Merge pull request #2156 from akohlmey/collected-small-changes

Collected changes for the next patch release
2020-06-15 14:40:27 -04:00
parent e083416dd8 0ca7270668
commit c987dfb2c9
195 changed files with 1369 additions and 1036 deletions
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@ -10,6 +10,7 @@ lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
 lib/kim/*             @ellio167
+lib/mesont/*          @iafoss

 # whole packages
 src/COMPRESS/*        @akohlmey
@ -25,6 +26,7 @@ src/USER-COLVARS/*    @giacomofiorin
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
 src/USER-MEAMC/*      @martok
+src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
@ -111,6 +113,7 @@ src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
+src/utils.*               @akohlmey @rbberger

 # tools
 tools/msi2lmp/*       @akohlmey
@ -123,6 +126,8 @@ unittest/*            @akohlmey @rbberger
 # cmake
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/presets/*.cmake @junghans @rbberger @akohlmey

 # python
 python/*              @rbberger
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@ -75,7 +75,9 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * 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 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). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions 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`, `make pdf` 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.
+* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
+* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
+* 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 <name>.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.

 Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.

--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
 - [ ] The added/updated documentation is integrated and tested with the documentation build system
 - [ ] The feature has been verified to work with the conventional build system
 - [ ] The feature has been verified to work with the CMake based build system
+- [ ] Suitable tests have been added to the unittest tree.
 - [ ] A package specific README file has been included or updated
 - [ ] One or more example input decks are included

--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@ -631,6 +631,8 @@ install(
 ###############################################################################
 if(BUILD_SHARED_LIBS)
  if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
    find_package(PythonInterp) # Deprecated since version 3.12
    if(PYTHONINTERP_FOUND)
        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@ -786,3 +788,6 @@ if(PKG_KSPACE)
    endif()
  endif()
 endif()
+if(BUILD_DOC)
+  message(STATUS "<<< Building HTML Manual >>>")
+endif()
--- a/cmake/Modules/Documentation.cmake
+++ b/cmake/Modules/Documentation.cmake
@ -2,10 +2,19 @@
 # Build documentation
 ###############################################################################
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
-if(BUILD_DOC)
-  find_package(PythonInterp 3 REQUIRED)

-  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+if(BUILD_DOC)
+  # Sphinx 3.x requires at least Python 3.5
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 REQUIRED)
+    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
+  else()
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
+    if(Python3_VERSION VERSION_LESS 3.5)
+      message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
+    endif()
+    set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
+  endif()

  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)

@ -25,11 +34,10 @@ if(BUILD_DOC)
  )

  # download mathjax distribution and unpack to folder "mathjax"
-  file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
-    "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-    EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
-
-  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
+    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
    file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
@ -37,11 +45,18 @@ if(BUILD_DOC)
  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
  file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)

+  # for increased browser compatibility
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
+    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
+      "${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
+  endif()
+
  # note, this may run in parallel with other tasks, so we must not use multiple processes here
  add_custom_command(
    OUTPUT html
    DEPENDS ${DOC_SOURCES} docenv requirements.txt
    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
+    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
  )

  # copy selected image files to html output tree
@ -56,17 +71,17 @@ if(BUILD_DOC)
  set(HTML_IMAGE_TARGETS "")
  foreach(_IMG ${HTML_EXTRA_IMAGES})
    string(PREPEND _IMG JPG/)
-    list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
+    list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
    add_custom_command(
      OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
-      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
+      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
      COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
    )
  endforeach()

  add_custom_target(
    doc ALL
-    DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
+    DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
  )

--- a/cmake/Modules/LAMMPSUtils.cmake
+++ b/cmake/Modules/LAMMPSUtils.cmake
@ -96,9 +96,15 @@ function(FetchPotentials pkgfolder potfolder)
      math(EXPR plusone "${blank}+1")
      string(SUBSTRING ${line} 0 ${blank} pot)
      string(SUBSTRING ${line} ${plusone} -1 sum)
-      message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-      file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${LAMMPS_POTENTIALS_DIR}/${pot}"
-        EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
+      if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
+        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+      endif()
+      if(NOT sum STREQUAL oldsum)
+        message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+          EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
+        file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
+      endif()
    endforeach()
  endif()
 endfunction(FetchPotentials)
--- a/cmake/Modules/Packages/USER-SCAFACOS.cmake
+++ b/cmake/Modules/Packages/USER-SCAFACOS.cmake
@ -14,6 +14,29 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
  message(STATUS "ScaFaCoS download requested - we will build our own")
+  # create variables to pass our compiler flags along to the subsystem compile
+  # need to apply -fallow-argument-mismatch, if the fortran compiler supports it
+  include(CheckFortranCompilerFlag)
+  check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
+  if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
+    set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
+  endif()
+  if(CMAKE_Fortran_FLAGS)
+    set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
+  else()
+    set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
+  endif()
+  if(CMAKE_CXX_FLAGS)
+      set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+    else()
+      set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
+  endif()
+  if(CMAKE_C_FLAGS)
+      set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
+    else()
+      set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
+  endif()
+
  include(ExternalProject)
  ExternalProject_Add(scafacos_build
    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
@ -22,9 +45,9 @@ if(DOWNLOAD_SCAFACOS)
                                             --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                             --with-internal-fftw --with-internal-pfft
                                             --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
-                                             FC=${CMAKE_MPI_Fortran_COMPILER}
-                                             CXX=${CMAKE_MPI_CXX_COMPILER}
-                                             CC=${CMAKE_MPI_C_COMPILER}
+                                             FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
+                                             CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
+                                             CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
                                             F77=
    BUILD_BYPRODUCTS
      <INSTALL_DIR>/lib/libfcs.a
--- a/cmake/presets/download.cmake
+++ b/cmake/presets/download.cmake
@ -0,0 +1,17 @@
+# preset that turns on packages with automatic downloads of sources of potentials
+# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)
+
--- a/cmake/presets/mingw-cross.cmake
+++ b/cmake/presets/mingw-cross.cmake
@ -4,7 +4,7 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                 USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
-                 USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
+                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
                 USER-YAFF)
--- a/doc/src/Build_basics.rst
+++ b/doc/src/Build_basics.rst
@ -225,7 +225,7 @@ A few example command lines are:

 For compiling with the Clang/LLVM compilers a CMake preset is provided that
 can be loaded with `-C ../cmake/presets/clang.cmake`.  Similarly,
-`-C ../cmake/presets/intel.cmake` should switch the 
+`-C ../cmake/presets/intel.cmake` should switch the

 In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
 compiler flags to tune for optimal performance on given hosts. By
@ -372,7 +372,8 @@ it.  The build step 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**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^

 Note that for creating a shared library, all the libraries it depends on
 must be compiled to be compatible with shared libraries.  This should be
@ -462,7 +463,8 @@ 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**\ :
+Documentation make option
+^^^^^^^^^^^^^^^^^^^^^^^^^

 The following make commands can be issued in the doc folder of the
 LAMMPS source distribution.
@ -489,7 +491,8 @@ your system.
   current LAMMPS version (HTML and PDF files), from the website
   `download page <https://lammps.sandia.gov/download.html>`_.

-**CMake build option**\ :
+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
@ -512,7 +515,8 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.

-**CMake build3**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -521,7 +525,8 @@ using CMake or Make.
 The generated binaries will also become part of the LAMMPS installation
 (see below).

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: bash

@ -545,7 +550,8 @@ 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 build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -553,7 +559,8 @@ you want to copy files to is protected.
   make                        # perform make after CMake command
   make install                # perform the installation into prefix

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 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
--- a/doc/src/Build_development.rst
+++ b/doc/src/Build_development.rst
@ -126,7 +126,7 @@ in the next section.

 .. note::

-   This unit test framework is new and still under development.
+   The unit test framework is new and still under development.
   The coverage is only minimal and will be expanded over time.
   Tests styles of the same kind of style (e.g. pair styles or
   bond styles) are performed with the same executable using
@ -237,12 +237,12 @@ and working.
     performed with automatically rescaled epsilon to account for
     additional loss of precision from code optimizations and different
     summation orders.
-   - When compiling with aggressive compiler optimization, some tests
+   - When compiling with (aggressive) compiler optimization, some tests
     are likely to fail.  It is recommended to inspect the individual
-     tests in detail to decide whether the specific error for a specific
+     tests in detail to decide, whether the specific error for a specific
     property is acceptable (it often is), or this may be an indication
-     of mis-compiled code (or undesired large of precision due to
-     reordering of operations).
+     of mis-compiled code (or an undesired large loss of precision due
+     to significant reordering of operations and thus less error cancellation).

 Collect and visualize code coverage metrics
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@ -60,12 +60,13 @@ This is the list of packages that may require additional steps.
 .. _compress:

 COMPRESS package
-------------------------------
+----------------

 To build with this package you must have the zlib compression library
 available on your system.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 If CMake cannot find the library, you can set these variables:

@ -74,10 +75,11 @@ If CMake cannot find the library, you can set these variables:
   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 If make cannot find the library, you can edit the file
-lib/compress/Makefile.lammps to specify the paths and library
+``lib/compress/Makefile.lammps`` to specify the paths and library
 name.

 ----------
@ -91,7 +93,8 @@ To build with this package, you must choose options for precision and
 which GPU hardware to build for. The GPU package currently supports
 three different types of backends: OpenCL, CUDA and HIP.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -159,7 +162,8 @@ and the linker to work correctly.
   cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
   make -j 4

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
 You can do this manually if you prefer; follow the instructions in
@ -208,10 +212,10 @@ your machine are not correct, the LAMMPS build will fail, and

 .. note::

-   If you re-build the GPU library in lib/gpu, you should always
-   un-install the GPU package in lammps/src, then re-install it and
+   If you re-build the GPU library in ``lib/gpu``, you should always
+   un-install the GPU package in ``lammps/src``, then re-install it and
   re-build LAMMPS.  This is because the compilation of files in the GPU
-   package uses the library settings from the lib/gpu/Makefile.machine
+   package uses the library settings from the ``lib/gpu/Makefile.machine``
   used to build the GPU library.

 ----------
@ -250,7 +254,8 @@ See the list of all KIM models here: https://openkim.org/browse/models
 the KIM API library with all its models, may take a long time (tens of
 minutes to hours) to build.  Of course you only need to do that once.)

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -282,7 +287,8 @@ 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**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download and build the KIM library manually if you prefer;
 follow the instructions in ``lib/kim/README``\ .  You can also do it in one
@ -300,7 +306,7 @@ invoke the ``lib/kim/Install.py`` script with the specified args.
  $ 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
+them to the ``LMP_INC`` variable through editing the ``Makefile.machine`` you are
 using.  For example:

 .. code-block:: make
@ -605,7 +611,8 @@ LATTE package
 To build with this package, you must download and build the LATTE
 library.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -618,7 +625,8 @@ already on your system (in a location CMake cannot find it),
 ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file,
 not the directory the library file is in.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download and build the LATTE library manually if you prefer;
 follow the instructions in ``lib/latte/README``\ .  You can also do it in
@ -634,11 +642,12 @@ args:
  $ 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
-"filelink.o", are created in lib/latte to point into the LATTE home
-dir.  When LAMMPS itself is built it will use these links.  You should
-also check that the Makefile.lammps file you create is appropriate for
-the compiler you use on your system to build LATTE.
+Note that 3 symbolic (soft) links, ``includelink`` and ``liblink`` and
+``filelink.o``, are created in ``lib/latte`` to point to required
+folders and files in the LATTE home directory.  When LAMMPS itself is
+built it will use these links.  You should also check that the
+``Makefile.lammps`` file you create is appropriate for the compiler you
+use on your system to build LATTE.

 ----------

@ -651,7 +660,8 @@ This package can optionally include support for messaging via sockets,
 using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
 be installed on your system.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -659,7 +669,8 @@ be installed on your system.
   -D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
   -D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 Before building LAMMPS, you must build the CSlib library in
 ``lib/message``\ .  You can build the CSlib library manually if you prefer;
@ -674,8 +685,8 @@ simply invoke the ``lib/message/Install.py`` script with the specified args:
  $ 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
-existing ``Makefile.lammps.\*`` and has settings to link with the ZeroMQ
+and ``lib/message/Makefile.lammps``.  The latter is copied from an
+existing ``Makefile.lammps.*`` and has settings to link with the ZeroMQ
 library if requested in the build.

 ----------
@ -691,7 +702,8 @@ library.  Building the MS-CG library requires that the GSL
 machine.  See the ``lib/mscg/README`` and ``MSCG/Install`` files for
 more details.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -706,7 +718,8 @@ filename (plus path) of the MSCG library file, not the directory the
 library file is in.  ``MSCG_INCLUDE_DIR`` is the directory the MSCG
 include file is in.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download and build the MS-CG library manually if you prefer;
 follow the instructions in ``lib/mscg/README``\ .  You can also do it in one
@ -734,16 +747,18 @@ not need to edit the ``lib/mscg/Makefile.lammps`` file.
 OPT package
 ---------------------

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 No additional settings are needed besides ``-D PKG_OPT=yes``

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-The compile flag "-restrict" must be used to build LAMMPS with the OPT
+The compile flag ``-restrict`` must be used to build LAMMPS with the OPT
 package when using Intel compilers.  It should be added to the CCFLAGS
-line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
-an example.
+line of your ``Makefile.machine``.  See
+``src/MAKE/OPTIONS/Makefile.opt`` for an example.

 ----------

@ -752,11 +767,13 @@ an example.
 POEMS package
 -------------------------

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 No additional settings are needed besides ``-D PKG_OPT=yes``

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ .
 You can do this manually if you prefer; follow the instructions in
@ -772,8 +789,8 @@ dir, using a command like these, which simply invoke the
  $ 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
-``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the
+``lib/poems/Makefile.lammps``.  The latter is copied from an existing
+``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
 POEMS library (though typically the settings are just blank).  If
 necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file
 for your system, which should define an ``EXTRAMAKE`` variable to specify
@ -791,7 +808,8 @@ library available on your system, which needs to be a Python 2.7
 version or a Python 3.x version.  See ``lib/python/README`` for more
 details.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -804,11 +822,12 @@ PYTHON_EXECUTABLE variable to specify which Python interpreter should
 be used.  Note note that you will also need to have the development
 headers installed for this version, e.g. python2-devel.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 The build uses the ``lib/python/Makefile.lammps`` file in the compile/link
 process to find Python.  You should only need to create a new
-``Makefile.lammps.\*`` file (and copy it to ``Makefile.lammps``\ ) if
+``Makefile.lammps.*`` file (and copy it to ``Makefile.lammps``) if
 the LAMMPS build fails.

 ----------
@ -822,7 +841,8 @@ To build with this package, you must download and build the `Voro++ library <vor

 .. _voro-home: http://math.lbl.gov/voro++

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -830,19 +850,20 @@ To build with this package, you must download and build the `Voro++ library <vor
   -D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
   -D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location)

-If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
+If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded and
 built inside the CMake build directory.  If the Voro++ library is
 already on your system (in a location CMake cannot find it),
-VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
-not the directory the library file is in.  VORO_INCLUDE_DIR is the
+``VORO_LIBRARY`` is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in.  ``VORO_INCLUDE_DIR`` is the
 directory the Voro++ include file is in.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download and build the Voro++ library manually if you prefer;
-follow the instructions in lib/voronoi/README.  You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/voronoi/Install.py script with the specified
+follow the instructions in ``lib/voronoi/README``.  You can also do it in
+one step from the ``lammps/src`` dir, using a command like these, which
+simply invoke the ``lib/voronoi/Install.py`` script with the specified
 args:

 .. code-block:: bash
@ -852,10 +873,10 @@ args:
  $ 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
-builds in src it will use these links.  You should not need to edit
-the lib/voronoi/Makefile.lammps file.
+Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
+created in lib/voronoi to point to the Voro++ source dir.  When LAMMPS
+builds in ``src`` it will use these links.  You should not need to edit
+the ``lib/voronoi/Makefile.lammps`` file.

