Merge remote-tracking branch 'upstream/master' into 2020

doc/src/Build_package.rst

@@ -136,6 +136,10 @@ src directory.
 .. _cmake_presets:
 
 CMake presets for installing many packages
+<<<<<<< HEAD
+=======
+""""""""""""""""""""""""""""""""""""""""""
+>>>>>>> upstream/master
 
 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@@ -168,7 +172,8 @@ one of them as a starting point and customize it to your needs.
    in a single cmake run, or change settings incrementally by running
    cmake with new flags.
 
-**Example:**
+Example
+"""""""
 
 .. code-block:: bash
 

doc/src/Commands_fix.rst

@@ -150,7 +150,10 @@ OPT.
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
+<<<<<<< HEAD
    * :doc:`pafi <fix_pafi>`
+=======
+>>>>>>> upstream/master
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

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/Speed_intel.rst

@@ -12,7 +12,8 @@ When offloading to a co-processor from a CPU, the same routine is run
 twice, once on the CPU and once with an offload flag. This allows
 LAMMPS to run on the CPU cores and co-processor cores simultaneously.
 
-**Currently Available USER-INTEL Styles:**
+Currently Available USER-INTEL Styles
+"""""""""""""""""""""""""""""""""""""
 
 * Angle Styles: charmm, harmonic
 * Bond Styles: fene, fourier, harmonic
@@ -31,9 +32,10 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
    support computing per-atom stress.  If any compute or fix in your
    input requires it, LAMMPS will abort with an error message.
 
-**Speed-ups to expect:**
+Speed-up to expect
+"""""""""""""""""""
 
-The speedups will depend on your simulation, the hardware, which
+The speedup will depend on your simulation, the hardware, which
 styles are used, the number of atoms, and the floating-point
 precision mode. Performance improvements are shown compared to
 LAMMPS *without using other acceleration packages* as these are
@@ -59,7 +61,8 @@ instructions to reproduce.
 
 ----------
 
-**Accuracy and order of operations:**
+Accuracy and order of operations
+""""""""""""""""""""""""""""""""
 
 In most molecular dynamics software, parallelization parameters
 (# of MPI, OpenMP, and vectorization) can change the results due
@@ -96,7 +99,8 @@ mode should not be used without appropriate validation.
 
 ----------
 
-**Quick Start for Experienced Users:**
+Quick Start for Experienced Users
+"""""""""""""""""""""""""""""""""
 
 LAMMPS should be built with the USER-INTEL package installed.
 Simulations should be run with 1 MPI task per physical *core*\ ,
@@ -136,7 +140,10 @@ For Intel Xeon Phi co-processors (Offload):
 
 ----------
 
-**Required hardware/software:**
+Required hardware/software
+""""""""""""""""""""""""""
+
+When using Intel compilers version 16.0 or later is required.
 
 When using Intel compilers version 16.0 or later is required.
 
@@ -159,7 +166,8 @@ For best performance, we recommend that the MCDRAM is configured in
 "Cache" mode can also be used, although the performance might be
 slightly lower.
 
-**Notes about Simultaneous Multithreading:**
+Notes about Simultaneous Multithreading
+"""""""""""""""""""""""""""""""""""""""
 
 Modern CPUs often support Simultaneous Multithreading (SMT). On
 Intel processors, this is called Hyper-Threading (HT) technology.
@@ -196,7 +204,8 @@ this information can normally be obtained with:
 
    cat /proc/cpuinfo
 
-**Building LAMMPS with the USER-INTEL package:**
+Building LAMMPS with the USER-INTEL package
+"""""""""""""""""""""""""""""""""""""""""""
 
 See the :ref:`Build extras <user-intel>` doc page for
 instructions.  Some additional details are covered here.
@@ -263,7 +272,8 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias
    in most of the example Makefiles is to use "-xHost", however this
    should not be used when cross-compiling.
 
-**Running LAMMPS with the USER-INTEL package:**
+Running LAMMPS with the USER-INTEL package
+""""""""""""""""""""""""""""""""""""""""""
 
 Running LAMMPS with the USER-INTEL package is similar to normal use
 with the exceptions that one should 1) specify that LAMMPS should use
@@ -304,7 +314,8 @@ almost all cases.
    recommended, especially when running on a machine with Intel
    Hyper-Threading technology disabled.
 
-**Run with the USER-INTEL package from the command line:**
+Run with the USER-INTEL package from the command line
+"""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 To enable USER-INTEL optimizations for all available styles used in
 the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for
@@ -339,7 +350,8 @@ launching MPI applications):
    mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
    mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
 
-**Or run with the USER-INTEL package by editing an input script:**
+Or run with the USER-INTEL package by editing an input script
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 As an alternative to adding command-line arguments, the input script
 can be edited to enable the USER-INTEL package. This requires adding
@@ -361,7 +373,8 @@ Alternatively, the :doc:`suffix intel <suffix>` command can be added to
 the input script to enable USER-INTEL styles for the commands that
 follow in the input script.
 
