Merge pull request #2296 from akohlmey/next_patch_version

Update version strings for next patch release

.gitattributes

@@ -0,0 +1,3 @@
+.gitattributes export-ignore
+.gitignore export-ignore
+.github export-ignore

.github/codecov.yml

@@ -0,0 +1,29 @@
+comment: false
+coverage:
+  notify:
+    slack:
+      default:
+        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
+        threshold: 10%
+        only_pulls: false
+        branches:
+          - "master"
+        flags:
+          - "unit"
+        paths:
+          - "src"
+  status:
+    project:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true
+    patch:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true

cmake/CMakeLists.txt

@@ -747,6 +747,12 @@ if (${_index} GREATER -1)
 endif()
 message(STATUS "<<< Linker flags: >>>")
 message(STATUS "Executable name:  ${LAMMPS_BINARY}")
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  get_target_property(OPTIONS lammps LINK_OPTIONS)
+  if(OPTIONS)
+    message(STATUS "Linker options:   ${OPTIONS}")
+  endif()
+endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
 endif()

cmake/Modules/Documentation.cmake

@@ -29,8 +29,8 @@ if(BUILD_DOC)
     OUTPUT requirements.txt
     DEPENDS docenv
     COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
   )
 
   # download mathjax distribution and unpack to folder "mathjax"

cmake/Modules/GTest.cmake

@@ -7,9 +7,11 @@ else()
 endif()
 
 include(ExternalProject)
+set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+mark_as_advanced(GTEST_URL)
 ExternalProject_Add(googletest
-                    GIT_REPOSITORY  https://github.com/google/googletest.git
-                    GIT_TAG         release-1.10.0
+                    URL ${GTEST_URL}
+                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

cmake/Modules/Packages/USER-SMD.cmake

@@ -9,8 +9,8 @@ if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
-    URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
+    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
+    URL_MD5 9e30f67e8531477de4117506fe44669b
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)

cmake/Modules/Testing.cmake

@@ -16,6 +16,36 @@ if(ENABLE_TESTING)
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
+  # check if a faster linker is available.
+  # only verified with GNU and Clang compilers and new CMake
+  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+      include(CheckCXXCompilerFlag)
+      set(CMAKE_CUSTOM_LINKER_DEFAULT default)
+      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
+      find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
+      find_program(HAVE_GOLD_LINKER_BIN ld.gold)
+      find_program(HAVE_BFD_LINKER_BIN ld.bfd)
+      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
+      elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
+      elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
+      endif()
+      set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
+      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
+      validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
+      mark_as_advanced(CMAKE_CUSTOM_LINKER)
+      if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
+        target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
+      endif()
+    endif()
+  endif()
+
   include(CTest)
 
   enable_testing()

doc/Makefile

@@ -83,7 +83,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
 	@mkdir -p html/JPG
-	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
+	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
 	@mkdir -p html/_static/mathjax
 	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
@@ -194,9 +194,7 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install --upgrade pip; \
-		pip install Sphinx; \
-		pip install sphinxcontrib-spelling ;\
-		pip install breathe; \
+		pip install --use-feature=2020-resolver -r requirements.txt; \
 		deactivate;\
 	)
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "21 July 2020" "2020-07-21"
+.TH LAMMPS "21 August 2020" "2020-08-21"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/requirements.txt

@@ -0,0 +1,4 @@
+Sphinx
+sphinxcontrib-spelling
+breathe
+Pygments

doc/src/Build_development.rst

@@ -159,8 +159,8 @@ A test run is then a a collection multiple individual test runs each
 with many comparisons to reference results based on template input
 files, individual command settings, relative error margins, and
 reference data stored in a YAML format file with ``.yaml``
-suffix. Currently the programs ``pair_style``, ``bond_style``, and
-``angle_style`` are implemented.  They will compare forces, energies and
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
+``test_angle_style`` are implemented.  They will compare forces, energies and
 (global) stress for all atoms after a ``run 0`` calculation and after a
 few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
 with different settings and also for multiple accelerated styles. If a
@@ -172,7 +172,7 @@ Below is an example command and output:
 
 .. parsed-literal::
 
-   [tests]$ pair_style mol-pair-lj_cut.yaml
+   [tests]$ test_pair_style mol-pair-lj_cut.yaml
    [==========] Running 6 tests from 1 test suite.
    [----------] Global test environment set-up.
    [----------] 6 tests from PairStyle
@@ -259,6 +259,71 @@ and working.
      of mis-compiled code (or an undesired large loss of precision due
      to significant reordering of operations and thus less error cancellation).
 