 ----------

@ -864,23 +885,28 @@ the lib/voronoi/Makefile.lammps file.
 USER-ADIOS package
 -----------------------------------

-The USER-ADIOS package requires the `ADIOS I/O library <https://github.com/ornladios/ADIOS2>`_,
-version 2.3.1 or newer. Make sure that you have ADIOS built either with or
-without MPI to match if you build LAMMPS with or without MPI.
-ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
-and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
-installation and the instructions below are followed for the respective build systems.
+The USER-ADIOS package requires the `ADIOS I/O library
+<https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
+sure that you have ADIOS built either with or without MPI to match if
+you build LAMMPS with or without MPI.  ADIOS compilation settings for
+LAMMPS are automatically detected, if the PATH and LD_LIBRARY_PATH
+environment variables have been updated for the local ADIOS installation
+and the instructions below are followed for the respective build
+systems.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

   -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
   -D PKG_USER-ADIOS=yes

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-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:
+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:

 .. code-block:: bash

@ -901,18 +927,20 @@ USER-ATC package

 The USER-ATC package requires the MANYBODY package also be installed.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 No additional settings are needed besides "-D PKG_USER-ATC=yes"
 and "-D PKG_MANYBODY=yes".

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-Before building LAMMPS, you must build the ATC library in lib/atc.
+Before building LAMMPS, you must build the ATC library in ``lib/atc``.
 You can do this manually if you prefer; follow the instructions in
-lib/atc/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/atc/Install.py script with the specified args:
+``lib/atc/README``.  You can also do it in one step from the
+``lammps/src`` dir, using a command like these, which simply invoke the
+``lib/atc/Install.py`` script with the specified args:

 .. code-block:: bash

@ -921,19 +949,19 @@ lib/atc/Install.py script with the specified args:
  $ 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
-Makefile.lammps.\* and has settings needed to build LAMMPS with the ATC
-library.  If necessary, you can edit/create a new
-lib/atc/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
+The build should produce two files: ``lib/atc/libatc.a`` and
+``lib/atc/Makefile.lammps``.  The latter is copied from an existing
+``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
+ATC library.  If necessary, you can edit/create a new
+``lib/atc/Makefile.machine`` file for your system, which should define
+an ``EXTRAMAKE`` variable to specify a corresponding
+``Makefile.lammps.<machine>`` file.

 Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries.  As explained in lib/atc/README these
+LAPACK linear algebra libraries.  As explained in ``lib/atc/README`` these
 can either exist on your system, or you can use the files provided in
-lib/linalg.  In the latter case you also need to build the library in
-lib/linalg with a command like these:
+``lib/linalg``.  In the latter case you also need to build the library in
+``lib/linalg`` with a command like these:

 .. code-block:: bash

@ -947,19 +975,21 @@ lib/linalg with a command like these:
 .. _user-awpmd:

 USER-AWPMD package
-----------------------------------
+------------------

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-No additional settings are needed besides "-D PKG_USER-AQPMD=yes".
+No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-Before building LAMMPS, you must build the AWPMD library in lib/awpmd.
+Before building LAMMPS, you must build the AWPMD library in ``lib/awpmd``.
 You can do this manually if you prefer; follow the instructions in
-lib/awpmd/README.  You can also do it in one step from the lammps/src
+``lib/awpmd/README``.  You can also do it in one step from the ``lammps/src``
 dir, using a command like these, which simply invoke the
-lib/awpmd/Install.py script with the specified args:
+``lib/awpmd/Install.py`` script with the specified args:

 .. code-block:: bash

@ -968,19 +998,19 @@ lib/awpmd/Install.py script with the specified args:
  $ 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
-Makefile.lammps.\* and has settings needed to build LAMMPS with the
+The build should produce two files: ``lib/awpmd/libawpmd.a`` and
+``lib/awpmd/Makefile.lammps``.  The latter is copied from an existing
+``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
 AWPMD library.  If necessary, you can edit/create a new
-lib/awpmd/Makefile.machine file for your system, which should define
-an EXTRAMAKE variable to specify a corresponding
-Makefile.lammps.machine file.
+``lib/awpmd/Makefile.machine`` file for your system, which should define
+an ``EXTRAMAKE`` variable to specify a corresponding
+``Makefile.lammps.<machine>`` file.

-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries.  As explained in lib/awpmd/README
+Note that the ``Makefile.lammps`` file has settings for the BLAS and
+LAPACK linear algebra libraries.  As explained in ``lib/awpmd/README``
 these can either exist on your system, or you can use the files
-provided in lib/linalg.  In the latter case you also need to build the
-library in lib/linalg with a command like these:
+provided in ``lib/linalg``.  In the latter case you also need to build the
+library in ``lib/linalg`` with a command like these:

 .. code-block:: bash

@ -999,36 +1029,26 @@ USER-COLVARS package
 This package includes into the LAMMPS distribution the Colvars library, which
 can be built for the most part with all major versions of the C++ language.

-A few of the most recent features require C++11 support.  In particular, the
-library is optionally built together with the
-`Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also
-included in the LAMMPS distribution.  Lepton implements the
-`customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_
-feature, and requires C++11 support.

-See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of
-C++11-only features.
-
-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 This is the recommended build recipe: no additional settings are normally
-needed besides "-D PKG_USER-COLVARS=yes".
+needed besides ``-D PKG_USER-COLVARS=yes``.

-Building and linking of Lepton (or other C++11-only features) is enabled
-automatically when compilation is carried out with C++11 support, and disabled
-otherwise.  Optionally, Lepton build may be manually controlled with the flag
-"-D COLVARS_LEPTON=yes\|no".
-
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 Before building LAMMPS, one must build the Colvars library in lib/colvars.

-This can be done manually in the same folder by using or adapting one of the
-provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+This can be done manually in the same folder by using or adapting one of
+the provided Makefiles: for example, ``Makefile.g++`` for the GNU C++
+compiler.  C++11 compatibility may need to be enabled for some older
+compilers (as is done in the example makefile).

 In general, it is safer to use build setting consistent with the rest of
 LAMMPS.  This is best carried out from the LAMMPS src directory using a
-command like these, which simply invoke the lib/colvars/Install.py script with
+command like these, which simply invoke the ``lib/colvars/Install.py`` script with
 the specified args:

 .. code-block:: bash
@ -1039,7 +1059,7 @@ the specified args:
  $ 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
+use as build recipe.  If it does not already exist in ``lib/colvars``, it will be
 auto-generated by using compiler flags consistent with those parsed from the
 core LAMMPS makefiles.

@ -1050,9 +1070,9 @@ 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)

-The build should produce two files: the library lib/colvars/libcolvars.a
+The build should produce two files: the library ``lib/colvars/libcolvars.a``
 (which also includes Lepton objects if enabled) and the specification file
-lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+``lib/colvars/Makefile.lammps``.  The latter is auto-generated, and normally does
 not need to be edited.

 ----------
@ -1099,12 +1119,14 @@ try a different one, switch to a different build system, consider a
 global PLUMED installation or consider downloading PLUMED during the
 LAMMPS build.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
-must ensure that GSL is installed in locations that are specified in
-your environment.  There are then two additional commands that control
-the manner in which PLUMED is obtained and linked into LAMMPS.
+When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
+command you must ensure that GSL is installed in locations that are
+specified in your environment.  There are then two additional variables
+that control the manner in which PLUMED is obtained and linked into
+LAMMPS.

 .. code-block:: bash

@ -1114,21 +1136,22 @@ the manner in which PLUMED is obtained and linked into LAMMPS.
 If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
 downloaded (the version of PLUMED that will be downloaded is hard-coded
 to a vetted version of PLUMED, usually a recent stable release version)
-and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
-to "no" (the default), CMake will try to detect and link to an installed
-version of PLUMED.  For this to work, the PLUMED library has to be
-installed into a location where the pkg-config tool can find it or the
-PKG_CONFIG_PATH environment variable has to be set up accordingly.
-PLUMED should be installed in such a location if you compile it using
-the default make; make install commands.
+and built inside the CMake build directory.  If ``DOWNLOAD_PLUMED`` is
+set to "no" (the default), CMake will try to detect and link to an
+installed version of PLUMED.  For this to work, the PLUMED library has
+to be installed into a location where the ``pkg-config`` tool can find
+it or the PKG_CONFIG_PATH environment variable has to be set up
+accordingly.  PLUMED should be installed in such a location if you
+compile it using the default make; make install commands.

-The PLUMED_MODE setting determines the linkage mode for the PLUMED
+The ``PLUMED_MODE`` setting determines the linkage mode for the PLUMED
 library.  The allowed values for this flag are "static" (default),
 "shared", or "runtime".  For a discussion of PLUMED linkage modes,
-please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
-mode is recommended.
+please see above.  When ``DOWNLOAD_PLUMED`` is enabled the static
+linkage mode is recommended.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 PLUMED needs to be installed before the USER-PLUMED package is installed
 so that LAMMPS can find the right settings when compiling and linking
@ -1149,9 +1172,9 @@ from the src folder through the following make args:
  $ 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
+Note that 2 symbolic (soft) links, ``includelink`` and ``liblink`` are
 created in lib/plumed that point to the location of the PLUMED build to
-use. A new file lib/plumed/Makefile.lammps is also created with settings
+use. A new file ``lib/plumed/Makefile.lammps`` is also created with settings
 suitable for LAMMPS to compile and link PLUMED using the desired linkage
 mode. After this step is completed, you can install the USER-PLUMED
 package and compile LAMMPS in the usual manner:
@ -1186,9 +1209,10 @@ To build with this package you must have the HDF5 software package
 installed on your system, which should include the h5cc compiler and
 the HDF5 library.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-No additional settings are needed besides "-D PKG_USER-H5MD=yes".
+No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.

 This should auto-detect the H5MD library on your system.  Several
 advanced CMake H5MD options exist if you need to specify where it is
@ -1196,26 +1220,27 @@ installed.  Use the ccmake (terminal window) or cmake-gui (graphical)
 tools to see these options and set them interactively from their user
 interfaces.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-Before building LAMMPS, you must build the CH5MD library in lib/h5md.
-You can do this manually if you prefer; follow the instructions in
-lib/h5md/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/h5md/Install.py script with the specified args:
+Before building LAMMPS, you must build the CH5MD library in
+``lib/h5md``.  You can do this manually if you prefer; follow the
+instructions in ``lib/h5md/README``.  You can also do it in one step
+from the ``lammps/src`` dir, using a command like these, which simply
+invoke the ``lib/h5md/Install.py`` script with the specified args:

 .. code-block:: bash

  $ 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
-Makefile.lammps.\* and has settings needed to build LAMMPS with the
+The build should produce two files: ``lib/h5md/libch5md.a`` and
+``lib/h5md/Makefile.lammps``.  The latter is copied from an existing
+``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
 system HDF5 library.  If necessary, you can edit/create a new
-lib/h5md/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
+``lib/h5md/Makefile.machine`` file for your system, which should define
+an EXTRAMAKE variable to specify a corresponding
+``Makefile.lammps.<machine>`` file.

 ----------

@ -1230,7 +1255,8 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
 used in tandem with the USER-INTEL package to good effect, as explained
 on the :doc:`Speed intel <Speed_intel>` doc page.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -1249,11 +1275,12 @@ Best performance is achieved with Intel hardware, Intel compilers, as well as
 the Intel TBB and MKL libraries. However, the code also compiles, links, and
 runs with other compilers and without TBB and MKL.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 Choose which hardware to compile for in Makefile.machine via the
-following settings.  See src/MAKE/OPTIONS/Makefile.intel_cpu\* and
-Makefile.knl files for examples. and src/USER-INTEL/README for
+following settings.  See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and
+``Makefile.knl`` files for examples. and ``src/USER-INTEL/README`` for
 additional information.

 For CPUs:
@ -1320,7 +1347,8 @@ define an ``EXTRAMAKE`` variable to specify a corresponding
 USER-MOLFILE package
 ---------------------------------------

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -1335,13 +1363,14 @@ folder of the local VMD installation in use. LAMMPS ships with a
 couple of default header files that correspond to a popular VMD
 version, usually the latest release.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-The lib/molfile/Makefile.lammps file has a setting for a dynamic
+The ``lib/molfile/Makefile.lammps`` file has a setting for a dynamic
 loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
-file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
+file.  See ``lib/molfile/README`` and ``lib/molfile/Makefile.lammps`` for
 details. It is also possible to configure a different folder with
 the VMD molfile plugin header files. LAMMPS ships with a couple of
 default headers, but these are not compatible with all VMD versions,
@ -1358,22 +1387,24 @@ USER-NETCDF package
 To build with this package you must have the NetCDF library installed
 on your system.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
+No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.

 This should auto-detect the NETCDF library if it is installed on your
 system at standard locations.  Several advanced CMake NETCDF options
-exist if you need to specify where it was installed.  Use the ccmake
-(terminal window) or cmake-gui (graphical) tools to see these options
-and set them interactively from their user interfaces.
+exist if you need to specify where it was installed.  Use the ``ccmake``
+(terminal window) or ``cmake-gui`` (graphical) tools to see these
+options and set them interactively from their user interfaces.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-The lib/netcdf/Makefile.lammps file has settings for NetCDF include
+The ``lib/netcdf/Makefile.lammps`` file has settings for NetCDF include
 and library files which LAMMPS needs to build with this package.  If
 the settings are not valid for your system, you will need to edit the
-Makefile.lammps file.  See lib/netcdf/README for details.
+``Makefile.lammps`` file.  See ``lib/netcdf/README`` for details.

 ----------

@ -1382,18 +1413,20 @@ Makefile.lammps file.  See lib/netcdf/README for details.
 USER-OMP package
 -------------------------------

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-No additional settings are required besides "-D PKG_USER-OMP=yes".  If
+No additional settings are required besides ``-D PKG_USER-OMP=yes``.  If
 CMake detects OpenMP support, the USER-OMP code will be compiled with
 multi-threading support enabled, otherwise as optimized serial code.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 To enable multi-threading support in the USER-OMP package (and other
-styles supporting OpenMP) the following compile and link flags must
-be added to your Makefile.machine file.
-See src/MAKE/OPTIONS/Makefile.omp for an example.
+styles supporting OpenMP) the following compile and link flags must be
+added to your Makefile.machine file.  See
+``src/MAKE/OPTIONS/Makefile.omp`` for an example.

 .. parsed-literal::

@ -1403,8 +1436,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
   LINKFLAGS: -qopenmp             # for Intel compilers on Linux

 For other platforms and compilers, please consult the documentation
-about OpenMP support for your compiler. Please see the note about
-how to address compatibility :ref:`issues with the 'default(none)' directive <default-none-issues>` of some compilers.
+about OpenMP support for your compiler.

