Merge branch 'develop' into always-exceptions

# Conflicts:
#	src/library.cpp

doc/src/Bibliography.rst

@@ -203,7 +203,7 @@ Bibliography
    A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
 
 **(CasP)**
-   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+   CasP webpage: http://www.casp-program.org/
 
 **(Cawkwell2012)**
    A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).

doc/src/Build_extras.rst

@@ -140,6 +140,8 @@ CMake build
                                 # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D CUDA_BUILD_MULTIARCH=value  # enables building CUDA kernels for all supported GPU architectures
+                                  # value = yes (default) or no
    -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
                                       # value = yes (default) or no
 
@@ -158,41 +160,49 @@ CMake build
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
 
-CMake can detect which version of the CUDA toolkit is used and thus will try
-to include support for **all** major GPU architectures supported by this toolkit.
-Thus the GPU_ARCH setting is merely an optimization, to have code for
-the preferred GPU architecture directly included rather than having to wait
-for the JIT compiler of the CUDA driver to translate it.
+CMake can detect which version of the CUDA toolkit is used and thus will
+try to include support for **all** major GPU architectures supported by
+this toolkit.  Thus the GPU_ARCH setting is merely an optimization, to
+have code for the preferred GPU architecture directly included rather
+than having to wait for the JIT compiler of the CUDA driver to translate
+it.  This behavior can be turned off (e.g. to speed up compilation) by
+setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
 
-When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
-is required and a GPU architecture of Kepler or later, which must *also* be
-supported by the CUDA toolkit in use **and** the CUDA driver in use.
-When compiling for OpenCL, OpenCL version 1.2 or later is required and the
-GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
+When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
+CUDA toolkit is required and a GPU architecture of Kepler or later,
+which must *also* be supported by the CUDA toolkit in use **and** the
+CUDA driver in use.  When compiling for OpenCL, OpenCL version 1.2 or
+later is required and the GPU must be supported by the GPU driver and
+OpenCL runtime bundled with the driver.
 
-When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
-using the traditional build procedure. CMake will detect files generated by that
-process and will terminate with an error and a suggestion for how to remove them.
+When building with CMake, you **must NOT** build the GPU library in
+``lib/gpu`` using the traditional build procedure. CMake will detect
+files generated by that process and will terminate with an error and a
+suggestion for how to remove them.
 
-If you are compiling for OpenCL, the default setting is to download, build, and
-link with a static OpenCL ICD loader library and standard OpenCL headers.  This
-way no local OpenCL development headers or library needs to be present and only
-OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
-desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+If you are compiling for OpenCL, the default setting is to download,
+build, and link with a static OpenCL ICD loader library and standard
+OpenCL headers.  This way no local OpenCL development headers or library
+needs to be present and only OpenCL compatible drivers need to be
+installed to use OpenCL.  If this is not desired, you can set
+:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
-The GPU library has some multi-thread support using OpenMP.  If LAMMPS is built
-with ``-D BUILD_OMP=on`` this will also be enabled.
+The GPU library has some multi-thread support using OpenMP.  If LAMMPS
+is built with ``-D BUILD_OMP=on`` this will also be enabled.
 
-If you are compiling with HIP, note that before running CMake you will have to
-set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
-and the linker to work correctly.
+If you are compiling with HIP, note that before running CMake you will
+have to set appropriate environment variables. Some variables such as
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
+necessary for :code:`hipcc` and the linker to work correctly.
 
-Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
-code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
-set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
-yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
-should only use this option in preparations to run on Aurora system at ANL.
+.. versionadded:: 3Aug2022
+
+Using the CHIP-SPV implementation of HIP is supported. It allows one to
+run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
+CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
+command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
+the use of HIP for Intel GPUs is experimental. You should only use this
+option in preparations to run on Aurora system at Argonne.
 
 .. code:: bash
 

doc/src/Developer_grid.rst

@@ -92,8 +92,8 @@ Arguments for these methods can be values returned by the
 *setup_grid()* method (described below), which define the extent of
 the grid cells (owned+ghost) the processor owns.  These 4 methods
 allocate memory for 2d (first two) and 3d (second two) grid data.  The
-two methods that end in "_one" allocate an array which stores a single
-value per grid cell.  The two that end in "_multi" allocate an array
+two methods that end in "_offset" allocate an array which stores a single
+value per grid cell.  The two that end in "_last" allocate an array
 which stores *Nvalues* per grid cell.
 