-**Tuning for Performance:**
+Tuning for Performance
+""""""""""""""""""""""
 
 .. note::
 
@@ -431,7 +444,8 @@ series processors will always perform better using MCDRAM. Please
 consult your system documentation for the best approach to specify
 that MPI runs are performed in MCDRAM.
 
-**Tuning for Offload Performance:**
+Tuning for Offload Performance
+""""""""""""""""""""""""""""""
 
 The default settings for offload should give good performance.
 
@@ -521,7 +535,8 @@ the pair styles in the USER-INTEL package currently support the
 :doc:`run_style respa <run_style>` command; only the "pair" option is
 supported.
 
-**References:**
+References
+""""""""""
 
 * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
 * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).

doc/src/Speed_omp.rst

@@ -8,18 +8,21 @@ improper), several Kspace styles, and a few fix styles.  It uses
 the OpenMP interface for multi-threading, but can also be compiled
 without OpenMP support, providing optimized serial styles in that case.
 
-**Required hardware/software:**
+Required hardware/software
+""""""""""""""""""""""""""
 
 To enable multi-threading, your compiler must support the OpenMP interface.
 You should have one or more multi-core CPUs, as multiple threads can only be
 launched by each MPI task on the local node (using shared memory).
 
-**Building LAMMPS with the USER-OMP package:**
+Building LAMMPS with the USER-OMP package
+"""""""""""""""""""""""""""""""""""""""""
 
 See the :ref:`Build extras <user-omp>` doc page for
 instructions.
 
-**Run with the USER-OMP package from the command line:**
+Run with the USER-OMP package from the command line
+"""""""""""""""""""""""""""""""""""""""""""""""""""
 
 These examples assume one or more 16-core nodes.
 
@@ -52,7 +55,8 @@ details, including the default values used if it is not specified.  It
 also gives more details on how to set the number of threads via the
 OMP_NUM_THREADS environment variable.
 
-**Or run with the USER-OMP package by editing an input script:**
+Or run with the USER-OMP package by editing an input script
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 The discussion above for the mpirun/mpiexec command, MPI tasks/node,
 and threads/MPI task is the same.
@@ -70,7 +74,8 @@ per MPI task to use.  The command doc page explains other options and
 how to set the number of threads via the OMP_NUM_THREADS environment
 variable.
 
-**Speed-ups to expect:**
+Speed-up to expect
+""""""""""""""""""
 
 Depending on which styles are accelerated, you should look for a
 reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
@@ -92,7 +97,8 @@ sub-section.
 A description of the multi-threading strategy used in the USER-OMP
 package and some performance examples are `presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_
 
-**Guidelines for best performance:**
+Guidelines for best performance
+"""""""""""""""""""""""""""""""
 
 For many problems on current generation CPUs, running the USER-OMP
 package with a single thread/task is faster than running with multiple

doc/src/Speed_opt.rst

@@ -7,15 +7,18 @@ Technologies).  It contains a handful of pair styles whose compute()
 methods were rewritten in C++ templated form to reduce the overhead
 due to if tests and other conditional code.
 
-**Required hardware/software:**
+Required hardware/software
+""""""""""""""""""""""""""
 
-None.
+Any hardware. Any compiler.
 
-**Building LAMMPS with the OPT package:**
+Building LAMMPS with the OPT package
+""""""""""""""""""""""""""""""""""""
 
 See the :ref:`Build extras <opt>` doc page for instructions.
 
-**Run with the OPT package from the command line:**
+Run with the OPT package from the command line
+""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: bash
 
@@ -25,7 +28,8 @@ See the :ref:`Build extras <opt>` doc page for instructions.
 Use the "-sf opt" :doc:`command-line switch <Run_options>`, which will
 automatically append "opt" to styles that support it.
 
-**Or run with the OPT package by editing an input script:**
+Or run with the OPT package by editing an input script
+""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
 "opt" suffix to individual styles in your input script, e.g.
@@ -34,13 +38,15 @@ Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
 
    pair_style lj/cut/opt 2.5
 
-**Speed-ups to expect:**
+Speed-up to expect
+""""""""""""""""""
 
 You should see a reduction in the "Pair time" value printed at the end
 of a run.  On most machines for reasonable problem sizes, it will be a
 5 to 20% savings.
 