 ----------

@ -1414,19 +1446,20 @@ USER-QMMM package
 ---------------------------------

 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.
+need to build LAMMPS as a library.  A LAMMPS executable with :doc:`fix
+qmmm <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**\ :
+CMake build
+^^^^^^^^^^^

 When using CMake, building a LAMMPS library is required and it is
 recommended to build a shared library, since any libraries built from
@ -1443,17 +1476,18 @@ would be:

 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
+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
+(pwqmmm.x) in the ``lib/qmmm`` folder.  You need to make certain, that

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-Before building LAMMPS, you must build the QMMM library in lib/qmmm.
+Before building LAMMPS, you must build the QMMM library in ``lib/qmmm``.
 You can do this manually if you prefer; follow the first two steps
-explained in lib/qmmm/README.  You can also do it in one step from the
-lammps/src dir, using a command like these, which simply invoke the
-lib/qmmm/Install.py script with the specified args:
+explained in ``lib/qmmm/README``.  You can also do it in one step from
+the ``lammps/src`` dir, using a command like these, which simply invoke
+the ``lib/qmmm/Install.py`` script with the specified args:

 .. code-block:: bash

@ -1462,18 +1496,18 @@ lib/qmmm/Install.py script with the specified args:
  $ 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
-Makefile.lammps.\* and has settings needed to build LAMMPS with the
+The build should produce two files: ``lib/qmmm/libqmmm.a`` and
+``lib/qmmm/Makefile.lammps``.  The latter is copied from an existing
+``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
 QMMM library (though typically the settings are just blank).  If
-necessary, you can edit/create a new lib/qmmm/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
+necessary, you can edit/create a new ``lib/qmmm/Makefile.<machine>`` file
+for your system, which should define an ``EXTRAMAKE`` variable to
+specify 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 (via "make couple"), go back to
-the lib/qmmm folder and follow the instructions in the README file 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.

@ -1488,26 +1522,28 @@ To build with this package, you must download and build the QUIP
 library.  It can be obtained from GitHub.  For support of GAP
 potentials, additional files with specific licensing conditions need
 to be downloaded and configured.  See step 1 and step 1.1 in the
-lib/quip/README file for details on how to do this.
+``lib/quip/README`` file for details on how to do this.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

   -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)

 CMake will not download and build the QUIP library.  But once you have
-done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should
+done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
 work.  Set QUIP_LIBRARY if CMake cannot find the QUIP library.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 The download/build procedure for the QUIP library, described in
-lib/quip/README file requires setting two environment variables,
+``lib/quip/README`` file requires setting two environment variables,
 QUIP_ROOT and QUIP_ARCH.  These are accessed by the
 lib/quip/Makefile.lammps file which is used when you compile and link
 LAMMPS with this package.  You should only need to edit
-Makefile.lammps if the LAMMPS build can not use its settings to
+``Makefile.lammps`` if the LAMMPS build can not use its settings to
 successfully build on your system.

 ----------
@ -1517,11 +1553,13 @@ successfully build on your system.
 USER-SCAFACOS package
 -----------------------------------------

-To build with this package, you must download and build the `ScaFaCoS Coulomb solver library <scafacos-home_>`_
+To build with this package, you must download and build the `ScaFaCoS
+Coulomb solver library <scafacos-home_>`_

 .. _scafacos-home: http://www.scafacos.de

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -1536,22 +1574,23 @@ SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
 file, not the directory the library file is in.  SCAFACOS_INCLUDE_DIR
 is the directory the ScaFaCoS include file is in.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download and build the ScaFaCoS library manually if you
-prefer; follow the instructions in lib/scafacos/README.  You can also
-do it in one step from the lammps/src dir, using a command like these,
-which simply invoke the lib/scafacos/Install.py script with the
+prefer; follow the instructions in ``lib/scafacos/README``.  You can also
+do it in one step from the ``lammps/src`` dir, using a command like these,
+which simply invoke the ``lib/scafacos/Install.py`` script with the
 specified args:

 make lib-scafacos                         # print help message
 make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>
 make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos

-Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-created in lib/scafacos to point to the ScaFaCoS src dir.  When LAMMPS
+Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
+created in ``lib/scafacos`` to point to the ScaFaCoS src dir.  When LAMMPS
 builds in src it will use these links.  You should not need to edit
-the lib/scafacos/Makefile.lammps file.
+the ``lib/scafacos/Makefile.lammps`` file.

 ----------

@ -1563,24 +1602,26 @@ USER-SMD package
 To build with this package, you must download the Eigen3 library.
 Eigen3 is a template library, so you do not need to build it.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. 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)

-If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
+If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be downloaded and
 inside the CMake build directory.  If the Eigen3 library is already on
-your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
+your system (in a location CMake cannot find it), ``EIGEN3_INCLUDE_DIR``
 is the directory the Eigen3++ include file is in.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 You can download the Eigen3 library manually if you prefer; follow the
-instructions in lib/smd/README.  You can also do it in one step from
-the lammps/src dir, using a command like these, which simply invoke
-the lib/smd/Install.py script with the specified args:
+instructions in ``lib/smd/README``.  You can also do it in one step from
+the ``lammps/src`` dir, using a command like these, which simply invoke
+the ``lib/smd/Install.py`` script with the specified args:

 .. code-block:: bash

@ -1588,9 +1629,9 @@ the lib/smd/Install.py script with the specified args:
  $ 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
-this link.  You should not need to edit the lib/smd/Makefile.lammps
+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
+this link.  You should not need to edit the ``lib/smd/Makefile.lammps``
 file.

 ----------
@ -1603,21 +1644,23 @@ USER-VTK package
 To build with this package you must have the VTK library installed on
 your system.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

-No additional settings are needed besides "-D PKG_USER-VTK=yes".
+No additional settings are needed besides ``-D PKG_USER-VTK=yes``.

 This should auto-detect the VTK library if it is installed on your
 system at standard locations.  Several advanced VTK options exist if
-you need to specify where it was installed.  Use the ccmake (terminal
-window) or cmake-gui (graphical) tools to see these options and set
+you need to specify where it was installed.  Use the ``ccmake`` (terminal
+window) or ``cmake-gui`` (graphical) tools to see these options and set
 them interactively from their user interfaces.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

-The lib/vtk/Makefile.lammps file has settings for accessing VTK files
+The ``lib/vtk/Makefile.lammps`` file has settings for accessing VTK files
 and its library, which LAMMPS needs to build with this package.  If
 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
+``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.
+edit the ``Makefile.lammps`` file.  See ``lib/vtk/README`` for details.
--- a/doc/src/Build_link.rst
+++ b/doc/src/Build_link.rst
@ -1,12 +1,12 @@
 Link LAMMPS as a library to another code
 ========================================

-LAMMPS is designed as a library of C++ objects and can thus be
+LAMMPS is designed as a library of C++ objects that can be
 integrated into other applications including Python scripts.
 The files ``src/library.cpp`` and ``src/library.h`` define a
 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.
+library <Howto_library>` page for a description of the interface
+and how to use 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 a file
@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
   communicator with a subset of MPI ranks to the function creating the
   LAMMPS instance.

----------
-
-**Link with LAMMPS as a static library**\ :
+Link with LAMMPS as a static library
+------------------------------------

 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*.
+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.

-*CMake build*\ :
+CMake build
+^^^^^^^^^^^

 This assumes that LAMMPS has been configured without setting a
 ``LAMMPS_MACHINE`` name, installed with "make install", and the
@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
   mpicxx -o caller caller.o -$(pkgconf liblammps --libs)

-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 This assumes that LAMMPS has been compiled in the folder
 ``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
 need to include all flags, libraries, and paths for the coupled
 executable, that are also required to link the LAMMPS executable.

-*CMake build*\ :
+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*
+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.

-.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
-
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 After you have compiled a static LAMMPS library using the conventional
 build system for example with "make mode=static serial". And you also
@ -110,10 +111,10 @@ change to:
   g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
     -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs

-Note, that you need to link with "g++" instead of "gcc", since the
-LAMMPS library is C++ code.  You can display the currently applied
-settings for building LAMMPS for the "serial" machine target by using
-the command:
+Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
+written your code in C, since LAMMPS itself 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

@ -123,25 +124,24 @@ Which should output something like:

 .. code-block:: bash

-   # Compiler: 
+   # Compiler:
   CXX=g++
-   # Linker: 
+   # Linker:
   LD=g++
-   # Compilation: 
+   # Compilation:
   CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
-   # Linking: 
+   # Linking:
   LDFLAGS=-g -O
-   # Libraries: 
+   # Libraries:
   LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/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
+equivalent and replace "serial" with the corresponding "machine" name
 of the makefile.

----------
-
-**Link with LAMMPS as a shared library**\ :
+Link with LAMMPS as a shared library
+------------------------------------

 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
@ -151,7 +151,8 @@ 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:

-*CMake build*\ :
+CMake build
+^^^^^^^^^^^

 The commands with a shared LAMMPS library compiled with the CMake
 build process are the same as for the static library.
@ -161,10 +162,11 @@ build process are the same as for the static library.
   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
   mpicxx -o caller caller.o -$(pkgconf --libs)

-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 The commands with a shared LAMMPS library compiled with the
-traditional make build using "make mode=shared serial" becomes:
+traditional make build using ``make mode=shared serial`` becomes:

 .. code-block:: bash

@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
        libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)

----------
-
-**Calling the LAMMPS library**\ :
-
-Either flavor of library (static or shared) allows one or more LAMMPS
-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.
-
-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 from a shared library through the `ctypes python module <ctypes_>`_.
-
-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.
-
-.. _ctypes: https://docs.python.org/3/library/ctypes.html
--- a/doc/src/Build_package.rst
+++ b/doc/src/Build_package.rst
@ -45,7 +45,8 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.

-**CMake build**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: csh

@ -72,7 +73,8 @@ once with CMake.
   invoke cmake.  CMake will give an error if that is not the case,
   indicating how you can un-install all packages in the src dir.

-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: bash

@ -108,7 +110,8 @@ once with make.
   within the same command.  You can include or exclude multiple packages
   in a single make command, e.g. make yes-colloid no-manybody.

-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^

 Any package can be included or excluded in a LAMMPS build, independent
 of all other packages.  However, some packages include files derived
@ -132,7 +135,7 @@ src directory.

 .. _cmake_presets:

-**CMake shortcuts for installing many packages**\ :
+CMake presets for installing many packages

 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@ -148,13 +151,14 @@ one of them as a starting point and customize it to your needs.

 .. code-block:: bash

-    cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
-    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most 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/intel.cmake   [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-    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 packages
+    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
+    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/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers

 .. note::
@ -184,7 +188,8 @@ one of them as a starting point and customize it to your needs.

 ----------

-**Make shortcuts for installing many packages**\ :
+Make shortcuts for installing many packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

 The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.
--- a/doc/src/Build_settings.rst
+++ b/doc/src/Build_settings.rst
@ -44,7 +44,8 @@ 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.

-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -74,7 +75,12 @@ to assist:
   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
   -D MKL_LIBRARIES=path

-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
+
+To change the FFT library to be used and its options, you have to edit
+your machine Makefile. Below are examples how the makefile variables
+could be changed.

 .. code-block:: make

@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
 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**\ :
+CMake build
+^^^^^^^^^^^

 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
 distribution.  It is portable across all platforms.  Depending on the size
@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
 version 3.X; the legacy version 2.1.X is no longer supported.

 Building FFTW for your box should be as simple as ``./configure; make;
-make install``\ .  The install command typically requires root privileges
+make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
 the "--prefix" option of configure.  Type ``./configure --help`` to see
 various options.
@ -169,20 +176,25 @@ ARRAY mode.

 .. _size:

-Size of LAMMPS data types
+Size of LAMMPS integer types
 ------------------------------------

-LAMMPS has a few integer data types which can be defined as 4-byte or
-8-byte integers.  The default setting of "smallbig" is almost always
-adequate.
+LAMMPS has a few integer data types which can be defined as either
+4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
+The default setting of "smallbig" is almost always adequate.

-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

   -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall

-**Makefile.machine setting**\ :
+Traditional build
+^^^^^^^^^^^^^^^^^
+
+If you want a setting different from the default, you need to edit your
+machine Makefile.

 .. code-block:: make

@ -190,7 +202,8 @@ adequate.

 The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified

-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^

 The default "smallbig" setting allows for simulations with:

@ -251,7 +264,8 @@ PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
 outputs movie files in MPEG format.  Using these options requires the
 following settings:

-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -276,7 +290,8 @@ variables:
   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
   -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable

-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: make

@ -295,7 +310,8 @@ 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,
 that is a directory in your PATH environment variable.

-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^

 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.
@ -318,7 +334,8 @@ 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>`.

-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
                            # default is yes if CMake can find gzip, else no
   -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it

-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: make

   LMP_INC = -DLAMMPS_GZIP

-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^

 This option requires that your machine supports the "popen()" function
 in the standard runtime library and that a gzip executable can be
@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being
 aligned on 64-byte boundaries.

-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead.  When
 compiling LAMMPS for Windows systems, malloc() will always be used
 and this setting ignored.

-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: make

@ -398,13 +419,15 @@ types, the following setting will be needed.  It converts "long long"
 to a "long" data type, which should be the desired 8-byte integer on
 those systems:

-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)

-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: make

@ -420,17 +443,26 @@ 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 calling code.
 Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python. Of course the calling code has to be set up to
-*catch* exceptions from within LAMMPS.
+e.g. to Python. Of course, the calling code has to be set up to
+*catch* exceptions thrown from within LAMMPS.

-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^

 .. code-block:: bash

   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)

-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^

 .. code-block:: make

   LMP_INC = -DLAMMPS_EXCEPTIONS
+
+.. note::
+
+   When LAMMPS is running in parallel, it is not always possible to
+   cleanly recover from an exception since not all parallel ranks may
+   throw an exception and thus other MPI ranks may get stuck waiting for
+   messages from the ones with errors.
--- a/doc/src/Commands_input.rst
+++ b/doc/src/Commands_input.rst
@ -31,9 +31,9 @@ does something different than this sequence:
   run      100

 In the first case, the specified timestep (0.5 fs) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
-timestep is used for the 2nd one.
+simulations of 100 timesteps each.  In the second case, the default
+timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
+timestep is used for the second one.

 (2) Some commands are only valid when they follow other commands.  For
 example you cannot set the temperature of a group of atoms until atoms
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@ -78,7 +78,7 @@ OPT.
   * :doc:`coul/long/soft (o) <pair_fep_soft>`
   * :doc:`coul/msm (o) <pair_coul>`
   * :doc:`coul/slater/cut <pair_coul_slater>`
-   * :doc:`coul/slater/long <pair_coul_slater>`   
+   * :doc:`coul/slater/long <pair_coul_slater>`
   * :doc:`coul/shield <pair_coul_shield>`
   * :doc:`coul/streitz <pair_coul>`
   * :doc:`coul/wolf (ko) <pair_coul>`
--- a/doc/src/Developer/developer.tex
+++ b/doc/src/Developer/developer.tex
@ -142,7 +142,7 @@ follows:
  minimize.

 \item The Special class walks the bond topology of a molecular system
-  to find 1st, 2nd, 3rd neighbors of each atom.  It is invoked by
+  to find first, second, third neighbors of each atom.  It is invoked by
  several commands, like read\_data, read\_restart, and replicate.