+Unit tests for timestepping related fixes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A substantial subset of :doc:`fix styles <fix>` are invoked regularly
+during MD timestepping and manipulate per-atom properties like
+positions, velocities, and forces.  For those fix styles, testing can be
+done in a very similar fashion as for force fields and thus there is a
+test program `test_fix_timestep` that shares a lot of code, properties,
+and command line flags with the force field style testers described in
+the previous section.
+
+This tester will set up a small molecular system run with verlet run
+style for 4 MD steps, then write a binary restart and continue for
+another 4 MD steps. At this point coordinates and velocities are
+recorded and compared to reference data. Then the system is cleared,
+restarted and running the second 4 MD steps again and the data is
+compared to the same reference. That is followed by another restart
+after which per atom type masses are replaced with per-atom masses and
+the second 4 MD steps are repeated again and compared to the same
+reference.  Also global scalar and vector data of the fix is recorded
+and compared.  If the fix is a thermostat and thus the internal property
+``t_target`` can be extracted, then this is compared to the reference
+data.  The tests are repeated with the respa run style.
+
+If the fix has a multi-threaded version in the USER-OMP package, then
+the entire set of tests is repeated for that version as well.
+
+For this to work, some additional conditions have to be met by the
+YAML format test inputs.
+
+- The fix to be tested (and only this fix), should be listed in the
+  ``prerequisites:`` section
+- The fix to be tested must be specified in the ``post_commands:``
+  section with the fix-ID ``test``.  This section may contain other
+  commands and other fixes (e.g. an instance of fix nve for testing
+  a thermostat or force manipulation fix)
+- For fixes that can tally contributions to the global virial, the
+  line ``fix_modify test virial yes`` should be included in the
+  ``post_commands:`` section of the test input.
+- For thermostat fixes the target temperature should be ramped from
+  an arbitrary value (e.g. 50K) to a pre-defined target temperature
+  entered as ``${t_target}``.
+- For fixes that have thermostatting support included, but do not
+  have it enabled in the input (e.g. fix rigid with default settings),
+  the ``post_commands:`` section should contain the line
+  ``variable t_target delete`` to disable the target temperature ramp
+  check to avoid false positives.
+
+Use custom linker for faster link times when ENABLE_TESTING is active
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When compiling LAMMPS with enabled tests, most test executables will
+need to be linked against the LAMMPS library.  Since this can be a very
+large library with many C++ objects when many packages are enabled, link
+times can become very long on machines that use the GNU BFD linker (e.g.
+Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
+or the ``gold`` linker available with GNU binutils can speed up this step
+substantially. CMake will by default test if any of the two can be
+enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
+selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
+Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
+``default`` option will use the system default linker otherwise, the
+linker is chosen explicitly.  This option is only available for the
+GNU or Clang C++ compiler.
+
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Build_windows.rst

@@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu
 from within Windows and from there on, you can pretty much use that
 shell like you are running on an Ubuntu Linux machine (e.g. installing
 software via apt-get and more). For more details on that, please
-see :doc:`this tutorial <Howto_bash>`
+see :doc:`this tutorial <Howto_wsl>`
 
 .. _gnu:
 

doc/src/Commands_bond.rst

@@ -46,6 +46,7 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 
 .. _angle:

doc/src/Commands_fix.rst

@@ -98,6 +98,7 @@ OPT.
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`momentum (k) <fix_momentum>`
+   * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`
    * :doc:`mscg <fix_mscg>`
    * :doc:`msst <fix_msst>`

doc/src/Errors_warnings.rst

@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    incorrect periodic images of atoms in interaction lists.  To avoid, either use
    :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
 
+*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
+
+   Since LAMMPS stores topology data with individual atoms, all atoms
+   comprising a bond, angle, dihedral or improper must be present on any
+   sub-domain that "owns" the atom with the information, either as a
+   local or a ghost atom. The communication cutoff is what determines up
+   to what distance from a sub-domain boundary ghost atoms are created.
+   The communication cutoff is by default the largest non-bonded cutoff
+   plus the neighbor skin distance, but for short or non-bonded cutoffs
+   and/or long bonds, this may not be sufficient. This warning indicates
+   that there is an increased risk of a simulation stopping unexpectedly
+   because of Bond/Angle/Dihedral/Improper atoms missing.  It can be
+   silenced by manually setting the communication cutoff via
+   :doc:`comm_modify cutoff <comm_modify>`.  However, since the
+   heuristic used to determine the estimate is not always accurate, it
+   is not changed automatically and the warning may be ignored depending
+   on the specific system being simulated.
+
 *Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
    Self-explanatory.
 

doc/src/Howto.rst

@@ -19,7 +19,7 @@ Tutorials howto
    Howto_cmake
    Howto_github
    Howto_pylammps
-   Howto_bash
+   Howto_wsl
 
