed using
 the :doc:`minimize <minimize>` command.  A parallel tempering
 (replica-exchange) simulation can be run using the
 :doc:`temper <temper>` command.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Eqs/angle_class2_p6.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

doc/src/Eqs/box.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-a &=& {\rm lx} \\
-b^2 &=&  {\rm ly}^2 +  {\rm xy}^2 \\
-c^2 &=&  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
-\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
-\cos{\beta} &=& \frac{\rm xz}{c} \\
-\cos{\gamma} &=& \frac{\rm xy}{b} \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/box_inverse.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-{\rm lx} &=& a \\
-{\rm xy} &=& b \cos{\gamma}  \\
-{\rm xz} &=& c \cos{\beta}\\
-{\rm ly}^2 &=&   b^2 - {\rm xy}^2 \\
-{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
-{\rm lz}^2 &=&  c^2 - {\rm xz}^2 - {\rm yz}^2 \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/centro_symmetry.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
-$$
-
-\end{document}

doc/src/Eqs/cna_cutoff1.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cna_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_cutoff.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cnp_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_eq.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} |^2
-$$
-
-\end{document}

doc/src/Eqs/compute_dpd.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ 
-   U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
-   U^{chem} = \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
-   U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\
-   \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/compute_fep_bar.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
-
-\end{document}

doc/src/Eqs/compute_fep_fdti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
-    A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
-  A(\lambda_i)}{\delta} \]
-
-\end{document}

doc/src/Eqs/compute_fep_fep.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
-- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
-      U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_lambda.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
-  \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_fep_ti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
-    U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
-    U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_u.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[  U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
-
-\end{document}

doc/src/Eqs/compute_fep_vol.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
-    \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
-\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
-
-\end{document}

doc/src/Eqs/compute_gyration.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
-$$
-
-\end{document}

doc/src/Eqs/compute_msd_nongauss.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
-$$
-
-\end{document}

doc/src/Eqs/compute_saed1.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  I=\frac{F^{*}F}{N}
-$$
-
-\end{document}
-

doc/src/Eqs/compute_saed2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-

doc/src/Eqs/compute_saed3.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
-$$
-\end{document}
-

doc/src/Eqs/compute_shape_parameters.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
- c = l_z - 0.5(l_y+l_x) \\
- b = l_y - l_x \\
- k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
-\end{eqnarray*}
-
-\end{document}
-

doc/src/Eqs/compute_sna_atom1.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom2.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom3.tex

@@ -1,16 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
-
-\begin{equation}
-B_{j_1,j_2,j}  = \\
-\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
-\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
-u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom4.tex

@@ -1,14 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\label{eqn:f_c}
-f_c(r)  & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
-& = & 0,  r > R_{ii'}
-\end{eqnarray*}
-
-
-\end{document}

doc/src/Eqs/compute_sna_atom5.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{equation}
-- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial {\bf r}_i}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom6.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{eqnarray*}
-- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
-\end{eqnarray*}
-
-\end{document}