 \item The Atom class stores all per-atom arrays.  More precisely, they
--- a/doc/src/Errors_debug.rst
+++ b/doc/src/Errors_debug.rst
@ -23,7 +23,7 @@ We use it to show how to identify the origin of a segmentation fault.
     double *special_lj = force->special_lj;
     int newton_pair = force->newton_pair;
  +  double comx = 0.0;
-   
+
     inum = list->inum;
     ilist = list->ilist;
  @@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
@ -31,7 +31,7 @@ We use it to show how to identify the origin of a segmentation fault.
         }
       }
  -  }
-   
+
  +    comx += atom->rmass[i]*x[i][0]; /* BUG */
  +  }
  +  printf("comx = %g\n",comx);
@ -42,7 +42,7 @@ After recompiling LAMMPS and running the input you should get something like thi

 .. code-block:

-   $ ./lmp -in in.melt 
+   $ ./lmp -in in.melt
   LAMMPS (19 Mar 2020)
   OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
     using 1 OpenMP thread(s) per MPI task
@ -98,11 +98,11 @@ drop back to the GDB prompt.
     Unit style    : lj
     Current step  : 0
     Time step     : 0.005
-   
+
   Program received signal SIGSEGV, Segmentation fault.
   0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
   139      comx += atom->rmass[i]*x[i][0]; /* BUG */
-   (gdb) 
+   (gdb)

 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
@ -119,7 +119,7 @@ the current function back to "main()".
   #4  0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
   #5  0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
   #6  0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
-   (gdb) 
+   (gdb)

 You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
@ -189,12 +189,12 @@ the console are not mixed.

 .. code-block::

-   $ valgrind ./lmp -in in.melt 
+   $ valgrind ./lmp -in in.melt
   ==1933642== Memcheck, a memory error detector
   ==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
   ==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
   ==1933642== Command: ./lmp -in in.melt
-   ==1933642== 
+   ==1933642==
   LAMMPS (19 Mar 2020)
   OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
     using 1 OpenMP thread(s) per MPI task
@ -228,7 +228,7 @@ the console are not mixed.
   ==1933642==    by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
   ==1933642==    by 0x409339: main (main.cpp:65)
   ==1933642==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
-   ==1933642== 
+   ==1933642==

 As you can see, the stack trace information is similar to that obtained
 from GDB. In addition you get a more specific hint about what cause the
--- a/doc/src/Errors_messages.rst
+++ b/doc/src/Errors_messages.rst
@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   are defined.

 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
   processor.  Typically this is because the pairwise cutoff is set too
   short or the bond has blown apart and an atom is too far away.

@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   the atoms are too far apart to make a valid bond.

 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
   Typically this is because the pairwise cutoff is set too short or the
   bond has blown apart and an atom is too far away.

@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   are too far apart to make a valid bond.

 *Bond atoms %d %d missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
   processor.  Typically this is because the pairwise cutoff is set too
   short or the bond has blown apart and an atom is too far away.

 *Bond atoms missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
   processor.  Typically this is because the pairwise cutoff is set too
   short or the bond has blown apart and an atom is too far away.

@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   template does not qualify.

 *Cannot use fix box/relax on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
   dimensions must be periodic.  E.g. if the xy component is specified,
   then the y dimension must be periodic.

@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   also keyword tri or xy, this is wrong.

 *Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
-   When specifying scaling on a tilt factor component, the 2nd of the two
+   When specifying scaling on a tilt factor component, the second of the two
   dimensions must be periodic.  E.g. if the xy component is specified,
   then the y dimension must be periodic.

@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   This would be changing the same box dimension twice.

 *Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
   dimensions must be periodic.  E.g. if the xy component is specified,
   then the y dimension must be periodic.

@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
   Self-explanatory.

 *Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.

 *Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.

 *Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.

 *Cannot use fix pour rigid and not molecule*
   Self-explanatory.
@ -7192,7 +7192,7 @@ keyword to allow for additional bonds to be formed
   does not exist.

 *Replacing a fix, but new style != old style*
-   A fix ID can be used a 2nd time, but only if the style matches the
+   A fix ID can be used a second time, but only if the style matches the
   previous fix.  In this case it is assumed you with to reset a fix's
   parameters.  This error may mean you are mistakenly re-using a fix ID
   when you do not intend to.
--- a/doc/src/Errors_warnings.rst
+++ b/doc/src/Errors_warnings.rst
@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
   Self-explanatory.

 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
   processor.  Typically this is because the pairwise cutoff is set too
   short or the bond has blown apart and an atom is too far away.

 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
   Typically this is because the pairwise cutoff is set too short or the
   bond has blown apart and an atom is too far away.

 *Bond atoms missing at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
   processor.  Typically this is because the pairwise cutoff is set too
   short or the bond has blown apart and an atom is too far away.

@ -486,7 +486,7 @@ This will most likely cause errors in kinetic fluctuations.
   a new style.

 *No Kspace calculation with verlet/split*
-   The 2nd partition performs a kspace calculation so the kspace_style
+   The second partition performs a kspace calculation so the kspace_style
   command must be used.

 *No automatic unit conversion to XTC file format conventions possible for units lj*
--- a/doc/src/Examples.rst
+++ b/doc/src/Examples.rst
@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:

 Running the simulation produces the files *dump.indent* and
 *log.lammps*\ .  You can visualize the dump file of snapshots with a
-variety of 3rd-party tools highlighted on the
+variety of third-party tools highlighted on the
 `Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
 web site.

--- a/doc/src/Howto_chunk.rst
+++ b/doc/src/Howto_chunk.rst
@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.

 (7) An example for using one set of per-chunk values for molecule
-chunks, to create a 2nd set of micelle-scale chunks (clustered
+chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.

 (8) An example for using one set of per-chunk values (dipole moment
--- a/doc/src/Howto_cmake.rst
+++ b/doc/src/Howto_cmake.rst
@ -114,19 +114,19 @@ summary screen will look like this:
   -- Detecting CXX compiler ABI info - done
   -- Detecting CXX compile features
   -- Detecting CXX compile features - done
-   -- Found Git: /usr/bin/git (found version "2.25.2") 
+   -- Found Git: /usr/bin/git (found version "2.25.2")
   -- Running check for auto-generated files from make-based build system
-   -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1") 
-   -- Found MPI: TRUE (found version "3.1")  
+   -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
+   -- Found MPI: TRUE (found version "3.1")
   -- Looking for C++ include omp.h
   -- Looking for C++ include omp.h - found
-   -- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-   -- Found OpenMP: TRUE (found version "4.5")  
-   -- Found JPEG: /usr/lib64/libjpeg.so (found version "62") 
-   -- Found PNG: /usr/lib64/libpng.so (found version "1.6.37") 
-   -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-   -- Found GZIP: /usr/bin/gzip  
-   -- Found FFMPEG: /usr/bin/ffmpeg  
+   -- Found OpenMP_CXX: -fopenmp (found version "4.5")
+   -- Found OpenMP: TRUE (found version "4.5")
+   -- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
+   -- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
+   -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
+   -- Found GZIP: /usr/bin/gzip
+   -- Found FFMPEG: /usr/bin/ffmpeg
   -- Performing Test COMPILER_SUPPORTS-ffast-math
   -- Performing Test COMPILER_SUPPORTS-ffast-math - Success
   -- Performing Test COMPILER_SUPPORTS-march=native
@ -143,7 +143,7 @@ summary screen will look like this:
    * JPEG
    * PNG
    * ZLIB
-   
+
   -- <<< Build configuration >>>
      Build type:       RelWithDebInfo
      Install path:     /home/akohlmey/.local
@ -157,7 +157,7 @@ summary screen will look like this:
         Options:       -ffast-math;-march=native
   -- <<< Linker flags: >>>
   -- Executable name:  lmp
-   -- Static library flags:    
+   -- Static library flags:
   -- <<< MPI flags >>>
   -- MPI includes:     /usr/include/mpich-x86_64
   -- MPI libraries:    /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
@ -291,7 +291,7 @@ Some common CMake variables

 .. list-table::
   :header-rows: 1
-   
+
   * - Variable
     - Description
   * - ``CMAKE_INSTALL_PREFIX``
@ -313,13 +313,13 @@ Some common CMake variables
     - Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
   * - ``CXX_COMPILER_LAUNCHER``
     - tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
-       
+
 Some common LAMMPS specific variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

 .. list-table::
   :header-rows: 1
-   
+
   * - Variable
     - Description
   * - ``BUILD_MPI``
@ -438,7 +438,7 @@ the target name to the command. Example: ``cmake --build . --target all`` or
   * - ``clean``
     - remove all generated files

-   
+
 Choosing generators
 -------------------

--- a/doc/src/Howto_coreshell.rst
+++ b/doc/src/Howto_coreshell.rst
@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle).  The
 groups, one for the core atoms, another for the shell atoms.
 Non-polarized ions which might also be included in the treated system
 should not be included into either of these groups, they are taken
-into account by the *group-ID* (2nd argument) of the compute.  The
+into account by the *group-ID* (second argument) of the compute.  The
 groups can be defined using the :doc:`group *type*\ <group>` command.
 Note that to perform thermostatting using this definition of
 temperature, the :doc:`fix modify temp <fix_modify>` command should be
--- a/doc/src/Howto_multiple.rst
+++ b/doc/src/Howto_multiple.rst
@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
 on the 3 partitions one after the other until all were finished.
 Initially, 3 simulations would be started simultaneously, one on each
 partition.  When one finished, that partition would then start
-the 4th simulation, and so forth, until all 8 were completed.
+the fourth simulation, and so forth, until all 8 were completed.
--- a/doc/src/Howto_restart.rst
+++ b/doc/src/Howto_restart.rst
@ -28,7 +28,7 @@ scripts are based on.  If that script had the line
 added to it, it would produce 2 binary restart files (tmp.restart.50
 and tmp.restart.100) as it ran.

-This script could be used to read the 1st restart file and re-run the
+This script could be used to read the first restart file and re-run the
 last 50 timesteps:

 .. code-block:: LAMMPS
--- a/doc/src/Howto_triclinic.rst
+++ b/doc/src/Howto_triclinic.rst
@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
 **x** is the vector in the LAMMPS basis.

 There is no requirement that a triclinic box be periodic in any
-dimension, though it typically should be in at least the 2nd dimension
+dimension, though it typically should be in at least the second dimension
 of the tilt (y in xy) if you want to enforce a shift in periodic
 boundary conditions across that boundary.  Some commands that work
 with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
 To avoid extremely tilted boxes (which would be computationally
 inefficient), LAMMPS normally requires that no tilt factor can skew
 the box more than half the distance of the parallel box length, which
-is the 1st dimension in the tilt factor (x for xz).  This is required
+is the first dimension in the tilt factor (x for xz).  This is required
 both when the simulation box is created, e.g. via the
 :doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
 as well as when the box shape changes dynamically during a simulation,
@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
 command), then the box is "flipped" to an equivalent shape with a tilt
 factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` doc page for further details.

-One exception to this rule is if the 1st dimension in the tilt
+One exception to this rule is if the first dimension in the tilt
 factor (x for xy) is non-periodic.  In that case, the limits on the
 tilt factor are not enforced, since flipping the box in that dimension
 does not change the atom positions due to non-periodicity.  In this
--- a/doc/src/Intro_nonfeatures.rst
+++ b/doc/src/Intro_nonfeatures.rst
@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
  molecular builder that will generate complex molecular models.  See
  the :doc:`Tools <Tools>` doc page for details on tools packaged with
  LAMMPS.  The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
-  describes a variety of 3rd party tools for this task.  Furthermore,
+  describes a variety of third party tools for this task.  Furthermore,
  some LAMMPS internal commands allow to reconstruct, or selectively add
  topology information, as well as provide the option to insert molecule
  templates instead of atoms for building bulk molecular systems.
--- a/doc/src/Manual.rst
+++ b/doc/src/Manual.rst
@ -32,11 +32,12 @@ a brief description of the basic code structure of LAMMPS.

 ----------

-Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
+Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
 every LAMMPS command.

 .. _lws: https://lammps.sandia.gov

+.. _user_documentation:
 .. toctree::
   :maxdepth: 2
   :numbered: 3
--- a/doc/src/Manual_build.rst
+++ b/doc/src/Manual_build.rst
@ -1,60 +1,62 @@
 Building the LAMMPS manual
 **************************

-Depending on how you obtained LAMMPS, the doc directory has up
-to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
-plus 2 e-book format files:
+Depending on how you obtained LAMMPS and whether you have built the
+manual yourself, this directory has a number of sub-directories and
+files. Here is a list with descriptions:

 .. code-block:: bash

-   src             # content files for LAMMPS documentation
-   html            # HTML version of the LAMMPS manual (see html/Manual.html)
-   utils           # tools and settings for building the documentation
-   docenv          # virtualenv for processing the manual sources
-   doctrees        # temporary data from processing the manual
-   mathjax         # code and fonts for rendering math in html
-   Manual.pdf      # large PDF version of entire manual
-   Developer.pdf   # small PDF with info about how LAMMPS is structured
-   LAMMPS.epub     # Manual in ePUB e-book format
-   LAMMPS.mobi     # Manual in MOBI e-book format
-   lammps.1        # man page for the lammps command
-   msi2lmp.1       # man page for the msi2lmp command
+   README           # brief info about the documentation
+   src              # content files for LAMMPS documentation
+   html             # HTML version of the LAMMPS manual (see html/Manual.html)
+   utils            # tools and settings for building the documentation
+   lammps.1         # man page for the lammps command
+   msi2lmp.1        # man page for the msi2lmp command
+   Manual.pdf       # large PDF version of entire manual
+   Developer.pdf    # small PDF with info about how LAMMPS is structured
+   LAMMPS.epub      # Manual in ePUB e-book format
+   LAMMPS.mobi      # Manual in MOBI e-book format
+   docenv           # virtualenv folder for processing the manual sources
+   doctrees         # temporary data from processing the manual
+   mathjax          # code and fonts for rendering math in html
+   doxygen          # doxygen configuration and output
+   .gitignore       # list of files and folders to be ignored by git
+   doxygen-warn.log # logfile with warnings from running doxygen
+   github-development-workflow.md   # notes on the LAMMPS development workflow
+   include-file-conventions.md      # notes on LAMMPS' include file conventions

-If you downloaded LAMMPS as a tarball from the web site, the html folder
-and the PDF files should be included.
+If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
+the html folder and the PDF files should be included.

 If you downloaded LAMMPS from the public git repository, then the HTML
 and PDF files are not included.  Instead you need to create them, in one
 of two ways:

 a. You can "fetch" the current HTML and PDF files from the LAMMPS web
-   site.  Just type "make fetch".  This should download a html_www
+   site.  Just type ``make fetch``.  This should download a html_www
   directory and Manual_www.pdf/Developer_www.pdf files.  Note that if
   new LAMMPS features have been added more recently than the date of
   your LAMMPS version, the fetched documentation will include those
   changes (but your source code will not, unless you update your local
   repository).

-b. You can build the HTML or PDF files yourself, by typing "make html"
-   or "make pdf".  This requires various tools including Sphinx, git,
-   and the MathJax javascript library, which the build process will attempt
-   to download automatically into a virtual environment in the folder
-   doc/docenv and the folder mathjax, respectively, if not already available.
-   This download is required only once, unless you type "make clean-all".
-   After that, viewing and  processing of the documentation can be done
-   without internet access.  To generate the PDF version of the manual,
-   the PDFLaTeX software and several LaTeX packages are required as well.
-   However, those cannot be installed automatically at the moment.
+b. You can build the HTML or PDF files yourself, by typing ``make html``
+   or ``make pdf``.  This requires various tools and files.  Some of them
+   have to be installed (more on that below). For the rest the build
+   process will attempt to download and install them into a python
+   virtual environment and local folders.  This download is required
+   only once, unless you type ``make clean-all``.  After that, viewing and
+   processing of the documentation can be done without internet access.