 .. code-block:: c++

doc/src/Howto_2d.rst

@@ -13,9 +13,9 @@ box with a single z plane of atoms - e.g.
 
 .. code-block:: LAMMPS
 
-   create box 1 -10 10 -10 10 -0.25 0.25
+   create_box 1 -10 10 -10 10 -0.25 0.25
 
-If using the :doc:`read data <read_data>` command to read in a file of
+If using the :doc:`read_data <read_data>` command to read in a file of
 atom coordinates, set the "zlo zhi" values to be finite but narrow,
 similar to the create_box command settings just described.  For each
 atom in the file, assign a z coordinate so it falls inside the

doc/src/Howto_bpm.rst

@@ -79,9 +79,9 @@ As bonds can be broken between neighbor list builds, the
 bond styles. There are two possible settings which determine how pair
 interactions work between bonded particles.  First, one can overlay
 pair forces with bond forces such that all bonded particles also
-feel pair interactions. This can be accomplished by using the *overlay/pair*
-keyword present in all bpm bond styles and by using the following special
-bond settings
+feel pair interactions. This can be accomplished by setting the *overlay/pair*
+keyword present in all bpm bond styles to *yes* and requires using the
+following special bond settings
 
    .. code-block:: LAMMPS
 
@@ -107,7 +107,17 @@ bond lists is expensive.  By setting the lj weight for 1-2 bonds to
 zero, this turns off pairwise interactions.  Even though there are no
 charges in BPM models, setting a nonzero coul weight for 1-2 bonds
 ensures all bonded neighbors are still included in the neighbor list
-in case bonds break between neighbor list builds.
+in case bonds break between neighbor list builds. If bond breakage is
+disabled during a simulation run by setting the *break* keyword to *no*,
+a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
+from the neighbor list builds
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 0 1 1
+
+This can be useful for post-processing, or to determine pair interaction
+properties between distinct bonded particles.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using

doc/src/Modify_style.rst

@@ -28,20 +28,34 @@ Include files (varied)
   packages and hard-to-find bugs have regularly manifested in the
   past.
 
-- Header files, especially those defining a "style", should only use
-  the absolute minimum number of include files and **must not**
-  contain any ``using`` statements. Typically, that would only be the
-  header for the base class.  Instead, any include statements should
-  be put in the corresponding implementation files and forward
-  declarations be used.  For implementation files, the "include what
-  you use" principle should be employed.  However, there is the
-  notable exception that when the ``pointers.h`` header is included
-  (or one of the base classes derived from it) certain headers will
-  always be included and thus do not need to be explicitly specified.
-  These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`,
-  `utils.h`, `vector`, `fmt/format.h`, `climits`, `cinttypes`.  This
-  also means any such file can assume that `FILE`, `NULL`, and
-  `INT_MAX` are defined.
+- Header files, especially those defining a "style", should only use the
+  absolute minimum number of include files and **must not** contain any
+  ``using`` statements. Typically, that would only be the header for the
+  base class.  Instead, any include statements should be put in the
+  corresponding implementation files and forward declarations be used.
+  For implementation files, the "include what you use" principle should
+  be employed.  However, there is the notable exception that when the
+  ``pointers.h`` header is included (or the header of one of the classes
+  derived from it), certain headers will *always* be included and thus
+  do not need to be explicitly specified.  These are: `mpi.h`,
+  `cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`, `vector`,
+  `fmt/format.h`, `climits`, `cinttypes`.  This also means any such file
+  can assume that `FILE`, `NULL`, and `INT_MAX` are defined.
+
+- Class members variables should not be initialized in the header file,
+  but instead should be initialized either in the initializer list of
+  the constructor or explicitly assigned in the body of the constructor.
+  If the member variable is relevant to the functionality of a class
+  (for example when it stores a value from a command line argument), the
+  member variable declaration is followed by a brief comment explaining
+  its purpose and what its values can be.  Class members that are
+  pointers should always be initialized to ``nullptr`` in the
+  initializer list of the constructor.  This reduces clutter in the
+  header and avoids accessing uninitialized pointers, which leads to
+  hard to debug issues, class members are often implicitly initialized
+  to ``NULL`` on the first use (but *not* after a :doc:`clear command
+  <clear>`).  Please see the files ``reset_atoms_mol.h`` and
+  ``reset_atoms_mol.cpp`` as an example.
 