 General howto
 =============

doc/src/Howto_bash.rst

@@ -1,264 +0,0 @@
-Using LAMMPS with Bash on Windows
-=================================
-
-**written by Richard Berger**
-
-----------
-
-Starting with Windows 10 you can install Linux tools directly in Windows. This
-allows you to compile LAMMPS following the same procedure as on a real Ubuntu
-Linux installation. Software can be easily installed using the package manager
-via apt-get and all files are accessible in both the Windows Explorer and your
-Linux shell (bash). This avoids switching to a different operating system or
-installing a virtual machine. Everything runs on Windows.
-
-.. seealso::
-
-   You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
-
-Installing Bash on Windows
---------------------------
-
-Prerequisites
-^^^^^^^^^^^^^
-
-* Windows 10 (64bit only)
-* Latest updates installed
-
-Enable developer mode
-^^^^^^^^^^^^^^^^^^^^^
-
-You enable this feature by first opening Windows Settings and enabling
-Developer mode. Go to the Windows settings and search for "developer". This
-will allow you to install software which comes from outside of the Windows
-Store.  You might be prompted to reboot your compute. Please do so.
-
-.. image:: JPG/bow_tutorial_01_small.png
-   :target: JPG/bow_tutorial_01.png
-
-.. image:: JPG/bow_tutorial_02_small.png
-   :target: JPG/bow_tutorial_02.png
-
-.. image:: JPG/bow_tutorial_03_small.png
-   :target: JPG/bow_tutorial_03.png
-
-Install Windows Subsystem for Linux
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Next you must ensure that the Window Subsystem for Linux is installed. Again,
-search for "enable windows features" in the Settings dialog. This opens a
-dialog with a list of features you can install. Add a checkmark to Windows
-Subsystem for Linux (Beta) and press OK.
-
-.. image:: JPG/bow_tutorial_04_small.png
-   :target: JPG/bow_tutorial_04.png
-
-.. image:: JPG/bow_tutorial_05.png
-   :target: JPG/bow_tutorial_05.png
-
-Install Bash for Windows
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-After installation completes, type "bash" in the Windows Start menu search.
-Select the first found option. This will launch a command-line window which
-will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
-enter. This will then download Ubuntu for Windows.
-
-.. image:: JPG/bow_tutorial_06.png
-
-.. image:: JPG/bow_tutorial_07.png
-
-During installation, you will be asked for a new password. This will be used
-for installing new software and running commands with sudo.
-
-.. image:: JPG/bow_tutorial_08.png
-
-Type exit to close the command-line window.
-
-Go to the Start menu and type "bash" again. This time you will see a "Bash on
-Ubuntu on Windows" Icon. Start this program.
-
-.. image:: JPG/bow_tutorial_09.png
-
-Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
-
-.. image:: JPG/bow_tutorial_10.png
-
-----------
-
-Compiling LAMMPS in Bash on Windows
------------------------------------
-
-The installation of LAMMPS in this environment is identical to working inside
-of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
-
-Installing prerequisite packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-First upgrade all existing packages using
-
-.. code-block:: bash
-
-   sudo apt update
-   sudo apt upgrade -y
-
-Next install the following packages, which include compilers and libraries
-needed for various LAMMPS features:
-
-.. code-block:: bash
-
-   sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
-
-Files in Ubuntu on Windows
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
-user home directory /home/[username]\ . You can access your Windows user directory
-using the /mnt/c/Users/[username] folder.
-
-Download LAMMPS
-^^^^^^^^^^^^^^^
-
-Obtain a copy of the LAMMPS code and go into it using "cd"
-
-Option 1: Downloading LAMMPS tarball using wget
-"""""""""""""""""""""""""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
-   tar xvzf lammps-stable.tar.gz
-   cd lammps-31Mar17
-
-Option 2: Obtaining LAMMPS code from GitHub
-"""""""""""""""""""""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   git clone https://github.com/lammps/lammps.git
-   cd lammps
-
-Compiling LAMMPS
-^^^^^^^^^^^^^^^^
-
-At this point you can compile LAMMPS like on Ubuntu Linux.
-
-Compiling serial version
-""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   cd src/
-   make -j 4 serial
-
-This will create an executable called lmp_serial in the src/ directory
-
-Compiling MPI version
-"""""""""""""""""""""
-
-.. code-block:: bash
-
-   cd src/
-   make -j 4 mpi
-
-This will create an executable called lmp_mpi in the src/ directory
-
-----------
-
-Finally, please note the absolute path of your src folder. You can get this using
-
-.. code-block:: bash
-
-   pwd
-
-or
-
-.. code-block:: bash
-
-   echo $PWD
-
-To run any examples you need the location of the executable. For now, let us
-save this location in a temporary variable
-
-.. code-block:: bash
-
-   LAMMPS_DIR=$PWD
-
-----------
-
-Running an example script
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Once compiled you can execute some of the LAMMPS examples. Switch into the
-examples/melt folder
-
-.. code-block:: bash
-
-   cd ../examples/melt
-
-The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
-version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
-version as follows:
-
-.. code-block:: bash
-
-   $LAMMPS_DIR/lmp_serial -in in.melt
-
-or
-
-.. code-block:: bash
-
-   mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
-
-Note the use of our variable $LAMMPS_DIR, which expands into the full path of
-the LAMMPS src folder we saved earlier.
-
-Adding your executable directory to your PATH
-"""""""""""""""""""""""""""""""""""""""""""""
-
-You can avoid having to type the full path of your LAMMPS binary by adding its
-parent folder to the PATH environment variable as follows:
-
-.. code-block:: bash
-
-   export PATH=$LAMMPS_DIR:$PATH
-
-Input scripts can then be run like this:
-
-.. code-block:: bash
-
-   lmp_serial -in in.melt
-
-or
-
-.. code-block:: bash
-
-   mpirun -np 4 lmp_mpi -in in.melt
-
-However, this PATH variable will not persist if you close your bash window.
-To persist this setting edit the $HOME/.bashrc file using your favorite editor
-and add this line
-
-.. code-block:: bash
-
-   export PATH=/full/path/to/your/lammps/src:$PATH
-
-**Example:**
-
-For an executable lmp_serial with a full path
-
-.. code-block:: bash
-
-   /home/richard/lammps/src/lmp_serial
-
-the PATH variable should be
-
-.. code-block:: bash
-
-   export PATH=/home/richard/lammps/src:$PATH
-
-.. note::
-
-   This should give you a jump start when trying to run LAMMPS on Windows.
-   To become effective in this environment I encourage you to look into Linux
-   tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)