-**Guidelines for best performance:**
+Guidelines for best performance
+"""""""""""""""""""""""""""""""
 
 Just try out an OPT pair style to see how it performs.
 

doc/src/angle_charmm.rst

@@ -92,7 +92,10 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/angle_class2.rst

@@ -135,7 +135,10 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/angle_coeff.rst

@@ -92,4 +92,7 @@ Related commands
 
 :doc:`angle_style <angle_style>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine.rst

@@ -60,4 +60,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine_buck6d.rst

@@ -68,4 +68,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine_delta.rst

@@ -62,4 +62,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`, :doc:`angle_style cosine/squared <angle_cosine_squared>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine_periodic.rst

@@ -70,7 +70,10 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/angle_cosine_shift.rst

@@ -61,4 +61,7 @@ Related commands
 :doc:`angle_coeff <angle_coeff>`,
 :doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine_shift_exp.rst

@@ -74,4 +74,7 @@ Related commands
 :doc:`angle_style cosine/shift <angle_cosine_shift>`,
 :doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cosine_squared.rst

@@ -62,4 +62,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_cross.rst

@@ -62,4 +62,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_dipole.rst

@@ -113,7 +113,10 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`, :doc:`angle_hybrid <angle_hybrid>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/angle_fourier.rst

@@ -58,4 +58,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_fourier_simple.rst

@@ -57,4 +57,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_harmonic.rst

@@ -69,4 +69,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_hybrid.rst

@@ -95,4 +95,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_mm3.rst

@@ -57,4 +57,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_none.rst

@@ -37,4 +37,7 @@ Related commands
 
 :doc:`angle_style zero <angle_zero>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_quartic.rst

@@ -65,4 +65,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_sdk.rst

@@ -73,4 +73,7 @@ Related commands
 :doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
 :doc:`pair_style lj/sdk/coul/long <pair_sdk>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_table.rst

@@ -130,7 +130,8 @@ one that matches the specified keyword.
 
 ----------
 
-**Restart info:**
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 This angle style writes the settings for the "angle_style table"
 command to :doc:`binary restart files <restart>`, so a angle_style
@@ -152,4 +153,7 @@ Related commands
 
 :doc:`angle_coeff <angle_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/angle_zero.rst

@@ -51,4 +51,7 @@ Related commands
 
 :doc:`angle_style none <angle_none>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/atom_modify.rst

@@ -160,7 +160,11 @@ The *first* and *sort* options cannot be used together.  Since sorting
 is on by default, it will be turned off if the *first* keyword is
 used with a group-ID that is not "all".
 
-**Related commands:** none
+Related commands
+""""""""""""""""
+
+none
+
 
 Default
 """""""

doc/src/balance.rst

@@ -548,4 +548,7 @@ Related commands
 
 .. _pizza: https://pizza.sandia.gov
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_class2.rst

@@ -65,7 +65,10 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/bond_coeff.rst

@@ -87,4 +87,7 @@ Related commands
 
 :doc:`bond_style <bond_style>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_fene.rst

@@ -74,7 +74,10 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/bond_fene_expand.rst

@@ -72,7 +72,10 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/bond_gromos.rst

@@ -59,4 +59,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_harmonic.rst

@@ -65,4 +65,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_harmonic_shift.rst

@@ -65,4 +65,7 @@ Related commands
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
 :doc:`bond_harmonic <bond_harmonic>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_harmonic_shift_cut.rst

@@ -64,4 +64,7 @@ Related commands
 :doc:`bond_harmonic <bond_harmonic>`,
 :doc:`bond_style harmonic/shift <bond_harmonic_shift>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_hybrid.rst

@@ -76,4 +76,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_mm3.rst

@@ -55,7 +55,10 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/bond_morse.rst

@@ -60,4 +60,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_none.rst

@@ -31,8 +31,15 @@ Restrictions
 """"""""""""
  none
 
-**Related commands:** none
+Related commands
+""""""""""""""""
+
+none
+
 
 :doc:`bond_style zero <bond_zero>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_nonlinear.rst

@@ -60,7 +60,10 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none
 
 ----------
 

doc/src/bond_oxdna.rst

@@ -108,7 +108,9 @@ Related commands
 :doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
 :doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
-**Default:**
+Default
+"""""""
+
 
 none
 

doc/src/bond_quartic.rst

@@ -108,4 +108,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_special.rst

@@ -103,4 +103,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_table.rst

@@ -128,7 +128,8 @@ one that matches the specified keyword.
 
 ----------
 
-**Restart info:**
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 This bond style writes the settings for the "bond_style table"
 command to :doc:`binary restart files <restart>`, so a bond_style
@@ -150,4 +151,7 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_write.rst

@@ -70,4 +70,7 @@ Related commands
 :doc:`bond_style table <bond_table>`,
 :doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/bond_zero.rst

@@ -50,4 +50,7 @@ Related commands
 
 :doc:`bond_style none <bond_none>`
 
-**Default:** none
+Default
+"""""""
+
+none

doc/src/box.rst

@@ -58,7 +58,11 @@ This command cannot be used after the simulation box is defined by a
 :doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
 :doc:`read_restart <read_restart>` command.
 
-**Related commands:** none
+Related commands
+""""""""""""""""
+
+none
+
 
 Default
 """""""

doc/src/clear.rst

@@ -37,6 +37,13 @@ Restrictions
 """"""""""""
  none
 
-**Related commands:** none
+Related commands
+""""""""""""""""
 
-**Default:** none
+none
+
+
+Default
+"""""""
+
+none