 - System headers or headers from installed libraries are included with
   angular brackets (example: ``#include <vector>``), while local

doc/src/Tools.rst

@@ -93,6 +93,7 @@ Miscellaneous tools
    * :ref:`i-pi <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
+   * :ref:`LAMMPS GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
    * :ref:`singularity/apptainer <singularity_tool>`
@@ -634,6 +635,229 @@ you first need to use the :doc:`clear` command.
 
 ----------
 
+.. _lammps_gui:
+
+LAMMPS GUI
+----------
+
+.. versionadded:: 2Aug2023
+
+Overview
+^^^^^^^^
+
+LAMMPS GUI is essentially a small graphical text editor that is linked
+to the :ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run
+LAMMPS directly using the contents of the editor's text buffer as input.
+This is similar to what people usually would do using a text editor to
+edit the input and then a command line terminal window to run the input
+commands.  The main benefit is that this integrates very well with
+graphical desktop environments and that it is easier to use for
+beginners in running computations and thus very suitable for tutorials
+on LAMMPS.  A small difference is that for the LAMMPS GUI it is not
+require to first commit its buffer of the text editor to a file.
+
+Features
+^^^^^^^^
+
+The main window of the LAMMPS GUI is a generic text editor window with
+line numbers and syntax highlighting set up for LAMMPS input files.  It
+can be used to edit any kind of text file, though.  The output of a run
+is captured and displayed in a separate dialog window and *not* sent to
+the console or a log file (unless the :doc:`log command <log>` is used
+in the input.  The log window is regularly updated during the run and a
+progress bar for the run command shown at the bottom of the main window.
+Starting a new run will open another log windows.  The state of LAMMPS
+will be reset between two runs.  After the simulation is finished, an
+image of the simulated system can be created and shown in an image
+viewer window.  Ongoing runs can be stopped at the next iteration via
+triggering a timeout.
+
+When opening a file, the editor will determine the directory where the
+file resides and switch its current working directory to the folder of
+that file.  Many LAMMPS inputs contain commands that read other files,
+typically from the folder of the input file.  The GUI will always show
+the current working directory in the bottom.  The editor window can also
+receive (entire) files via drag-n-drop from a file manager GUI or a
+desktop environment.  When exiting the GUI with a modified buffer, a
+dialog asking to either cancel, ignore the modifications, or save the
+file with show up. Same when attempting to load a new file into a
+modified buffer.
+
+Hotkeys
+^^^^^^^
+
+Almost all functionality is accessible from the menu or via hotkeys.
+The following hotkeys are available (On macOS use the Command key
+instead of Ctrl (aka Control)).
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Hotkey
+     - Function
+     - Hotkey
+     - Function
+     - Hotkey
+     - Function
+     - Hotkey
+     - Function
+   * - Ctrl+N
+     - New File
+     - Ctrl+Z
+     - Undo edit
+     - Ctrl+V
+     - Paste text
+     - Ctrl+Q
+     - Quit (Main Window only)
+   * - Ctrl+O
+     - Open File
+     - Ctrl+Shift+Z
+     - Redo edit
+     - Ctrl+Enter
+     - Run LAMMPS
+     - Ctrl+W
+     - Close (Log and Image Window only)
+   * - CTRL+S
+     - Save File
+     - Ctrl+C
+     - Copy text
+     - Ctrl+/
+     - Stop Active Run
+     - Ctrl+P
+     - Preferences
+   * - Ctrl+Shift+S
+     - Save File As
+     - Ctrl+X
+     - Cut text
+     - Ctrl+I
+     - Create Snapshot Image
+     - Ctrl+Shift+/
+     - Quick Help
+
+Further editing keybindings `are documented with the Qt documentation
+<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
+case of conflicts the list above takes precedence.
+
+Parallelization
+^^^^^^^^^^^^^^^
+
+Due to its nature as a graphical application, it is not possible to use
+the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading is
+available and enabled by default.
+
+Prerequisites and portability
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+LAMMPS GUI is programmed in C++ based on the C++11 standard and using
+the `Qt GUI framework <https://www.qt.io/product/framework>`_.
+Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
+recommended Qt 6.x not (yet) supported. Furthermore, CMake version 3.16
+is required and LAMMPS must be configured with ``-D
+LAMMPS_EXCETIONS=on`` and ``-D BUILD_MPI=off``. It has been successfully
+compiled and tested on:
+
+- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
+- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
+- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
+- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
+
+Pre-compiled executables
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Pre-compiled LAMMPS executables including the GUI are currently
+available from https://download.lammps.org/static. You can unpack the
+archive (or mount the macOS disk image) and run the GUI directly in
+place. The folder may also be moved around and added to the ``PATH``
+environment variable so the executables will be found automatically. The
+LAMMPS GUI executable is called ``lammps-gui`` and takes no arguments or
+will interpret the first argument as filename to load.
+
+Compilation
+^^^^^^^^^^^
+
+The source for the LAMMPS GUI is included with the LAMMPS source code
+distribution in the folder `tools/lammps-gui` and thus it can be can be
+built as part of a regular LAMMPS compilation.
+:doc:`Using CMake <Howto_cmake>` is required.
+To enable its compilation the CMake variable ``-D BUILD_LAMMPS_GUI=on``
+must be set when creating the CMake configuration.  All other settings
+(compiler, flags, compile type) for LAMMPS GUI are then inherited from
+the regular LAMMPS build.  If the Qt library is packaged for Linux
+distributions, then its location is typically auto-detected since the
+required CMake configuration files are stored in a location where CMake
+can find them without additional help.  Otherwise, the location of the
+Qt library installation must be indicated by setting
+``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to a folder inside
+the Qt installation that contains the file ``Qt5Config.cmake``.
+
+It is also possible to build the LAMMPS GUI as a standalone executable
+(e.g. when LAMMPS has been compiled with traditional make), then the
+CMake configuration needs to be told where to find the LAMMPS headers
+and the LAMMPS library, via `-D LAMMPS_SOURCE_DIR=/path/to/lammps/src`.
+CMake will try to guess a build folder with the LAMMPS library from that
+path, but it can also be set with `-D LAMMPS_LIB_DIR=/path/to/lammps/lib`.
+
+Rather than linking to the LAMMPS library during compilation, it is also
+possible to compile the GUI with a plugin loader library that will load
+the LAMMPS library dynamically at runtime during the start of the GUI
+from a shared library; e.g. `liblammps.so` or `liblammps.dylib` or
+`liblammps.dll` (depending on the operating system).  This has the
+advantage that the LAMMPS library can be updated LAMMPS without having
+to recompile the GUI.  The ABI of the LAMMPS C-library interface is very
+stable and generally backward compatible.  This feature is enabled by
+setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then
+``-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
+would be the ``examples/COUPLE/plugin`` folder of the LAMMPS distribution.
+
+Platform notes
+^^^^^^^^^^^^^^
+
+macOS
+"""""
+
+When building on macOS, the build procedure will try to manufacture a
+drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
+target (i.e. `cmake --build <build dir> --target dmg` or `make dmg`.
+
+To build multi-arch executables that will run on both, arm64 and x86_64
+architectures natively, it is necessary to set the CMake variable ``-D
+CMAKE_OSX_ARCHITECTURES=arm64;x86_64``.  To achieve wide compatibility
+with different macOS versions, you can also set ``-D
+CMAKE_OSX_DEPLOYMENT_TARGET=11.0`` which will set compatibility to macOS
+11 (Big Sur) and later, even if you are compiling on a more recent macOS
+version.
+
+Windows
+"""""""
+
+On Windows currently only compilation from within Visual Studio 2022 is
+supported and tested. Using CMake and Ninja as build system is
+required. Qt needs to be installed, tested was a package downloaded from
+https://www.qt.io, into the ``C:\\Qt`` folder.  There is a custom
+`x64-GUI-MSVC` build configuration provided that will activate building
+the `lammps-gui.exe` executable in addition to LAMMPS.  When requesting
+an installation from the `Build` menu, it will create a compressed zip
+file with the executables and required dependent .dll files.  This zip
+file can be uncompressed and ``lammps-gui.exe`` run directly from there.
+The uncompressed folder can be added to the ``PATH`` environment and
+LAMMPS and LAMMPS GUI can be launched from anywhere from the command
+line.
+
+Linux
+"""""
+
+Version 5.12 or later of the Qt library and CMake version 3.16 are
+required and those are provided by, e.g., Ubuntu 20.04LTS.  Thus older
+Linux distributions are not likely to be supported, while more recent
+ones will work, even for pre-compiled executables (see above).  After
+compiling with ``cmake --build <build folder>``, use
+``cmake --build <build folder> --target tgz`` or ``make tgz`` to build
+a ``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
+support libraries.
+
+----------
+
 .. _arc:
 