doc/src/Howto_cmake.rst

@@ -47,7 +47,7 @@ using a shell like Bash.
 
 - Linux: any Terminal window will work
 - MacOS X: launch the Terminal application.
-- Windows 10: install and run the :doc:`Windows subsystem for Linux <Howto_bash>`
+- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
 
 We also assume that you have downloaded and unpacked a recent LAMMPS source code package
 or used Git to create a clone of the LAMMPS sources on your compilation machine.

doc/src/Howto_wsl.rst

@@ -0,0 +1,359 @@
+Using LAMMPS on Windows 10 with WSL
+###################################
+
+**written by Richard Berger**
+
+----------
+
+It's always been tricky for us to have LAMMPS users and developers work on
+Windows. We primarily develop LAMMPS to run on Linux clusters. To teach
+LAMMPS in workshop settings, we had to redirect Windows users to
+Linux Virtual Machines such as VirtualBox or Unix-like compilation with
+Cygwin.
+
+With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),
+Microsoft has added a new way to work on Linux-based code. The Windows
+Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual
+Machine that transparently integrates into Windows. All you need is to ensure
+you have the latest Windows updates installed and enable this new feature.
+Linux VMs are then easily installed using the Microsoft Store.
+
+In this tutorial, I'll show you how to set up and compile LAMMPS for both serial
+and MPI usage in WSL2.
+
+Installation
+============
+
+Upgrade to the latest Windows 10
+--------------------------------
+
+Type "Updates" in Windows Start and select "Check for Updates".
+
+.. image:: img/wsl_tutorial/updates.png
+   :scale: 50%
+
+Install all pending updates and reboot your system as many times as
+necessary. Continue until your Windows installation is updated.
+
+.. image:: img/wsl_tutorial/windows_update.png
+   :scale: 50%
+
+Verify your system has at least **version 2004 and build 19041 or later**. You
+can find this information by clicking on "OS build info".
+
+.. image:: img/wsl_tutorial/osinfo.png
+   :scale: 50%
+
+Enable WSL
+----------
+Next, we must install two additional Windows features to enable WSL support.
+Open a PowerShell window as an administrator. Type "PowerShell" in Windows
+Start and select "Run as Administrator".
+
+.. image:: img/wsl_tutorial/powershell.png
+   :scale: 50%
+
+Windows will ask you for administrator access. After you accept a new command
+line window will appear. Type in the following command to install WSL:
+
+.. code-block::
+
+   dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
+
+.. image:: img/wsl_tutorial/wsl_install1.png
+
+Next, enable the VirtualMachinePlatform feature using the following command:
+
+.. code-block::
+
+   dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
+
+.. image:: img/wsl_tutorial/wsl_install2.png
+
+Finally, reboot your system.
+
+Update WSL kernel component
+---------------------------
+
+Download and install the :download:`WSL Kernel Component Update <https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi>`.
+Afterwards, reboot your system.
+
+Set WSL2 as default
+-------------------
+
+Again, open PowerShell as administrator and run the following command:
+
+.. code-block:: powershell
+
+   wsl --set-default-version 2
+
+This command ensures that all future Linux installations will use WSL version 2.
+
+.. image:: img/wsl_tutorial/wsl_install3.png
+
+Install a Linux Distribution
+----------------------------
+Next, we need to install a Linux distribution via the Microsoft Store.
+Install `Ubuntu 20.04 LTS <ms-windows-store://pdp/?ProductId=9n6svws3rx71>`_.
+Once installed, you can launch it like any other application from the Start
+Menu.
+
+.. image:: img/wsl_tutorial/ubuntu_in_store.png
+   :scale: 50%
+
+Initial Setup
+^^^^^^^^^^^^^
+The first time you launch the Ubuntu Linux console, it will prompt you for a
+UNIX username and password. You will need this password to perform :code:`sudo`
+commands later. Once completed, your Linux shell is ready for use. All your
+actions and commands will run as the Linux user you specified.
+
+.. image:: img/wsl_tutorial/first_login.png
+   :scale: 50%
+
+Windows Explorer / WSL integration
+==================================
+
+Your Linux installation will have its own Linux filesystem, which contains
+the Ubuntu files. Your Linux user will have a regular Linux home directory in
+:code:`/home/<USERNAME>`. This directory is different from your Windows User
+directory. Windows and Linux filesystems are connected through WSL.
+
+All hard drives in Windows are accessible in the :code:`/mnt` directory in Linux.
+E.g., WSL maps the :code:`C` hard drive to the :code:`/mnt/c` directory. That means you
+can access your Windows User directory in :code:`/mnt/c/Users/<WINDOWS_USERNAME>`.
+
+The Windows Explorer can also access the Linux filesystem. To illustrate this
+integration, open an Ubuntu console and navigate to a directory of your
+choice. To view this location in Windows Explorer, use the :code:`explorer.exe .`
+command (do not forget the final dot!).
+
+.. image:: img/wsl_tutorial/wsl_integration.png
+   :scale: 50%
+
+--------
+
+Compiling LAMMPS
+================
+
+You now have a fully functioning Ubuntu installation and can follow most
+guides to install LAMMPS on a Linux system. Here are some of the essential
+steps to follow:
+
+Install prerequisite packages
+-----------------------------
+
+Before we can begin, we need to download the necessary compiler toolchain and
+libraries to compile LAMMPS. In our Ubuntu-based Linux installation, we will
+use the :code:`apt` package manager to install additional packages.
+
+First, upgrade all existing packages using :code:`apt update` and :code:`apt upgrade`.
+
+.. code-block:: bash
+
+   sudo apt update
+   sudo apt upgrade -y