 ----------

-The generation of all documentation is managed by the Makefile in
-the doc directory.
+The generation of all documentation is managed by the Makefile in the
+doc directory. The following documentation related make commands are
+available:

 .. code-block:: bash

-   Documentation Build Options:
-
   make html          # generate HTML in html dir using Sphinx
   make pdf           # generate 2 PDF files (Manual.pdf,Developer.pdf)
                      #   in doc dir via htmldoc and pdflatex
@ -62,8 +64,10 @@ the doc directory.
                      #   as a tarball and unpack into html dir and 2 PDFs
   make epub          # generate LAMMPS.epub in ePUB format using Sphinx
   make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
+
   make clean         # remove intermediate RST files created by HTML build
   make clean-all     # remove entire build folder and any cached data
+
   make anchor_check  # check for duplicate anchor labels
   make style_check   # check for complete and consistent style lists
   make package_check # check for complete and consistent package lists
@ -74,29 +78,30 @@ the doc directory.
 Installing prerequisites for HTML build
 =======================================

-To run the HTML documentation build toolchain, Python 3 and virtualenv
-have to be installed.  Here are instructions for common setups:
+To run the HTML documentation build toolchain, python 3, git, doxygen,
+and virtualenv have to be installed locally.  Here are instructions for
+common setups:

 Ubuntu
 ------

 .. code-block:: bash

-   sudo apt-get install python-virtualenv
+   sudo apt-get install python-virtualenv git doxygen

 Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
 ------------------------------------------------------------------------------------

 .. code-block:: bash

-   sudo yum install python3-virtualenv
+   sudo yum install python3-virtualenv git doxygen

 Fedora (since version 22)
 -------------------------

 .. code-block:: bash

-   sudo dnf install python3-virtualenv
+   sudo dnf install python3-virtualenv git doxygen

 MacOS X
 -------
@ -120,22 +125,92 @@ Once Python 3 is installed, open a Terminal and type

 This will install virtualenv from the Python Package Index.

----------
+Installing prerequisites for PDF build
+======================================

-Installing prerequisites for epub build
-=======================================
+In addition to the tools needed for building the HTML format manual,
+a working LaTeX installation with support for PDFLaTeX and a selection
+of LaTeX styles/packages are required.

-ePUB
----
+Installing prerequisites for e-book reader builds
+=================================================

-Same as for HTML. This uses mostly the same tools and configuration
-files as the HTML tree. In addition it uses LaTeX to convert embedded
+In addition to the tools needed for building the HTML format manual,
+a working LaTeX installation with a few add-on LaTeX packages
+as well as the ``dvipng`` tool are required to convert embedded
 math expressions transparently into embedded images.

-For converting the generated ePUB file to a MOBI format file
-(for e-book readers, like Kindle, that cannot read ePUB), you
-also need to have the 'ebook-convert' tool from the "calibre"
-software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
-You first create the ePUB file and then convert it with 'make mobi'
-On the Kindle readers in particular, you also have support for
-PDF files, so you could download and view the PDF version as an alternative.
+For converting the generated ePUB file to a MOBI format file (for e-book
+readers, like Kindle, that cannot read ePUB), you also need to have the
+``ebook-convert`` tool from the "calibre" software
+installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+Typing ``make mobi`` will first create the ePUB file and then convert
+it.  On the Kindle readers in particular, you also have support for PDF
+files, so you could download and view the PDF version as an alternative.
+
+
+Instructions for Developers
+===========================
+
+When adding new styles or options to the LAMMPS code, corresponding
+documentation is required and either existing files in the ``src``
+folder need to be updated or new files added. These files are written
+in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
+
+Before contributing any documentation, please check that both the HTML
+and the PDF format documentation can translate without errors. Please also
+check the output to the console for any warnings or problems.  There will
+be multiple tests run automatically:
+
+- A test for correctness of all anchor labels and their references
+
+- A test that all LAMMPS packages (= folders with sources in
+  ``lammps/src``) are documented and listed.  A typical warning shows
+  the name of the folder with the suspected new package code and the
+  documentation files where they need to be listed:
+
+  .. parsed-literal::
+
+     Found 33 standard and 41 user packages
+     Standard package NEWPACKAGE missing in Packages_standard.rst
+     Standard package NEWPACKAGE missing in Packages_details.rst
+
+- A test that only standard, printable ASCII text characters are used.
+  This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
+  thus prints all offending lines with filename and line number
+  prepended to the screen.  Special characters like the Angstrom
+  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
+  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
+
+- A test whether all styles are documented and listed in their
+  respective overview pages.  A typical output with warnings looks like this:
+
+  .. parsed-literal::
+
+     Parsed style names w/o suffixes from C++ tree in ../src:
+        Angle styles:      21    Atom styles:       24
+        Body styles:        3    Bond styles:       17
+        Command styles:    41    Compute styles:   143
+        Dihedral styles:   16    Dump styles:       26
+        Fix styles:       223    Improper styles:   13
+        Integrate styles:   4    Kspace styles:     15
+        Minimize styles:    9    Pair styles:      234
+        Reader styles:      4    Region styles:      8
+     Compute style entry newcomp is missing or incomplete in Commands_compute.rst
+     Compute style entry newcomp is missing or incomplete in compute.rst
+     Fix style entry newfix is missing or incomplete in Commands_fix.rst
+     Fix style entry newfix is missing or incomplete in fix.rst
+     Pair style entry new is missing or incomplete in Commands_pair.rst
+     Pair style entry new is missing or incomplete in pair_style.rst
+     Found 6 issue(s) with style lists
+
+
+In addition, there is the option to run a spellcheck on the entire
+manual with ``make spelling``.  This requires `a library called enchant
+<https://github.com/AbiWord/enchant>`_.  To avoid printing out *false
+positives* (e.g. keywords, names, abbreviations) those can be added to
+the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
+
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+
+.. _lws: https://lammps.sandia.gov
--- a/doc/src/Modify_fix.rst
+++ b/doc/src/Modify_fix.rst
@ -27,7 +27,7 @@ derived class.  See fix.h for details.
 +---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_force           | called before force computation in setup (optional)                                        |
 +---------------------------+--------------------------------------------------------------------------------------------+
-| setup                     | called immediately before the 1st timestep and after forces are computed (optional)        |
+| setup                     | called immediately before the first timestep and after forces are computed (optional)      |
 +---------------------------+--------------------------------------------------------------------------------------------+
 | min_setup_pre_force       | like setup_pre_force, but for minimizations instead of MD runs (optional)                  |
 +---------------------------+--------------------------------------------------------------------------------------------+
--- a/doc/src/Modify_kspace.rst
+++ b/doc/src/Modify_kspace.rst
@ -10,12 +10,12 @@ Ewald.cpp is an example of computing K-space interactions.
 Here is a brief description of methods you define in your new derived
 class.  See kspace.h for details.

-+---------------+----------------------------------------------+
-| init          | initialize the calculation before a run      |
-+---------------+----------------------------------------------+
-| setup         | computation before the 1st timestep of a run |
-+---------------+----------------------------------------------+
-| compute       | every-timestep computation                   |
-+---------------+----------------------------------------------+
-| memory_usage  | tally of memory usage                        |
-+---------------+----------------------------------------------+
+---------------+------------------------------------------------+
+| init          | initialize the calculation before a run        |
+---------------+------------------------------------------------+
+| setup         | computation before the first timestep of a run |
+---------------+------------------------------------------------+
+| compute       | every-timestep computation                     |
+---------------+------------------------------------------------+
+| memory_usage  | tally of memory usage                          |
+---------------+------------------------------------------------+
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@ -490,7 +490,7 @@ interactions.  These include Ewald, particle-particle particle-mesh

 Building with this package requires a 1d FFT library be present on
 your system for use by the PPPM solvers.  This can be the KISS FFT
-library provided with LAMMPS, 3rd party libraries like FFTW, or a
+library provided with LAMMPS, third party libraries like FFTW, or a
 vendor-supplied FFT library.  See the :doc:`Build settings <Build_settings>` doc page for details on how to select
 different FFT options for your LAMPMS build.

--- a/doc/src/Python_library.rst
+++ b/doc/src/Python_library.rst
@ -254,12 +254,3 @@ following steps:
 * You should now be able to invoke the new interface function from a
  Python script.

----------
-
-.. autoclass:: lammps.lammps
-   :members:
-   :no-undoc-members:
-
-.. autoclass:: lammps.NeighList
-   :members:
-   :no-undoc-members:
--- a/doc/src/Python_test.rst
+++ b/doc/src/Python_test.rst
@ -10,7 +10,7 @@ and type:
   >>> lmp = lammps()

 If you get no errors, you're ready to use LAMMPS from Python.  If the
-2nd command fails, the most common error to see is
+second command fails, the most common error to see is

 .. parsed-literal::

--- a/doc/src/Run_options.rst
+++ b/doc/src/Run_options.rst
@ -324,17 +324,17 @@ physical processors is done by MPI before LAMMPS begins.  It may be
 useful in some cases to alter the rank order.  E.g. to insure that
 cores within each node are ranked in a desired order.  Or when using
 the :doc:`run_style verlet/split <run_style>` command with 2 partitions
-to insure that a specific Kspace processor (in the 2nd partition) is
-matched up with a specific set of processors in the 1st partition.
+to insure that a specific Kspace processor (in the second partition) is
+matched up with a specific set of processors in the first partition.
 See the :doc:`Speed tips <Speed_tips>` doc page for more details.

 If the keyword *nth* is used with a setting *N*\ , then it means every
 Nth processor will be moved to the end of the ranking.  This is useful
 when using the :doc:`run_style verlet/split <run_style>` command with 2
 partitions via the -partition command-line switch.  The first set of
-processors will be in the first partition, the 2nd set in the 2nd
+processors will be in the first partition, the second set in the second
 partition.  The -reorder command-line switch can alter this so that
-the 1st N procs in the 1st partition and one proc in the 2nd partition
+the first N procs in the first partition and one proc in the second partition
 will be ordered consecutively, e.g. as the cores on one physical node.
 This can boost performance.  For example, if you use "-reorder nth 4"
 and "-partition 9 3" and you are running on 12 processors, the
--- a/doc/src/angle_charmm.rst
+++ b/doc/src/angle_charmm.rst
@ -37,7 +37,7 @@ The *charmm* angle style uses the potential
   E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2

 with an additional Urey_Bradley term based on the distance :math:`r` between
-the 1st and 3rd atoms in the angle.  :math:`K`, :math:`\theta_0`,
+the first and third atoms in the angle.  :math:`K`, :math:`\theta_0`,
 :math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
 type.

--- a/doc/src/angle_coeff.rst
+++ b/doc/src/angle_coeff.rst
@ -31,7 +31,7 @@ Angle coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.

 N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterisk can be
+be used, as in the first example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
 form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A
@ -53,7 +53,7 @@ same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Angle Coeffs" section of a data file, the line that
-corresponds to the 1st example above would be listed as
+corresponds to the first example above would be listed as

 .. parsed-literal::

--- a/doc/src/angle_table.rst
+++ b/doc/src/angle_table.rst
@ -75,7 +75,7 @@ parenthesized comments):
   ...
   181 180.0 0.0 0.0

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
@ -99,7 +99,7 @@ is in the tabulated file (with effectively no preliminary
 interpolation), you should set Ntable = Nfile.

 The "FP" parameter is optional.  If used, it is followed by two values
-fplo and fphi, which are the 2nd derivatives at the innermost and
+fplo and fphi, which are the second derivatives at the innermost and
 outermost angle settings.  These values are needed by the spline
 construction routines.  If not specified by the "FP" parameter, they
 are estimated (less accurately) by the first two and last two
@ -110,9 +110,9 @@ equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix
 set to 180.0.

 Following a blank line, the next N lines list the tabulated values.
-On each line, the 1st value is the index from 1 to N, the 2nd value is
-the angle value (in degrees), the 3rd value is the energy (in energy
-units), and the 4th is -dE/d(theta) (also in energy units).  The 3rd
+On each line, the first value is the index from 1 to N, the second value is
+the angle value (in degrees), the third value is the energy (in energy
+units), and the fourth is -dE/d(theta) (also in energy units).  The third
 term is the energy of the 3-atom configuration for the specified
 angle.  The last term is the derivative of the energy with respect to
 the angle (in degrees, not radians).  Thus the units of the last term
--- a/doc/src/atc_control_momentum.rst
+++ b/doc/src/atc_control_momentum.rst
@ -15,7 +15,7 @@ Syntax
   fix_modify AtC control momentum glc_velocity
   fix_modify AtC control momentum hoover
   fix_modify AtC control momentum flux [faceset face_set_id, interpolate]
-   
+
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * control = name of the AtC sub-command
 * physics_type = *thermal* or *momentum*
@ -52,7 +52,7 @@ the finite element temperature.  *flux* is a similar mode, but rather
 adds energy to the atoms based on conservation of energy.

 *correction_max_iterations* sets the maximum number of iterations to
-compute the 2nd order in time correction term for lambda with the
+compute the second order in time correction term for lambda with the
 fractional step method. The method uses the same tolerance as the
 controller's matrix solver.

--- a/doc/src/atc_control_thermal.rst
+++ b/doc/src/atc_control_thermal.rst
@ -56,7 +56,7 @@ adds energy to the atoms based on conservation of energy. *hoover* and
 atoms.

 *correction_max_iterations* sets the maximum number of iterations to
-compute the 2nd order in time correction term for lambda with the
+compute the second order in time correction term for lambda with the
 fractional step method. The method uses the same tolerance as the
 controller's matrix solver.