 lmp2arc tool

doc/src/atc_add_molecule.rst

@@ -6,7 +6,7 @@ fix_modify AtC add_molecule command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>
 

doc/src/atc_add_species.rst

@@ -6,7 +6,7 @@ fix_modify AtC add_species command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> add_species <tag> <group|type> <ID>
 

doc/src/atc_atom_element_map.rst

@@ -6,7 +6,7 @@ fix_modify AtC atom_element_map command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> atom_element_map <eulerian|lagrangian> [<frequency>]
 

doc/src/atc_atom_weight.rst

@@ -6,7 +6,7 @@ fix_modify AtC atom_weight command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> atom_weight <method> <args>
 

doc/src/atc_atomic_charge.rst

@@ -6,7 +6,7 @@ fix_modify AtC atomic_charge command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> <include|omit> atomic_charge
 

doc/src/atc_boundary_dynamics.rst

@@ -6,7 +6,7 @@ fix_modify AtC boundary_dynamics command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>
 

doc/src/atc_boundary_faceset.rst

@@ -6,7 +6,7 @@ fix_modify AtC boundary_faceset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>
 

doc/src/atc_boundary_type.rst

@@ -6,7 +6,7 @@ fix_modify AtC boundary type command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary type <atom-type-id>
 

doc/src/atc_consistent_fe_initialization.rst

@@ -6,7 +6,7 @@ fix_modify AtC consistent_fe_initialization command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> consistent_fe_initialization <on|off>
 

doc/src/atc_control_localized_lambda.rst

@@ -6,7 +6,7 @@ fix_modify AtC control localized_lambda command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control localized_lambda <on|off>
 

doc/src/atc_control_momentum.rst

@@ -6,7 +6,7 @@ fix_modify AtC control momentum command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
    fix_modify AtC control momentum none

doc/src/atc_control_thermal.rst

@@ -6,7 +6,7 @@ fix_modify AtC control thermal command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
    fix_modify <AtC fixID> control thermal <control_type> <optional_args>

doc/src/atc_decomposition.rst

@@ -6,7 +6,7 @@ fix_modify AtC decomposition command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> decomposition <type>
 

doc/src/atc_electron_integration.rst

@@ -6,7 +6,7 @@ fix_modify AtC extrinsic electron_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> extrinsic electron_integration <integration_type> [<num_subcycle_steps>]
 

doc/src/atc_equilibrium_start.rst

@@ -6,7 +6,7 @@ fix_modify AtC equilibrium_start command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> equilibrium_start <on|off>
 

doc/src/atc_extrinsic_exchange.rst

@@ -6,7 +6,7 @@ fix_modify AtC extrinsic exchange command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> extrinsic exchange <on|off>
 

doc/src/atc_fe_md_boundary.rst

@@ -6,7 +6,7 @@ fix_modify AtC fe_md_boundary command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fe_md_boundary <faceset|interpolate|no_boundary>
 

doc/src/atc_filter_scale.rst

@@ -6,7 +6,7 @@ fix_modify AtC filter scale command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter scale <scale>
 

doc/src/atc_filter_type.rst

@@ -6,7 +6,7 @@ fix_modify AtC filter type command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter type <exponential|step|no_filter>
 

doc/src/atc_fix.rst

@@ -6,7 +6,7 @@ fix_modify AtC fix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fix <field> <nodeset> <constant|function>
 

doc/src/atc_fix_flux.rst

@@ -6,7 +6,7 @@ fix_modify AtC fix_flux command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fix_flux <field> <face_set> <value|function>
 