+
+Next, install the following packages with :code:`apt install`:
+
+
+.. code-block:: bash
+
+   sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev \
+                       libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip \
+                       python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev \
+                       hdf5-tools
+
+Download LAMMPS
+---------------
+
+Obtain a copy of the LAMMPS source code and go into it using the :code:`cd` command.
+
+Option 1: Download a LAMMPS tarball using wget
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+   wget https://github.com/lammps/lammps/archive/stable_3Mar2020.tar.gz
+   tar xvzf stable_3Mar2020.tar.gz
+   cd lammps
+
+Option 2: Download a LAMMPS development version from GitHub
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+   git clone --depth=1 https://github.com/lammps/lammps.git
+   cd lammps
+
+
+Configure and Compile LAMMPS with CMake
+---------------------------------------
+
+A beginner-friendly way to compile LAMMPS is to use CMake. Create a :code:`build`
+directory to compile LAMMPS and move into it. This directory will store the
+build configuration and any binaries generated during compilation.
+
+.. code-block:: bash
+
+   mkdir build
+   cd build
+
+There are countless ways to compile LAMMPS. It is beyond the scope of this
+tutorial. If you want to find out more about what can be enabled, please
+consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
+
+To compile a minimal version of LAMMPS, we're going to use a preset.
+Presets are a way to specify a collection of CMake options using a file.
+
+.. code-block:: bash
+
+   cmake ../cmake/presets/minimal.cmake ../cmake
+
+This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command.
+
+.. code-block:: bash
+
+   make -j 4
+
+The :code:`-j` option specifies how many parallel processes will perform the
+compilation. This option can significantly speed up compilation times. Use a
+number that corresponds to the number of processors in your system.
+
+After the compilation completes successfully, you will have an executable
+called :code:`lmp` in the :code:`build` directory.
+
+.. image:: img/wsl_tutorial/compilation_result.png
+   :scale: 50%
+
+Please take note of the absolute path of your :code:`build` directory. You will
+need to know the location to execute the LAMMPS binary later.
+
+One way of getting the absolute path of the current directory is through the
+:code:`$PWD` variable:
+
+.. code-block:: bash
+
+   # prints out the current value of the PWD variable
+   echo $PWD
+
+Let us save this value in a temporary variable :code:`LAMMPS_BUILD_DIR` for future use:
+
+.. code-block:: bash
+
+   LAMMPS_BUILD_DIR=$PWD
+
+The full path of the LAMMPS binary then is :code:`$LAMMPS_BUILD_DIR/lmp`.
+
+------------
+
+Running an example script
+=========================
+
+Now that we have a LAMMPS binary, we will run a script from the examples folder.
+
+Switch into the :code:`examples/melt` folder:
+
+.. code-block::
+
+   cd ../examples/melt
+
+To run this example in serial, use the following command line:
+
+.. code-block::
+
+   $LAMMPS_BUILD_DIR/lmp -in in.melt
+
+To run the same script in parallel using MPI with 4 processes, do the following:
+
+.. code-block:: bash
+
+   mpirun -np 4 $LAMMPS_BUILD_DIR/lmp -in in.melt
+
+If you run LAMMPS for the first time, the Windows Firewall might prompt you
+to confirm access. LAMMPS is accessing the network stack to enable parallel
+computation. Allow the access.
+
+.. image:: img/wsl_tutorial/windows_firewall.png
+   :scale: 75%
+
+In either serial or MPI case, LAMMPS executes and will output something similar to this:
+
+.. code-block::
+
+   LAMMPS (30 Jun 2020)
+   ...
+   ...
+   ...
+   Total # of neighbors = 151513
+   Ave neighs/atom = 37.878250
+   Neighbor list builds = 12
+   Dangerous builds not checked
+   Total wall time: 0:00:00
+
+**Congratulations! You've successfully compiled and executed LAMMPS on WSL!**
+
+Final steps
+===========
+
+It is cumbersome to always specify the path of your LAMMPS binary. You can
+avoid this by adding the absolute path of your :code:`build` directory to your PATH
+environment variable.
+
+.. code-block:: bash
+
+   export PATH=$LAMMPS_BUILD_DIR:$PATH
+
+You can then run LAMMPS input scripts like this:
+
+.. code-block:: bash
+
+   lmp -in in.melt
+
+or
+
+.. code-block:: bash
+
+   mpirun -np 4 lmp -in in.melt
+
+.. note::
+
+   The value of this :code:`PATH` variable will disappear once you close your
+   console window. To persist this setting edit the :code:`$HOME/.bashrc` file using your
+   favorite text editor and add this line:
+
+   .. code-block:: bash
+
+      export PATH=/full/path/to/your/lammps/build:$PATH
+
+   **Example:**
+   If the LAMMPS executable `lmp` has the following absolute path:
+
+   .. code-block:: bash
+
+      /home/<USERNAME>/lammps/build/lmp
+
+   the :code:`PATH` variable should be:
+
+
+   .. code-block:: bash
+
+      export PATH=/home/<USERNAME>/lammps/build:$PATH
+
+   Once set up, all your Ubuntu consoles will always have access to your :code:`lmp`
+   binary without having to specify its location.
+
+Conclusion
+==========
+I hope this gives you good overview on how to start compiling and running LAMMPS on
+Windows. WSL makes preparing and running scripts on Windows a much better
+experience.
+
+If you are completely new to Linux, I highly recommend investing some time in
+studying Linux online tutorials. E.g., tutorials about Bash Shell and Basic
+Unix commands (e.g., `Linux Journey <https://linuxjourney.com/>`_). Acquiring
+these skills will make you much more productive in this environment.
+
+.. seealso::
+
+   * `Windows Subsystem for Linux Documentation <https://docs.microsoft.com/en-us/windows/wsl/>`_