--- a/doc/src/atc_hardy_fields.rst
+++ b/doc/src/atc_hardy_fields.rst
@ -25,8 +25,8 @@ Syntax
  - temperature : temperature derived from the relative atomic kinetic energy
  - kinetic_temperature : temperature derived from the full kinetic energy
  - number_density : simple kernel estimation of number of atoms per unit volume
-  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
-  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
+  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
+  - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
  - potential_energy : potential energy per unit volume
  - kinetic_energy : kinetic energy per unit volume
@ -37,7 +37,7 @@ Syntax
  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
  - vacancy_concentration : volume fraction of vacancy content
  - type_concentration : volume fraction of a specific atom type
-  
+
 Examples
 """"""""

--- a/doc/src/atc_hardy_gradients.rst
+++ b/doc/src/atc_hardy_gradients.rst
@ -23,8 +23,8 @@ Syntax
  - temperature : temperature derived from the relative atomic kinetic energy
  - kinetic_temperature : temperature derived from the full kinetic energy
  - number_density : simple kernel estimation of number of atoms per unit volume
-  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
-  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
+  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
+  - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
  - potential_energy : potential energy per unit volume
  - kinetic_energy : kinetic energy per unit volume
--- a/doc/src/atc_hardy_kernel.rst
+++ b/doc/src/atc_hardy_kernel.rst
@ -25,7 +25,7 @@ Syntax
  - *quartic_bar* : <half_width>
  - *quartic_cylinder* : <radius>
  - *quartic_sphere* : <radius>
-    
+


 Examples
--- a/doc/src/atc_hardy_rates.rst
+++ b/doc/src/atc_hardy_rates.rst
@ -23,8 +23,8 @@ Syntax
  - temperature : temperature derived from the relative atomic kinetic energy
  - kinetic_temperature : temperature derived from the full kinetic energy
  - number_density : simple kernel estimation of number of atoms per unit volume
-  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
-  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
+  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
+  - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
  - potential_energy : potential energy per unit volume
  - kinetic_energy : kinetic energy per unit volume
--- a/doc/src/atc_remove_species.rst
+++ b/doc/src/atc_remove_species.rst
@ -38,7 +38,7 @@ Related AtC commands
 - :doc:`fix_modify AtC add_species <atc_add_species>`
 - :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
 - :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
-  
+
 Default
 """""""

--- a/doc/src/atc_set_reference_pe.rst
+++ b/doc/src/atc_set_reference_pe.rst
@ -22,7 +22,7 @@ Examples

   fix_modify AtC set reference_potential_energy
   fix_modify AtC set reference_potential_energy -0.05
-   fix_modify AtC set reference_potential_energy myPEvalues 
+   fix_modify AtC set reference_potential_energy myPEvalues

 Description
 """""""""""
--- a/doc/src/atc_time_integration.rst
+++ b/doc/src/atc_time_integration.rst
@ -33,11 +33,11 @@ Command to select the thermal or momentum time integration.
 Options for thermal time integration:

 *gear*
-  atomic velocity update with 2nd order Verlet, nodal temperature update
-  with 3rd or 4th order Gear, thermostats based on controlling power
+  atomic velocity update with second order Verlet, nodal temperature update
+  with third or fourth order Gear, thermostats based on controlling power

 *fractional_step*
-  atomic velocity update with 2nd order Verlet, mixed nodal temperature
+  atomic velocity update with second order Verlet, mixed nodal temperature
  update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
  thermostats based on controlling discrete energy changes

@ -46,18 +46,18 @@ Options for thermal time integration:
 Options for momentum time integration:

 *verlet*
-  atomic velocity update with 2nd order Verlet, nodal temperature update
-  with 2nd order Verlet, kinetostats based on controlling force
+  atomic velocity update with second order Verlet, nodal temperature update
+  with second order Verlet, kinetostats based on controlling force

 *fractional_step*
-  atomic velocity update with 2nd order Verlet, mixed nodal momentum
-  update, 2nd order Verlet for continuum and exact 2nd order Verlet for
+  atomic velocity update with second order Verlet, mixed nodal momentum
+  update, second order Verlet for continuum and exact second order Verlet for
  atomic contributions, kinetostats based on controlling discrete
  momentum changes

 *gear*
-  atomic velocity update with 2nd order Verlet, nodal temperature update
-  with 3rd or 4th order Gear, kinetostats based on controlling power.
+  atomic velocity update with second order Verlet, nodal temperature update
+  with third or fourth order Gear, kinetostats based on controlling power.

 ---------

--- a/doc/src/bond_coeff.rst
+++ b/doc/src/bond_coeff.rst
@ -32,7 +32,7 @@ Bond coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.

 N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterisk can be
+be used, as in the first example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple bond types.  This takes the
 form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of bond types,
 then an asterisk with no numeric values means all types from 1 to N.  A
@ -54,7 +54,7 @@ same format as the arguments of the bond_coeff command in an input
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Bond Coeffs" section of a data file, the line that
-corresponds to the 1st example above would be listed as
+corresponds to the first example above would be listed as

 .. parsed-literal::

--- a/doc/src/bond_fene.rst
+++ b/doc/src/bond_fene.rst
@ -38,8 +38,8 @@ The *fene* bond style uses the potential

 to define a finite extensible nonlinear elastic (FENE) potential
 :ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models.  The first
-term is attractive, the 2nd Lennard-Jones term is repulsive.  The
-first term extends to :math:`R_0`, the maximum extent of the bond.  The 2nd
+term is attractive, the second Lennard-Jones term is repulsive.  The
+first term extends to :math:`R_0`, the maximum extent of the bond.  The second
 term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.

 The following coefficients must be defined for each bond type via the
--- a/doc/src/bond_fene_expand.rst
+++ b/doc/src/bond_fene_expand.rst
@ -32,12 +32,12 @@ The *fene/expand* bond style uses the potential

 to define a finite extensible nonlinear elastic (FENE) potential
 :ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models.  The first
-term is attractive, the 2nd Lennard-Jones term is repulsive.
+term is attractive, the second Lennard-Jones term is repulsive.

 The *fene/expand* bond style is similar to *fene* except that an extra
 shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
 effectively change the bead size of the bonded atoms.  The first term
-now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
+now extends to :math:`R_0 + \Delta` and the second term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.

 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in
--- a/doc/src/bond_table.rst
+++ b/doc/src/bond_table.rst
@ -74,7 +74,7 @@ parenthesized comments):
   ...
   101 1.00 338.0000 -1352.0000

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
@ -109,9 +109,9 @@ equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix
 length is to the distance in the table with the lowest potential energy.

 Following a blank line, the next N lines list the tabulated values.
-On each line, the 1st value is the index from 1 to N, the 2nd value is
-the bond length r (in distance units), the 3rd value is the energy (in
-energy units), and the 4th is the force (in force units).  The bond
+On each line, the first value is the index from 1 to N, the second value is
+the bond length r (in distance units), the third value is the energy (in
+energy units), and the fourth is the force (in force units).  The bond
 lengths must range from a LO value to a HI value, and increase from
 one line to the next.  If the actual bond length is ever smaller than
 the LO value or larger than the HI value, then the calculation is
--- a/doc/src/boundary.rst
+++ b/doc/src/boundary.rst
@ -76,9 +76,9 @@ atoms becomes less than 50.0.  This can be useful if you start a
 simulation with an empty box or if you wish to leave room on one side
 of the box, e.g. for atoms to evaporate from a surface.

-For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
+For triclinic (non-orthogonal) simulation boxes, if the second dimension
 of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
-enforced with the tilt factor offset.  If the 1st dimension is
+enforced with the tilt factor offset.  If the first dimension is
 shrink-wrapped, then the shrink wrapping is applied to the tilted box
 face, to encompass the atoms.  E.g. for a positive xy tilt, the xlo
 and xhi faces of the box are planes tilting in the +y direction as y
--- a/doc/src/box.rst
+++ b/doc/src/box.rst
@ -38,7 +38,7 @@ skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` do
 boxes in LAMMPS.

 LAMMPS normally requires that no tilt factor can skew the box more
-than half the distance of the parallel box length, which is the 1st
+than half the distance of the parallel box length, which is the first
 dimension in the tilt factor (x for xz).  If *tilt* is set to
 *small*\ , which is the default, then an error will be
 generated if a box is created which exceeds this limit.  If *tilt*
--- a/doc/src/compute_adf.rst
+++ b/doc/src/compute_adf.rst
@ -82,9 +82,9 @@ neighbor atom in each requested ADF.
   is what is specified with the :doc:`neighbor <neighbor>` command.

 The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two
-ways.  An explicit numeric value can be used, as in the 1st example
+ways.  An explicit numeric value can be used, as in the first example
 above.  Or a wild-card asterisk can be used to specify a range of atom
-types as in the 2nd example above.
+types as in the second example above.
 This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
 number of atom types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
@ -92,12 +92,12 @@ all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

-If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the 1st example
+If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example
 above, this means that the ADF is computed where atoms of type *itypeN*
 are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN*
 are forming the angle.  If any of *itypeN*\ , *jtypeN*\ , or *ktypeN*
 represent a range of values via
-the wild-card asterisk, as in the 2nd example above, this means that the
+the wild-card asterisk, as in the second example above, this means that the
 ADF is computed where atoms of any of the range of types represented
 by *itypeN* are the central atom, and the angle is formed by two neighbors,
 one neighbor in the range of types represented by *jtypeN* and another neighbor
--- a/doc/src/compute_chunk_atom.rst
+++ b/doc/src/compute_chunk_atom.rst
@ -218,8 +218,8 @@ into ellipses.
 The created bins (and hence the chunk IDs) are numbered consecutively
 from 1 to the number of bins = *Nchunk*\ .  For *bin2d* and *bin3d*\ , the
 numbering varies most rapidly in the first dimension (which could be
-x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
-3rd dimension.  For *bin/sphere*\ , the bin with smallest radii is chunk
+x, y, or z), next rapidly in the second dimension, and most slowly in the
+third dimension.  For *bin/sphere*\ , the bin with smallest radii is chunk
 1 and the bni with largest radii is chunk Nchunk = *ncbin*\ .  For
 *bin/cylinder*\ , the numbering varies most rapidly in the dimension
 along the cylinder axis and most slowly in the radial direction.
@ -614,7 +614,7 @@ Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are
 scaled by the lattice spacing or reduced value of the *x* dimension.

 Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
-are scaled by the lattice spacing or reduced value of the 1st
+are scaled by the lattice spacing or reduced value of the first
 dimension perpendicular to the cylinder axis.  E.g. y for an x-axis
 cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.

--- a/doc/src/compute_coord_atom.rst
+++ b/doc/src/compute_coord_atom.rst
@ -63,7 +63,7 @@ keywords are listed, a single coordination number is calculated, which
 includes atoms of all types (same as the "\*" format, see below).

 The *typeN* keywords can be specified in one of two ways.  An explicit
-numeric value can be used, as in the 2nd example above.  Or a
+numeric value can be used, as in the second example above.  Or a
 wild-card asterisk can be used to specify a range of atom types.  This
 takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
 atom types, then an asterisk with no numeric values means all types
--- a/doc/src/compute_displace_atom.rst
+++ b/doc/src/compute_displace_atom.rst
@ -36,7 +36,7 @@ all effects due to atoms passing through periodic boundaries.

 A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.
-The 4th component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
+The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
 dz\*dz).

 The displacement of an atom is from its original position at the time
--- a/doc/src/compute_fep.rst
+++ b/doc/src/compute_fep.rst
@ -224,7 +224,7 @@ the pair\_\*.cpp file associated with the potential.

 Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for
-each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  I <= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same
 values. A wild-card asterisk can be used in place of or in conjunction
 with the I,J arguments to set the coefficients for multiple pairs of
--- a/doc/src/compute_group_group.rst
+++ b/doc/src/compute_group_group.rst
@ -64,7 +64,7 @@ If the *kspace* keyword is set to *yes*\ , which is not the default, and
 if a :doc:`kspace_style <kspace_style>` is defined, then the interaction
 energy will include a Kspace component which is the long-range
 Coulombic energy between all the atoms in the first group and all the
-atoms in the 2nd group.  Likewise, the interaction force calculated by
+atoms in the second group.  Likewise, the interaction force calculated by
 this compute will include the force on the compute group atoms due to
 long-range Coulombic interactions with atoms in the specified group2.

--- a/doc/src/compute_msd.rst
+++ b/doc/src/compute_msd.rst
@ -38,7 +38,7 @@ parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <comp

 A vector of four quantities is calculated by this compute.  The first 3
 elements of the vector are the squared dx,dy,dz displacements, summed
-and averaged over atoms in the group.  The 4th element is the total
+and averaged over atoms in the group.  The fourth element is the total
 squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
 averaged over atoms in the group.

--- a/doc/src/compute_msd_chunk.rst
+++ b/doc/src/compute_msd_chunk.rst
@ -36,7 +36,7 @@ they can be used to measure properties of a system.

 Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
-center-of-mass.  The 4th component is the total squared displacement,
+center-of-mass.  The fourth component is the total squared displacement,
 i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass.  These
 calculations include all effects due to atoms passing through periodic
 boundaries.
--- a/doc/src/compute_msd_nongauss.rst
+++ b/doc/src/compute_msd_nongauss.rst
@ -39,7 +39,7 @@ element of the vector is the total squared dx,dy,dz displacements
 drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
 fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
 dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
-group.  The 3rd component is the nonGaussian diffusion parameter NGP =
+group.  The third component is the nonGaussian diffusion parameter NGP =
 3\*drfourth/(5\*drsquared\*drsquared), i.e.

 .. math::
@ -68,7 +68,7 @@ page for an overview of LAMMPS output options.

 The vector values are "intensive".  The first vector value will be in
 distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
-the 3rd is dimensionless.
+the third is dimensionless.

 Restrictions
 """"""""""""
--- a/doc/src/compute_property_chunk.rst
+++ b/doc/src/compute_property_chunk.rst
@ -63,7 +63,7 @@ chunkID.  This means that the original chunk IDs (e.g. molecule IDs)
 will have been compressed to remove chunk IDs with no atoms assigned
 to them.  Thus a compressed chunk ID of 3 may correspond to an original
 chunk ID (molecule ID in this case) of 415.  The *id* attribute will
-then be 415 for the 3rd chunk.
+then be 415 for the third chunk.

 The *coordN* attributes can only be used if a *binning* style was used
 in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced
--- a/doc/src/compute_rdf.rst
+++ b/doc/src/compute_rdf.rst
@ -97,7 +97,7 @@ listed, then a separate histogram is generated for each
 *itype*\ ,\ *jtype* pair.

 The *itypeN* and *jtypeN* settings can be specified in one of two
-ways.  An explicit numeric value can be used, as in the 4th example
+ways.  An explicit numeric value can be used, as in the fourth example
 above.  Or a wild-card asterisk can be used to specify a range of atom
 types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
 number of atom types, then an asterisk with no numeric values means
@ -106,11 +106,11 @@ all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

-If both *itypeN* and *jtypeN* are single values, as in the 4th example
+If both *itypeN* and *jtypeN* are single values, as in the fourth example
 above, this means that a g(r) is computed where atoms of type *itypeN*
 are the central atom, and atoms of type *jtypeN* are the distribution
 atom.  If either *itypeN* and *jtypeN* represent a range of values via
-the wild-card asterisk, as in the 5th example above, this means that a
+the wild-card asterisk, as in the fifth example above, this means that a
 g(r) is computed where atoms of any of the range of types represented
 by *itypeN* are the central atom, and atoms of any of the range of
 types represented by *jtypeN* are the distribution atom.
--- a/doc/src/compute_temp_cs.rst
+++ b/doc/src/compute_temp_cs.rst
@ -49,7 +49,7 @@ respective group IDs, which can be defined using the
 must be the same and there should be one bond defined between a pair
 of atoms in the two groups.  Non-polarized ions which might also be
 included in the treated system should not be included into either of
-these groups, they are taken into account by the *group-ID* (2nd
+these groups, they are taken into account by the *group-ID* (second
 argument) of the compute.

 The temperature is calculated by the formula KE = dim/2 N k T, where
--- a/doc/src/compute_ti.rst
+++ b/doc/src/compute_ti.rst
@ -76,7 +76,7 @@ with respect to *lambda*\ .

 To perform this calculation, you provide one or more atom types as
 *atype*\ .  *Atype* can be specified in one of two ways.  An explicit
-numeric values can be used, as in the 1st example above.  Or a
+numeric values can be used, as in the first example above.  Or a
 wildcard asterisk can be used in place of or in conjunction with the
 *atype* argument to select multiple atom types.  This takes the form
 "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of atom types, then
--- a/doc/src/compute_vacf.rst
+++ b/doc/src/compute_vacf.rst
@ -33,7 +33,7 @@ A vector of four quantities is calculated by this compute.  The first 3
 elements of the vector are vx \* vx0 (and similarly for the y and z
 components), summed and averaged over atoms in the group.  Vx is the
 current x-component of velocity for the atom, vx0 is the initial
-x-component of velocity for the atom.  The 4th element of the vector
+x-component of velocity for the atom.  The fourth element of the vector
 is the total VACF, i.e. (vx\*vx0 + vy\*vy0 + vz\*vz0), summed and
 averaged over atoms in the group.