doc/src/atc_hardy_computes.rst

@@ -6,7 +6,7 @@ fix_modify AtC computes command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> computes <add|delete> <per-atom compute-ID> <volume|number>
 

doc/src/atc_hardy_fields.rst

@@ -6,7 +6,7 @@ fix_modify AtC fields command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fields <all|none>
    fix_modify <AtC fixID> fields <add|delete> <list_of_fields>

doc/src/atc_hardy_gradients.rst

@@ -6,7 +6,7 @@ fix_modify AtC gradients command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> gradients <add|delete> <list_of_fields>
 

doc/src/atc_hardy_kernel.rst

@@ -6,7 +6,7 @@ fix_modify AtC kernel command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> kernel <type> <parameters>
 

doc/src/atc_hardy_on_the_fly.rst

@@ -6,7 +6,7 @@ fix_modify AtC on_the_fly command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>
 

doc/src/atc_hardy_rates.rst

@@ -6,7 +6,7 @@ fix_modify AtC rates command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> rates <add|delete> <list_of_fields>
 

doc/src/atc_initial.rst

@@ -6,7 +6,7 @@ fix_modify AtC initial command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> initial <field> <nodeset> <constant|function>
 

doc/src/atc_internal_element_set.rst

@@ -6,7 +6,7 @@ fix_modify AtC internal_element_set command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> internal_element_set <element_set_name>
 

doc/src/atc_internal_quadrature.rst

@@ -6,7 +6,7 @@ fix_modify AtC internal_quadrature command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> internal_quadrature <on|off> [region]
 

doc/src/atc_kernel_bandwidth.rst

@@ -6,7 +6,7 @@ fix_modify AtC kernel_bandwidth command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> kernel_bandwidth <value>
 

doc/src/atc_lumped_lambda_solve.rst

@@ -6,7 +6,7 @@ fix_modify AtC control lumped_lambda_solve command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control lumped_lambda_solve <on|off>
 

doc/src/atc_mask_direction.rst

@@ -6,7 +6,7 @@ fix_modify AtC control mask_direction command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control mask_direction <direction> <on|off>
 

doc/src/atc_mass_matrix.rst

@@ -6,7 +6,7 @@ fix_modify AtC mass_matrix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mass_matrix <fe|md_fe>
 

doc/src/atc_material.rst

@@ -6,7 +6,7 @@ fix_modify AtC material command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> material <elementset_name> <material_id>
 

doc/src/atc_mesh_add_to_nodeset.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh add_to_nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 

doc/src/atc_mesh_create.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh create command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
 

doc/src/atc_mesh_create_elementset.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh create_elementset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 

doc/src/atc_mesh_create_faceset_box.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset box command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]
 

doc/src/atc_mesh_create_faceset_plane.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset plane command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]
 

doc/src/atc_mesh_create_nodeset.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh create_nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 

doc/src/atc_mesh_delete_elements.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh delete_elements command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh delete_elements <id>
 

doc/src/atc_mesh_nodeset_to_elementset.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh nodeset_to_elementset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>
 

doc/src/atc_mesh_output.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh output command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh output <file_prefix>
 

doc/src/atc_mesh_quadrature.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh quadrature command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh quatrature <quad>
 

doc/src/atc_mesh_read.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh read command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh read <f|p> <f|p> <f|p>
 

doc/src/atc_mesh_write.rst

@@ -6,7 +6,7 @@ fix_modify AtC mesh write command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh write <f|p> <f|p> <f|p>
 

doc/src/atc_output.rst

@@ -6,7 +6,7 @@ fix_modify AtC output command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output <filename_prefix> <frequency> [text|full_text|binary|vector_components|tensor_components]
    fix_modify <AtC fixID> output index [step|time]

doc/src/atc_output_boundary_integral.rst

@@ -6,7 +6,7 @@ fix_modify AtC output boundary_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output boundary_integral <fieldname> faceset [name]
 

doc/src/atc_output_contour_integral.rst

@@ -6,7 +6,7 @@ fix_modify AtC output contour_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output contour_integral <fieldname> faceset <name> [axis [x|y|z]]
 