doc/src/Python_examples.rst

@@ -80,16 +80,23 @@ See the python/README file for instructions on how to run them and the
 source code for individual scripts for comments about what they do.
 
 Here are screenshots of the vizplotgui_tool.py script in action for
-different visualization package options.  Click to see larger images:
+different visualization package options:
 
-.. image:: JPG/screenshot_gl_small.jpg
-   :target: JPG/screenshot_gl.jpg
+.. |pyex1| image:: img/screenshot_gl.jpg
+   :width: 24%
 
-.. image:: JPG/screenshot_atomeye_small.jpg
-   :target: JPG/screenshot_atomeye.jpg
+.. |pyex2| image:: img/screenshot_atomeye.jpg
+   :width: 24%
 
-.. image:: JPG/screenshot_pymol_small.jpg
-   :target: JPG/screenshot_pymol.jpg
+.. |pyex3| image:: img/screenshot_pymol.jpg
+   :width: 24%
+
+.. |pyex4| image:: img/screenshot_vmd.jpg
+   :width: 24%
+
+|pyex1|  |pyex2|  |pyex3|  |pyex4|
+
+.. raw:: html
+
+   Click to see larger versions of the images.
 
-.. image:: JPG/screenshot_vmd_small.jpg
-   :target: JPG/screenshot_vmd.jpg

doc/src/accel_styles.rst

@@ -0,0 +1,17 @@
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.

doc/src/angle_class2.rst

@@ -95,23 +95,7 @@ since it is the same value from the :math:`E_a` formula.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine.rst

@@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine_delta.rst

@@ -46,23 +46,7 @@ internally.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine_periodic.rst

@@ -54,23 +54,7 @@ geometry.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine_shift.rst

@@ -45,23 +45,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine_shift_exp.rst

@@ -56,23 +56,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_cosine_squared.rst

@@ -46,23 +46,7 @@ internally.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_dipole.rst

@@ -82,23 +82,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 Restrictions
 """"""""""""

doc/src/angle_fourier.rst

@@ -42,23 +42,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_fourier_simple.rst

@@ -41,23 +41,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_harmonic.rst

@@ -53,25 +53,7 @@ radian\^2.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package
-<Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix
-command-line switch <Run_options>` when you invoke LAMMPS, or you can
-use the :doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_quartic.rst

@@ -49,23 +49,7 @@ per radian\^2 or radian\^3 or radian\^4.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_sdk.rst

@@ -56,24 +56,7 @@ pair_style.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package
-<Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/angle_table.rst

@@ -126,23 +126,7 @@ one that matches the specified keyword.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/balance.rst

@@ -177,16 +177,16 @@ volume (area in 2d) assigned to each processor, as in the following 2d
 diagram where processor sub-domains are shown and particles are
 colored by the processor that owns them.
 