--- a/doc/src/dihedral_charmm.rst
+++ b/doc/src/dihedral_charmm.rst
@ -73,7 +73,7 @@ or :doc:`read_restart <read_restart>` commands:
 The weighting factor is required to correct for double counting
 pairwise non-bonded Lennard-Jones interactions in cyclic systems or
 when using the CHARMM dihedral style with non-CHARMM force fields.
-With the CHARMM dihedral style, interactions between the 1st and 4th
+With the CHARMM dihedral style, interactions between the first and fourth
 atoms in a dihedral are skipped during the normal non-bonded force
 computation and instead evaluated as part of the dihedral using
 special epsilon and sigma values specified with the
@ -93,7 +93,7 @@ which applies to all 1-4 interactions in the system.  For CHARMM force
 fields, the special_bonds 1-4 interaction scaling factor should be set
 to 0.0. Since the corresponding 1-4 non-bonded interactions are
 computed with the dihedral.  This means that if any of the weighting
-factors defined as dihedral coefficients (4th coeff above) are
+factors defined as dihedral coefficients (fourth coeff above) are
 non-zero, then you must use a pair style with "lj/charmm" and set the
 special_bonds 1-4 scaling factor to 0.0 (which is the
 default). Otherwise 1-4 non-bonded interactions in dihedrals will be
@ -115,7 +115,7 @@ details.

 Note that for AMBER force fields, which use pair styles with "lj/cut",
 the special_bonds 1-4 scaling factor should be set to the AMBER
-defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
+defaults (1/2 and 5/6) and all the dihedral weighting factors (fourth
 coeff above) must be set to 0.0. In this case, you can use any pair
 style you wish, since the dihedral does not need any Lennard-Jones
 parameter information and will not compute any 1-4 non-bonded
--- a/doc/src/dihedral_coeff.rst
+++ b/doc/src/dihedral_coeff.rst
@ -31,7 +31,7 @@ Dihedral coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.

 N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterisk can be
+be used, as in the first example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple dihedral types.  This takes the
 form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of dihedral types,
 then an asterisk with no numeric values means all types from 1 to N.  A
@ -53,7 +53,7 @@ same format as the arguments of the dihedral_coeff command in an input
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Dihedral Coeffs" section of a data file, the line that
-corresponds to the 1st example above would be listed as
+corresponds to the first example above would be listed as

 .. parsed-literal::

--- a/doc/src/dihedral_table.rst
+++ b/doc/src/dihedral_table.rst
@ -92,7 +92,7 @@ or blank lines.
   ...
   30 180.0 -0.707106781187

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections. The first line begins with a keyword which
 identifies the section. The line can contain additional text, but the
@ -102,10 +102,10 @@ any order) one or more parameters for the table. Each parameter is a
 keyword followed by one or more numeric values.

 Following a blank line, the next N lines list the tabulated values. On
-each line, the 1st value is the index from 1 to N, the 2nd value is
-the angle value, the 3rd value is the energy (in energy units), and
-the 4th is -dE/d(phi) also in energy units). The 3rd term is the
-energy of the 4-atom configuration for the specified angle.  The 4th
+each line, the first value is the index from 1 to N, the second value is
+the angle value, the third value is the energy (in energy units), and
+the fourth is -dE/d(phi) also in energy units). The third term is the
+energy of the 4-atom configuration for the specified angle.  The fourth
 term (when present) is the negative derivative of the energy with
 respect to the angle (in degrees, or radians depending on whether the
 user selected DEGREES or RADIANS).  Thus the units of the last term
@ -147,9 +147,9 @@ choice of angle units).

 The optional "NOF" keyword allows the user to omit the forces
 (negative energy derivatives) from the table file (normally located in
-the 4th column).  In their place, forces will be calculated
+the fourth column).  In their place, forces will be calculated
 automatically by differentiating the potential energy function
-indicated by the 3rd column of the table (using either linear or
+indicated by the third column of the table (using either linear or
 spline interpolation).

 The optional "DEGREES" keyword allows the user to specify angles in
@ -157,7 +157,7 @@ degrees instead of radians (default).

 The optional "RADIANS" keyword allows the user to specify angles in
 radians instead of degrees.  (Note: This changes the way the forces
-are scaled in the 4th column of the data file.)
+are scaled in the fourth column of the data file.)

 The optional "CHECKU" keyword is followed by a filename.  This allows
 the user to save all of the *Ntable* different entries in the
--- a/doc/src/dihedral_table_cut.rst
+++ b/doc/src/dihedral_table_cut.rst
@ -113,7 +113,7 @@ or blank lines.
   ...
   30 180.0 -0.707106781187

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections. The first line begins with a keyword which
 identifies the section. The line can contain additional text, but the
@ -123,10 +123,10 @@ any order) one or more parameters for the table. Each parameter is a
 keyword followed by one or more numeric values.

 Following a blank line, the next N lines list the tabulated values. On
-each line, the 1st value is the index from 1 to N, the 2nd value is
-the angle value, the 3rd value is the energy (in energy units), and
-the 4th is -dE/d(phi) also in energy units). The 3rd term is the
-energy of the 4-atom configuration for the specified angle.  The 4th
+each line, the first value is the index from 1 to N, the second value is
+the angle value, the third value is the energy (in energy units), and
+the fourth is -dE/d(phi) also in energy units). The third term is the
+energy of the 4-atom configuration for the specified angle.  The fourth
 term (when present) is the negative derivative of the energy with
 respect to the angle (in degrees, or radians depending on whether the
 user selected DEGREES or RADIANS).  Thus the units of the last term
@ -168,9 +168,9 @@ choice of angle units).

 The optional "NOF" keyword allows the user to omit the forces
 (negative energy derivatives) from the table file (normally located in
-the 4th column).  In their place, forces will be calculated
+the fourth column).  In their place, forces will be calculated
 automatically by differentiating the potential energy function
-indicated by the 3rd column of the table (using either linear or
+indicated by the third column of the table (using either linear or
 spline interpolation).

 The optional "DEGREES" keyword allows the user to specify angles in
@ -178,7 +178,7 @@ degrees instead of radians (default).

 The optional "RADIANS" keyword allows the user to specify angles in
 radians instead of degrees.  (Note: This changes the way the forces
-are scaled in the 4th column of the data file.)
+are scaled in the fourth column of the data file.)

 The optional "CHECKU" keyword is followed by a filename.  This allows
 the user to save all of the *Ntable* different entries in the
--- a/doc/src/dump_image.rst
+++ b/doc/src/dump_image.rst
@ -134,17 +134,23 @@ Only atoms in the specified group are rendered in the image.  The
 alter what atoms are included in the image.
 The filename suffix determines whether a JPEG, PNG, or PPM file is
 created with the *image* dump style.  If the suffix is ".jpg" or
-".jpeg", then a JPEG format file is created, if the suffix is ".png",
-then a PNG format is created, else a PPM (aka NETPBM) format file is
-created.  The JPEG and PNG files are binary; PPM has a text mode
-header followed by binary data. JPEG images have lossy compression;
-PNG has lossless compression; and PPM files are uncompressed but can
-be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ".gz" suffix is used.
+".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
+suffix is ".png", then a `PNG format <png_format_>`_ is created, else
+a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
+The JPEG and PNG files are binary; PPM has a text mode header followed
+by binary data. JPEG images have lossy compression, PNG has lossless
+compression, and PPM files are uncompressed but can be compressed with
+gzip, if LAMMPS has been compiled with -DLAMMPS_GZIP and a ".gz" suffix
+is used.
+
+.. _jpeg_format: https://jpeg.org/jpeg/
+.. _png_format: https://en.wikipedia.org/wiki/Portable_Network_Graphics
+.. _ppm_format: https://en.wikipedia.org/wiki/Netpbm

 Similarly, the format of the resulting movie is chosen with the
 *movie* dump style. This is handled by the underlying FFmpeg converter
-and thus details have to be looked up in the FFmpeg documentation.
+and thus details have to be looked up in the `FFmpeg documentation
+<http://ffmpeg.org/ffmpeg.html>`_.
 Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
 Additional settings of the movie compression like bitrate and
 framerate can be set using the :doc:`dump_modify <dump_modify>` command.
--- a/doc/src/dump_modify.rst
+++ b/doc/src/dump_modify.rst
@ -306,7 +306,7 @@ must enclose in quotes if it is more than one field.  The *int* and
 *float* keywords take a single format argument and are applied to all
 integer or floating-point quantities output.  The setting for *M
 string* also takes a single format argument which is used for the Mth
-value output in each line, e.g. the 5th column is output in high
+value output in each line, e.g. the fifth column is output in high
 precision for "format 5 %20.15g".

 .. note::
@ -419,7 +419,7 @@ be written, by processors 0,25,50,75.  Each will collect information
 from itself and the next 24 processors and write it to a dump file.

 For the *fileper* keyword, the specified value of Np means write one
-file for every Np processors.  For example, if Np = 4, every 4th
+file for every Np processors.  For example, if Np = 4, every fourth
 processor (0,4,8,12,etc) will collect information from itself and the
 next 3 processors and write it to a dump file.

@ -790,7 +790,7 @@ for the sequential style; otherwise the value is ignored.  It
 specifies the bin size to use within the range for assigning
 consecutive colors to.  For example, if the range is from -10.0 to
 10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
-the range.  The first will be from -10.0 <= color1 < -9.0, then 2nd
+the range.  The first will be from -10.0 <= color1 < -9.0, then second
 from -9.0 <= color2 < -8.0, etc.

 The *N* setting is how many entries follow.  The format of the entries
--- a/doc/src/dynamical_matrix.rst
+++ b/doc/src/dynamical_matrix.rst
@ -70,7 +70,7 @@ See the :doc:`Build package <Build_package>` doc page for more info.
 Related commands
 """"""""""""""""

-:doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`, 
+:doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`,

 :doc:`compute hma <compute_hma>` uses an analytic formulation of the
 Hessian provided by a pair_style's Pair::single_hessian() function,
--- a/doc/src/fix_adapt.rst
+++ b/doc/src/fix_adapt.rst
@ -229,7 +229,7 @@ specified, but are ignored.

 Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for
-each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  I <= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same values.

 A wild-card asterisk can be used in place of or in conjunction with
--- a/doc/src/fix_adapt_fep.rst
+++ b/doc/src/fix_adapt_fep.rst
@ -199,7 +199,7 @@ specified, but are ignored.

 Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for
-each, as in the 1st example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  I <= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same values.

 A wild-card asterisk can be used in place of or in conjunction with
--- a/doc/src/fix_ave_chunk.rst
+++ b/doc/src/fix_ave_chunk.rst
@ -435,7 +435,7 @@ column is only used if the *compress* keyword was set to *yes* for the
 the original chunk IDs (e.g. molecule IDs) will have been compressed
 to remove chunk IDs with no atoms assigned to them.  Thus a compressed
 chunk ID of 3 may correspond to an original chunk ID or molecule ID of
-415.  The OrigID column will list 415 for the 3rd chunk.
+415.  The OrigID column will list 415 for the third chunk.

 The CoordN columns only appear if a *binning* style was used in the
 :doc:`compute chunk/atom <compute_chunk_atom>` command.  For *bin/1d*\ ,
--- a/doc/src/fix_ave_correlate.rst
+++ b/doc/src/fix_ave_correlate.rst
@ -321,7 +321,7 @@ accessed on timesteps that are multiples of *Nfreq* since that is when
 averaging is performed.  The global array has # of rows = *Nrepeat*
 and # of columns = Npair+2.  The first column has the time delta (in
 timesteps) between the pairs of input values used to calculate the
-correlation, as described above.  The 2nd column has the number of
+correlation, as described above.  The second column has the number of
 samples contributing to the correlation average, as described above.
 The remaining Npair columns are for I,J pairs of the N input values,
 as determined by the *type* keyword, as described above.
--- a/doc/src/fix_ave_histo.rst
+++ b/doc/src/fix_ave_histo.rst
@ -346,10 +346,10 @@ values:
 * 4 = max value of all input values, including ones not histogrammed

 The global array has # of rows = Nbins and # of columns = 3.  The
-first column has the bin coordinate, the 2nd column has the count of
-values in that histogram bin, and the 3rd column has the bin count
+first column has the bin coordinate, the second column has the count of
+values in that histogram bin, and the third column has the bin count
 divided by the total count (not including missing counts), so that the
-values in the 3rd column sum to 1.0.
+values in the third column sum to 1.0.

 The vector and array values calculated by this fix are all treated as
 intensive.  If this is not the case, e.g. due to histogramming
--- a/doc/src/fix_bond_create.rst
+++ b/doc/src/fix_bond_create.rst
@ -154,13 +154,13 @@ of type *angletype*\ , with parameters assigned by the corresponding
 .. note::

   LAMMPS stores and maintains a data structure with a list of the
-   1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
+   first, second, and third neighbors of each atom (within the bond topology of
   the system) for use in weighting pairwise interactions for bonded
-   atoms.  Note that adding a single bond always adds a new 1st neighbor
-   but may also induce \*many\* new 2nd and 3rd neighbors, depending on the
+   atoms.  Note that adding a single bond always adds a new first neighbor
+   but may also induce \*many\* new second and third neighbors, depending on the
   molecular topology of your system.  The "extra special per atom"
   parameter must typically be set to allow for the new maximum total
-   size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 2
+   size (first + second + third neighbors) of this per-atom list.  There are 2
   ways to do this.  See the :doc:`read_data <read_data>` or
   :doc:`create_box <create_box>` commands for details.

@ -172,12 +172,12 @@ of type *angletype*\ , with parameters assigned by the corresponding
   considered for pairwise interactions, using the weighting rules set by
   the :doc:`special_bonds <special_bonds>` command.  Consider a new bond
   created between atoms I,J.  If J has a bonded neighbor K, then K
-   becomes a 2nd neighbor of I.  Even if the *atype* keyword is not used
+   becomes a second neighbor of I.  Even if the *atype* keyword is not used
   to create angle I-J-K, the pairwise interaction between I and K will
   be potentially turned off or weighted by the 1-3 weighting specified
   by the :doc:`special_bonds <special_bonds>` command.  This is the case
   even if the "angle yes" option was used with that command.  The same
-   is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and
+   is true for third neighbors (1-4 interactions), the *dtype* keyword, and
   the "dihedral yes" option used with the
   :doc:`special_bonds <special_bonds>` command.

--- a/doc/src/fix_box_relax.rst
+++ b/doc/src/fix_box_relax.rst
@ -371,7 +371,7 @@ the meaning of the xy,xz,yz tilt factors.

 The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
 for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
-can only be used if the 2nd dimension in the keyword is periodic,
+can only be used if the second dimension in the keyword is periodic,
 and if the tilt factor is not coupled to the barostat via keywords
 *tri*\ , *yz*\ , *xz*\ , and *xy*\ .

--- a/doc/src/fix_cmap.rst
+++ b/doc/src/fix_cmap.rst
@ -66,7 +66,7 @@ in the body of the data file like this with N lines:
          N       3     314     315     317      318    330

 The first column is an index from 1 to N to enumerate the CMAP terms;
-it is ignored by LAMMPS.  The 2nd column is the "type" of the
+it is ignored by LAMMPS.  The second column is the "type" of the
 interaction; it is an index into the CMAP force field file.  The
 remaining 5 columns are the atom IDs of the atoms in the two 4-atom
 dihedrals that overlap to create the CMAP 5-body interaction.  Note
--- a/doc/src/fix_deform.rst
+++ b/doc/src/fix_deform.rst
@ -104,7 +104,7 @@ can be modeled using the :ref:`USER-UEF package <PKG-USER-UEF>` and its :doc:`fi

 For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be
 shrink-wrapped.  For the *xy*\ , *yz*\ , *xz* parameters, the associated
-2nd dimension cannot be shrink-wrapped.  Dimensions not varied by this
+second dimension cannot be shrink-wrapped.  Dimensions not varied by this
 command can be periodic or non-periodic.  Dimensions corresponding to
 unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.