doc/src/atc_output_nodeset.rst

@@ -6,7 +6,7 @@ fix_modify AtC output nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output nodeset <nodeset_name> <operation>
 

doc/src/atc_output_volume_integral.rst

@@ -6,7 +6,7 @@ fix_modify AtC output volume_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output volume_integral <elementset_name> <field>
 

doc/src/atc_pair_interactions.rst

@@ -9,7 +9,7 @@ fix_modify AtC bond_interactions command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> pair_interactions <on|off>
    fix_modify <AtC fixID> bond_interactions <on|off>

doc/src/atc_poisson_solver.rst

@@ -6,7 +6,7 @@ fix_modify AtC poisson_solver command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> poisson_solver mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
 

doc/src/atc_read_restart.rst

@@ -6,7 +6,7 @@ fix_modify AtC read_restart command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> read_restart <file_name>
 

doc/src/atc_remove_molecule.rst

@@ -6,7 +6,7 @@ fix_modify AtC remove_molecule command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_molecule <tag>
 

doc/src/atc_remove_source.rst

@@ -6,7 +6,7 @@ fix_modify AtC remove_source command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_source <field> <element_set>
 

doc/src/atc_remove_species.rst

@@ -6,7 +6,7 @@ fix_modify AtC remove_species command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_species <tag>
 

doc/src/atc_reset_atomic_reference.rst

@@ -6,7 +6,7 @@ fix_modify AtC reset_atomic_reference_positions command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> reset_atomic_reference_positions
 

doc/src/atc_reset_time.rst

@@ -6,7 +6,7 @@ fix_modify AtC reset_time command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> reset_time <value>
 

doc/src/atc_sample_frequency.rst

@@ -6,7 +6,7 @@ fix_modify AtC sample_frequency command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> sample_frequency <freq>
 

doc/src/atc_set_reference_pe.rst

@@ -6,7 +6,7 @@ fix_modify AtC set reference_potential_energy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]
 

doc/src/atc_source.rst

@@ -6,7 +6,7 @@ fix_modify AtC source command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> source <field> <element_set> <value|function>
 

doc/src/atc_source_integration.rst

@@ -6,7 +6,7 @@ fix_modify AtC source_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> source_integration <fe|atom>
 

doc/src/atc_temperature_definition.rst

@@ -6,7 +6,7 @@ fix_modify AtC temperature_definition command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> temperature_definition <kinetic|total>
 

doc/src/atc_time_filter.rst

@@ -6,7 +6,7 @@ fix_modify AtC filter command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter <on|off|equilibrate>
 

doc/src/atc_time_integration.rst

@@ -6,7 +6,7 @@ fix_modify AtC time_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> time_integration <descriptor>
 

doc/src/atc_track_displacement.rst

@@ -6,7 +6,7 @@ fix_modify AtC track_displacement command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> track_displacement <on|off>
 

doc/src/atc_unfix.rst

@@ -6,7 +6,7 @@ fix_modify AtC unfix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> unfix <field> <nodeset>
 

doc/src/atc_unfix_flux.rst

@@ -6,7 +6,7 @@ fix_modify AtC unfix_flux command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> unfix_flux <field> <face_set> <value|function>
 

doc/src/atc_write_atom_weights.rst

@@ -6,7 +6,7 @@ fix_modify AtC write_atom_weights command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> write_atom_weights <filename> <frequency>
 

doc/src/atc_write_restart.rst

@@ -6,7 +6,7 @@ fix_modify AtC write_restart command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> write_restart <file_name>
 

doc/src/bond_bpm_rotational.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/rotational keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
 
   .. parsed-literal::
 
@@ -80,32 +80,32 @@ respectively.  Details on the calculations of shear displacements and
 angular displacements can be found in :ref:`(Wang) <Wang2009>` and
 :ref:`(Wang and Mora) <Wang2009b>`.
 