-.. list-table::
+.. |balance1| image:: img/balance_uniform.jpg
+   :width: 32%
 
-   * - .. figure:: JPG/balance_uniform_small.jpg
-          :target: JPG/balance_uniform.jpg
+.. |balance2| image:: img/balance_nonuniform.jpg
+   :width: 32%
 
-     - .. figure:: JPG/balance_nonuniform_small.jpg
-          :target: JPG/balance_nonuniform.jpg
+.. |balance3| image:: img/balance_rcb.jpg
+   :width: 32%
 
-     - .. figure:: JPG/balance_rcb_small.jpg
-          :target: JPG/balance_rcb.jpg
+|balance1|  |balance2|  |balance3|
 
 The leftmost diagram is the default partitioning of the simulation box
 across processors (one sub-box for each of 16 processors); the middle

doc/src/bond_class2.rst

@@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_fene.rst

@@ -54,23 +54,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_fene_expand.rst

@@ -52,23 +52,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_gromos.rst

@@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_harmonic.rst

@@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_harmonic_shift.rst

@@ -48,23 +48,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_harmonic_shift_cut.rst

@@ -46,23 +46,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_morse.rst

@@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_none.rst

@@ -13,7 +13,7 @@ Syntax
 Examples
 """"""""
 
-.. code-blocK:: LAMMPS
+.. code-block:: LAMMPS
 
    bond_style none
 

doc/src/bond_nonlinear.rst

@@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_quartic.rst

@@ -88,23 +88,7 @@ status of broken bonds or permanently delete them, e.g.:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/bond_special.rst

@@ -0,0 +1,106 @@
+.. index:: bond_style special
+
+bond_style special command
+=================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style special
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   bond_style special
+   bond_coeff 0.5 0.5
+
+Description
+"""""""""""
+
+The *special* bond style can be used to create conceptual bonds which
+effectively impose weightings on the pairwise Lennard Jones and/or
+Coulombic interactions between selected pairs of particles in the
+system.  The form of the pairwise interaction will be whatever is
+computed by the :doc:`pair_style <pair_style>` command defined for the
+system; this command defines the weightings for its two terms.
+
+This command can thus be useful to apply weightings that cannot be
+handled by the :doc:`special_bonds <special_bonds>` command, such as
+on 1-5 or 1-6 interactions.  Or it can be used to add pairwise forces
+between one or more pairs of atoms that otherwise would not be include
+in the :doc:`pair_style <pair_style>` computation.
+
+The potential for this bond style has the form
+
+.. math::
+
+   E =  w_{LJ} E_{LJ} + w_{Coul} E_{Coul}
+
+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
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* :math:`w_{LJ}` weight (0.0 to 1.0) on pairwise Lennard-Jones interactions
+
+* :math:`w_{Coul}` weight (0.0 to 1.0) on pairwise Coulombic interactions
+
+----------
+
+Normally this bond style should be used in conjunction with one (or
+more) other bond styles which compute forces between atoms directly
+bonded to each other in a molecule.  This means the :doc:`bond_style
+hybrid <bond_hybrid>` command should be used with bond_style special
+as one of its sub-styles.
+
+Note that the same as for any other bond style, pairs of bonded atoms
+must be enumerated in the data file read by the :doc:`read_data
+<read_data>` command.  Thus if this command is used to weight all 1-5
+interactions in the system, all the 1-5 pairs of atoms must be listed
+in the "Bonds" section of the data file.
+
+This bond style imposes strict requirements on settings made with the
+:doc:`special_bonds <special_bonds>` command.  These requirements
+ensure that the new bonds created by this style do not create spurious
+1-2, 1-3, or 1-4 interactions within the molecular topology.
+
+Specifically 1-2 interactions must have weights of zero, 1-3
+interactions must either have weights of unity or :doc:`special_bonds
+angle yes <special_bonds>` must be used, and 1-4 interactions must
+have weights of unity or :doc:`special_bonds dihedral yes <special_bonds>`
+must be used.
+
+If this command is used to create bonded interactions between
+particles that are further apart than usual (e.g. 1-5 or 1-6
+interactions), this style may require an increase in the communication
+cutoff via the :doc:`comm_modify cutoff <comm_modify>` command.  If
+LAMMPS cannot find a partner atom in a bond, an error will be issued.
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+This bond style requires the use of a :doc:`pair_style <pair_style>` which
+computes a pairwise additive interaction and provides the ability to
+compute interactions for individual pairs of atoms.  Manybody potentials
+are not compatible in general, but also some other pair styles are missing
+the required functionality and thus will cause an error.
+
+This command is not compatible with long-range Coulombic interactions. If a
+`kspace_style <kspace_style>` is declared, an error will be issued.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
+
+**Default:** none

doc/src/bond_style.rst

@@ -98,6 +98,7 @@ accelerated styles exist.
 * :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
 * :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
 * :doc:`quartic <bond_quartic>` - breakable quartic bond
+* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
 * :doc:`table <bond_table>` - tabulated by bond length
 