@ -463,7 +463,7 @@ and the final tilt factor at the end of the simulation would be 0.0.
 During each flip event, atoms are remapped into the new box in the
 appropriate manner.

-The one exception to this rule is if the 1st dimension in the tilt
+The one exception to this rule is if the first dimension in the tilt
 factor (x for xy) is non-periodic.  In that case, the limits on the
 tilt factor are not enforced, since flipping the box in that dimension
 does not change the atom positions due to non-periodicity.  In this
@ -601,7 +601,7 @@ Restrictions
 You cannot apply x, y, or z deformations to a dimension that is
 shrink-wrapped via the :doc:`boundary <boundary>` command.

-You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
+You cannot apply xy, yz, or xz deformations to a second dimension (y in
 xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.

 Related commands
--- a/doc/src/fix_eos_table.rst
+++ b/doc/src/fix_eos_table.rst
@ -66,7 +66,7 @@ parenthesized comments):
   ...
   500 10.0 0.500

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
@ -86,8 +86,8 @@ to match exactly what is in the tabulated file (with effectively no
 preliminary interpolation), you should set Ntable = Nfile.

 Following a blank line, the next N lines list the tabulated values.
-On each line, the 1st value is the index from 1 to N, the 2nd value is
-the internal temperature (in temperature units), the 3rd value is the
+On each line, the first value is the index from 1 to N, the second value is
+the internal temperature (in temperature units), the third value is the
 internal energy (in energy units).

 Note that the internal temperature and internal energy values must
--- a/doc/src/fix_eos_table_rx.rst
+++ b/doc/src/fix_eos_table_rx.rst
@ -106,7 +106,7 @@ parenthesized comments):
   ...
   500 10.0 0.500 ... 1.0000

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
@ -121,8 +121,8 @@ What LAMMPS does is a preliminary interpolation by creating splines
 using the Nfile tabulated values as nodal points.

 Following a blank line, the next N lines list the tabulated values.
-On each line, the 1st value is the index from 1 to N, the 2nd value is
-the internal temperature (in temperature units), the 3rd value until
+On each line, the first value is the index from 1 to N, the second value is
+the internal temperature (in temperature units), the third value until
 the *m+3* value are the internal energies of the m species (in energy units).

 Note that all internal temperature and internal energy values must
--- a/doc/src/fix_external.rst
+++ b/doc/src/fix_external.rst
@ -109,20 +109,42 @@ etc.
 To use this fix during energy minimization, the energy corresponding
 to the added forces must also be set so as to be consistent with the
 added forces.  Otherwise the minimization will not converge correctly.
+Correspondingly, the global virial needs to be updated to be use this
+fix with variable cell calculations (e.g. :doc:`fix box/relax <fix_box_relax>`
+or :doc:`fix npt <fix_nh>`).

-This can be done from the external driver by calling this public
-method of the FixExternal class:
+This can be done from the external driver by calling these public
+methods of the FixExternal class:

 .. code-block:: c++

-   void set_energy(double eng);
+   void set_energy_global(double eng);
+   void set_virial_global(double *virial);

-where eng is the potential energy.  Eng is an extensive quantity,
+where *eng* is the potential energy, and *virial* an array of the 6
+stress tensor components.  Eng is an extensive quantity,
 meaning it should be the sum over per-atom energies of all affected
 atoms.  It should also be provided in :doc:`energy units <units>`
 consistent with the simulation.  See the details below for how to
 insure this energy setting is used appropriately in a minimization.

+Additional public methods that the caller can use to update system
+properties are:
+
+.. code-block:: c++
+
+   void set_energy_peratom(double *eng);
+   void set_virial_peratom(double **virial);
+   void set_vector_length(int n);
+   void set_vector(int idx, double val);
+
+These allow to set per-atom energy contributions, per-atom stress
+contributions, the length and individual values of a global vector
+of properties that the caller code may want to communicate  to LAMMPS
+(e.g. for use in :doc:`fix ave/time <fix_ave_time>` or in
+:doc:`equal-style variables <variable>` or for
+:doc:`custom thermo output <thermo_style>`.
+
 ----------

 **Restart, fix_modify, output, run start/stop, minimize info:**
--- a/doc/src/fix_nh.rst
+++ b/doc/src/fix_nh.rst
@ -432,7 +432,7 @@ equilibrium liquids can not support a shear stress and that
 equilibrium solids can not support shear stresses that exceed the
 yield stress.

-One exception to this rule is if the 1st dimension in the tilt factor
+One exception to this rule is if the first dimension in the tilt factor
 (x for xy) is non-periodic.  In that case, the limits on the tilt
 factor are not enforced, since flipping the box in that dimension does
 not change the atom positions due to non-periodicity.  In this mode,
@ -673,7 +673,7 @@ Restrictions

 *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
 periodic.  *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
-simulation domain is triclinic and the 2nd dimension in the keyword
+simulation domain is triclinic and the second dimension in the keyword
 (\ *y* dimension in *xy*\ ) is periodic.  *Z*\ , *xz*\ , and *yz*\ , cannot be
 barostatted for 2D simulations.  The :doc:`create_box <create_box>`,
 :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -687,7 +687,7 @@ is not allowed in the Nose/Hoover formulation.

 The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
 for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
-can only be used if the 2nd dimension in the keyword is periodic,
+can only be used if the second dimension in the keyword is periodic,
 and if the tilt factor is not coupled to the barostat via keywords
 *tri*\ , *yz*\ , *xz*\ , and *xy*\ .

@ -710,7 +710,7 @@ Default

 The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
 ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
-flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
+flip = yes, scaleyz = scalexz = scalexy = yes if periodic in second
 dimension and not coupled to barostat, otherwise no.

 ----------
--- a/doc/src/fix_npt_cauchy.rst
+++ b/doc/src/fix_npt_cauchy.rst
@ -354,7 +354,7 @@ equilibrium liquids can not support a shear stress and that
 equilibrium solids can not support shear stresses that exceed the
 yield stress.

-One exception to this rule is if the 1st dimension in the tilt factor
+One exception to this rule is if the first dimension in the tilt factor
 (x for xy) is non-periodic.  In that case, the limits on the tilt
 factor are not enforced, since flipping the box in that dimension does
 not change the atom positions due to non-periodicity.  In this mode,
@ -555,7 +555,7 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>

 *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
 periodic.  *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
-simulation domain is triclinic and the 2nd dimension in the keyword
+simulation domain is triclinic and the second dimension in the keyword
 (\ *y* dimension in *xy*\ ) is periodic.  *Z*\ , *xz*\ , and *yz*\ , cannot be
 barostatted for 2D simulations.  The :doc:`create_box <create_box>`,
 :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -569,7 +569,7 @@ is not allowed in the Nose/Hoover formulation.

 The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
 for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
-can only be used if the 2nd dimension in the keyword is periodic,
+can only be used if the second dimension in the keyword is periodic,
 and if the tilt factor is not coupled to the barostat via keywords
 *tri*\ , *yz*\ , *xz*\ , and *xy*\ .

@ -626,7 +626,7 @@ Default
 The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
 ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
 cauchystat = no,
-scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
+scaleyz = scalexz = scalexy = yes if periodic in second dimension and
 not coupled to barostat, otherwise no.

 ----------
--- a/doc/src/fix_poems.rst
+++ b/doc/src/fix_poems.rst
@ -39,7 +39,7 @@ useful for treating a large biomolecule as a collection of connected,
 coarse-grained particles.

 The coupling, associated motion constraints, and time integration is
-performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS) <poems_>`_ which computes the
+performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the
 constrained rigid-body motion of articulated (jointed) multibody
 systems :ref:`(Anderson) <Anderson>`.  POEMS was written and is distributed
 by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
@ -48,8 +48,6 @@ and other members of his group at Rensselaer Polytechnic Institute
 copyright information on POEMS and other details, please refer to the
 documents in the poems directory distributed with LAMMPS.

-.. _poems: http://www.rpi.edu/~anderk5/lab
-
 This fix updates the positions and velocities of the rigid atoms with
 a constant-energy time integration, so you should not update the same
 atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
@ -123,7 +121,7 @@ command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 Restrictions
 """"""""""""

-This fix is part of the POEMS package.  It is only enabled if LAMMPS
+This fix is part of the :ref:`POEMS <PKG-POEMS>` package.  It is only enabled if LAMMPS
 was built with that package, which also requires the POEMS library be
 built and linked with LAMMPS.  See the :doc:`Build package <Build_package>` doc page for more info.

--- a/doc/src/fix_precession_spin.rst
+++ b/doc/src/fix_precession_spin.rst
@ -158,7 +158,7 @@ atom_style "spin" was declared.  See the :doc:`Build package <Build_package>` do
 The *precession/spin* style can only be declared once. If more
 than one precession type (for example combining an anisotropy and a Zeeman interactions)
 has to be declared, they have to be chained in the same command
-line (as shown in the examples above). 
+line (as shown in the examples above).

 Related commands
 """"""""""""""""
--- a/doc/src/fix_recenter.rst
+++ b/doc/src/fix_recenter.rst
@ -116,7 +116,7 @@ Restrictions
 """"""""""""

 This fix should not be used with an x,y,z setting that causes a large
-shift in the system on the 1st timestep, due to the requested COM
+shift in the system on the first timestep, due to the requested COM
 being very different from the initial COM.  This could cause atoms to
 be lost, especially in parallel.  Instead, use the
 :doc:`displace_atoms <displace_atoms>` command, which can be used to
--- a/doc/src/fix_restrain.rst
+++ b/doc/src/fix_restrain.rst
@ -162,7 +162,7 @@ the restraint is
 .. math::

   E = 0 \qquad\quad\quad ,if\;r \ge r_0
-   
+
 with the following coefficients:

 * :math:`K` (energy/distance\^2)
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@ -248,7 +248,7 @@ differences may accumulate to produce divergent trajectories.
   will be built only at the very first *run* command and maintained for
   as long as the rigid fix is defined. For example, you might think you
   could displace the atoms in a body or add a large velocity to each atom
-   in a body to make it move in a desired direction before a 2nd run is
+   in a body to make it move in a desired direction before a second run is
   performed, using the :doc:`set <set>` or
   :doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
   commands.  But these commands will not affect the internal attributes
@ -727,7 +727,7 @@ In all case, the rigid bodies and non-rigid particles both contribute
 to the global pressure and the box is scaled the same by any of the
 barostatting fixes.

-You could even use the 2nd and 3rd options for a non-hybrid simulation
+You could even use the second and third options for a non-hybrid simulation
 consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do.  The
 barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
 and change the box dimensions, but not time integrate any particles.
--- a/doc/src/fix_rigid_meso.rst
+++ b/doc/src/fix_rigid_meso.rst
@ -108,7 +108,7 @@ internal energy and extrapolated velocity are also updated.
   will be built only at the very first *run* command and maintained for
   as long as the rigid fix is defined. For example, you might think you
   could displace the particles in a body or add a large velocity to each particle
-   in a body to make it move in a desired direction before a 2nd run is
+   in a body to make it move in a desired direction before a second run is
   performed, using the :doc:`set <set>` or
   :doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
   commands.  But these commands will not affect the internal attributes
--- a/doc/src/fix_rx.rst
+++ b/doc/src/fix_rx.rst
@ -18,7 +18,7 @@ Syntax
 * file = filename containing the reaction kinetic equations and Arrhenius parameters
 * localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function
 * matrix = *sparse, dense* format for the stoichiometric matrix
-* solver = *lammps_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method
+* solver = *lammps_rk4,rkf45* = rk4 is an explicit fourth order Runge-Kutta method; rkf45 is an adaptive fourth-order Runge-Kutta-Fehlberg method
 * minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
 * maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
 * relTol = relative tolerance for the rkf45 solver (rkf45 only)
@ -61,9 +61,9 @@ of *m* ordinary differential equations (ODEs) that describe the change
 in concentration of a given species as a function of time are then
 constructed based on the *n* reaction rate equations.

-The ODE systems are solved over the full DPD timestep *dt* using either a 4th
+The ODE systems are solved over the full DPD timestep *dt* using either a fourth
 order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified
-by the *lammps_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method
+by the *lammps_rk4* keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method
 with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep
 for the rk4 method is optionally specified immediately after the rk4
 keyword. The ODE step-size is set as *dt/num_steps*. Smaller
@ -76,7 +76,7 @@ can be specified by the user or estimated internally. It is recommended that the
 specify *h0* since this will generally reduced the number of ODE integration steps
 required. *h0* is defined as *dt / min_steps* if min_steps >= 1. If min_steps == 0,
 *h0* is estimated such that an explicit Euler method would likely produce
-an acceptable solution. This is generally overly conservative for the 4th-order
+an acceptable solution. This is generally overly conservative for the fourth-order
 method and users are advised to specify *h0* as some fraction of the DPD timestep.
 For small DPD timesteps, only one step may be necessary depending upon the tolerances.
 Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness
@ -172,7 +172,7 @@ parenthesized comments):
   ...
   1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     1.66E+06 0.0 0.69

-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.

--- a/doc/src/fix_saed_vtk.rst
+++ b/doc/src/fix_saed_vtk.rst
@ -45,7 +45,7 @@ Description
 """""""""""

 Time average computed intensities from :doc:`compute saed <compute_saed>` and
-write output to a file in the 3rd generation vtk image data format for
+write output to a file in the third generation vtk image data format for
 visualization directly in parallelized visualization software packages
 like ParaView and VisIt. Note that if no time averaging is done, this
 command can be used as a convenient way to simply output diffraction
@ -92,7 +92,7 @@ averaging is done; values are simply generated on timesteps

 ----------

-The output for fix ave/time/saed is a file written with the 3rd generation
+The output for fix ave/time/saed is a file written with the third generation
 vtk image data formatting.  The filename assigned by the *file* keyword is
 appended with _N.vtk where N is an index (0,1,2...) to account for multiple
 diffraction intensity outputs.
@ -156,7 +156,7 @@ running or windowed average.

 The *file* keyword allows a filename to be specified.  Every *Nfreq*
 steps, the vector of saed intensity data is written to a new file using
-the 3rd generation vtk format.  The base of each file is assigned by
+the third generation vtk format.  The base of each file is assigned by
 the *file* keyword and this string is appended with _N.vtk where N is
 an index (0,1,2...) to account for situations with multiple diffraction
 intensity outputs.
--- a/doc/src/fix_smd.rst
+++ b/doc/src/fix_smd.rst
@ -126,7 +126,7 @@ displacement).

 The force is the total force on the group of atoms by the spring.  In
 the case of the *couple* style, it is the force on the fix group
-(group-ID) or the negative of the force on the 2nd group (group-ID2).
+(group-ID) or the negative of the force on the second group (group-ID2).
 The vector values calculated by this fix are "extensive".

 No parameter of this fix can be used with the *start/stop* keywords of
--- a/doc/src/fix_spring.rst
+++ b/doc/src/fix_spring.rst
@ -118,7 +118,7 @@ various :doc:`output commands <Howto_output>`.  The first 3 quantities
 in the vector are xyz components of the total force added to the group
 of atoms by the spring.  In the case of the *couple* style, it is the
 force on the fix group (group-ID) or the negative of the force on the
-2nd group (group-ID2).  The 4th quantity in the vector is the
+second group (group-ID2).  The fourth quantity in the vector is the
 magnitude of the force added by the spring, as a positive value if
 (r-R0) > 0 and a negative value if (r-R0) < 0.  This sign convention
 can be useful when using the spring force to compute a potential of
--- a/Show More
+++ b/Show More