 ----------

doc/src/bond_table.rst

@@ -124,23 +124,7 @@ one that matches the specified keyword.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/comm_style.rst

@@ -55,8 +55,7 @@ commands.  The decomposition can be changed via the
 Restrictions
 """"""""""""
 
-Communication style *tiled* cannot be used with *triclinic* simulation
-cells.
+None
 
 Related commands
 """"""""""""""""

doc/src/compute_coord_atom.rst

@@ -115,23 +115,7 @@ too frequently.
 ----------
 
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 
 ----------

doc/src/compute_orientorder_atom.rst

@@ -146,23 +146,7 @@ too frequently.
 ----------
 
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 
 ----------

doc/src/compute_pressure.rst

@@ -112,23 +112,7 @@ where "thermo_temp" is the ID of a similarly defined compute of style
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/compute_saed.rst

@@ -57,8 +57,8 @@ is computed from the structure factor F using the equations:
 
 .. math::
 
-  I = & \frac{F^{*}F}{N} \\
-  F(\mathbf{k}) = & \sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k} \cdot \mathbf{r}_j)
+   I = & \frac{F^{*}F}{N} \\
+   F(\mathbf{k}) = & \sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k} \cdot \mathbf{r}_j)
 
 Here, K is the location of the reciprocal lattice node, :math:`r_j` is the
 position of each atom, :math:`f_j` are atomic scattering factors.
@@ -68,8 +68,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a)  by
 the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
 
-.. image:: JPG/saed_mesh_small.jpg
-   :target: JPG/saed_mesh.jpg
+.. image:: img/saed_mesh.jpg
+   :scale: 75%
    :align: center
 
 For a mesh defined by the simulation domain, a rectilinear grid is
@@ -103,8 +103,8 @@ mesh and a *dR_Ewald* thick surface of the Ewald sphere.  See the
 example 3D intensity data and the intersection of a [010] zone axis
 in the below image.
 
-.. image:: JPG/saed_ewald_intersect_small.jpg
-   :target: JPG/saed_ewald_intersect.jpg
+.. image:: img/saed_ewald_intersect.jpg
+   :scale: 75%
    :align: center
 
 The atomic scattering factors, fj, accounts for the reduction in
@@ -116,8 +116,8 @@ The analytic approximation is computed using the formula
 
 .. math::
 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
-  a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
+   f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
+   a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
 
 Coefficients parameterized by :ref:`(Fox) <Fox>` are assigned for each
 atom type designating the chemical symbol and charge of each atom

doc/src/compute_temp.rst

@@ -69,23 +69,7 @@ thermostatting.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/compute_temp_partial.rst

@@ -69,23 +69,7 @@ thermostatting.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/compute_xrd.rst

@@ -71,8 +71,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a)
 by the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
 
-.. image:: JPG/xrd_mesh_small.jpg
-   :target: JPG/xrd_mesh.jpg
+.. image:: img/xrd_mesh.jpg
+   :scale: 75%
    :align: center
 
 For a mesh defined by the simulation domain, a rectilinear grid is

doc/src/create_atoms.rst

@@ -257,8 +257,7 @@ individual lattice points being "above" or "below" the mathematical
 expression for the sinusoidal curve.  If a finer lattice were used,
 the sinusoid would appear to be "smoother".  Also note the use of the
 "xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords which
-converts lattice spacings to distance.  Click on the image for a
-larger version.
+converts lattice spacings to distance.
 
 .. code-block:: LAMMPS
 
@@ -275,10 +274,14 @@ larger version.
    create_atoms    1 box var v set x xx set y yy
    write_dump      all atom sinusoid.lammpstrj
 
-.. image:: JPG/sinusoid_small.jpg
-   :target: JPG/sinusoid.jpg
+.. image:: img/sinusoid.jpg
+   :scale: 50%
    :align: center
 
+.. raw:: html
+
+   Click on the image for a larger version.
+
 The *rotate* keyword allows specification of the orientation
 at which molecules are inserted.  The axis of rotation is
 determined by the rotation vector (Rx,Ry,Rz) that goes through the

doc/src/dihedral_charmm.rst

@@ -125,23 +125,7 @@ computed.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_class2.rst

@@ -154,23 +154,7 @@ listed under a *BondBond13 Coeffs* heading and you must leave out the
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_cosine_shift_exp.rst

@@ -56,23 +56,7 @@ commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_fourier.rst

@@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_harmonic.rst

@@ -60,23 +60,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_helix.rst

@@ -51,23 +51,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_multi_harmonic.rst

@@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------
 

doc/src/dihedral_nharmonic.rst

@@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
-:doc:`suffix <suffix>` command in your input script.
-
-See the :doc:`Speed packages <Speed_packages>` doc page for more
-instructions on how to use the accelerated styles effectively.
+.. include:: accel_styles.rst
 
 ----------