-Bonds will break under sufficient stress. A breaking criteria is calculated
+Bonds will break under sufficient stress. A breaking criterion is calculated
 
 .. math::
 
-   B = \mathrm{max}\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
-       \frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \}
+   B = \mathrm{max}\left\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
+       \frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \right\}
 
 where :math:`|f_s|` is the magnitude of the shear force and
 :math:`|\tau_b|` and :math:`|\tau_t|` are the magnitudes of the
-bending and twisting forces, respectively. The corresponding variables
+bending and twisting torques, respectively. The corresponding variables
 :math:`f_{r,c}` :math:`f_{s,c}`, :math:`\tau_{b,c}`, and
 :math:`\tau_{t,c}` are critical limits to each force or torque.  If
 :math:`B` is ever equal to or exceeds one, the bond will break.  This
-is done by setting by setting its type to 0 such that forces and
+is done by setting the bond type to 0 such that forces and
 torques are no longer computed.
 
 After computing the base magnitudes of the forces and torques, they
 can be optionally multiplied by an extra factor :math:`w` to smoothly
 interpolate forces and torques to zero as the bond breaks. This term
-is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be
-added or removed using the *smooth* keyword.
+is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be added
+or removed by setting the *smooth* keyword to *yes* or *no*, respectively.
 
 Finally, additional damping forces and torques are applied to the two
 particles. A force is applied proportional to the difference in the
 normal velocity of particles using a similar construction as
-dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
+dissipative particle dynamics :ref:`(Groot) <Groot3>`:
 
 .. math::
 
@@ -115,8 +115,8 @@ where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
 radial normal vector, and :math:`\vec{v}` is the velocity difference
 between the two particles. Similarly, tangential forces are applied to
 each atom proportional to the relative differences in sliding
-velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
-al.) <Wang20152>`) along with their associated torques. The rolling and
+velocities with a constant prefactor :math:`\gamma_s` :ref:`(Wang et
+al.) <Wang20152>` along with their associated torques. The rolling and
 twisting components of the relative angular velocities of the two
 atoms are also damped by applying torques with prefactors of
 :math:`\gamma_r` and :math:`\gamma_t`, respectively.
@@ -139,21 +139,23 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`\gamma_r`      (force*distance/velocity units)
 * :math:`\gamma_t`      (force*distance/velocity units)
 
-However, the *normalize* option will normalize the radial and shear forces
-by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
+If the *normalize* keyword is set to *yes*, the radial and shear forces
+will be normalized by :math:`r_0` such that :math:`k_r` and :math:`k_s`
+must be given in force units.
 
 By default, pair forces are not calculated between bonded particles.
-Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* option. These settings require specific
+Pair forces can alternatively be overlaid on top of bond forces by setting
+the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the `:doc: how to
-<Howto_BPM>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to
+<Howto_bpm>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break* option is used, then LAMMPS assumes bonds should not break
+If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
-However, if a bond does break, it will trigger an error.
+However, if a bond reaches a damage criterion greater than one,
+it will trigger an error.
 
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
@@ -232,16 +234,15 @@ This bond style is part of the BPM package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-By default if pair interactions are to be disabled, this bond style
-requires setting
+By default if pair interactions between bonded atoms are to be disabled,
+this bond style requires setting
 
 .. code-block:: LAMMPS
 
    special_bonds lj 0 1 1 coul 1 1 1
 
-and :doc:`newton <newton>` must be set to bond off.  If the
-*overlay/pair* option is used, this bond style alternatively requires
-setting
+and :doc:`newton <newton>` must be set to bond off.  If the *overlay/pair*
+keyword is set to *yes*, this bond style alternatively requires setting
 
 .. code-block:: LAMMPS
 

doc/src/bond_bpm_spring.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/spring keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
 
   .. parsed-literal::
 
@@ -72,13 +72,13 @@ particles based on a model described by Clemmer and Robbins
 where :math:`k` is a stiffness, :math:`r` is the current distance
 and :math:`r_0` is the initial distance between the two particles, and
 :math:`w` is an optional smoothing factor discussed below. Bonds will
-break at a strain of :math:`\epsilon_c`.  This is done by setting by
-setting its type to 0 such that forces are no longer computed.
+break at a strain of :math:`\epsilon_c`.  This is done by setting
+the bond type to 0 such that forces are no longer computed.
 
 An additional damping force is applied to the bonded
 particles.  This forces is proportional to the difference in the
 normal velocity of particles using a similar construction as
-dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
+dissipative particle dynamics :ref:`(Groot) <Groot4>`:
 
 .. math::
 
@@ -88,9 +88,10 @@ where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
 radial normal vector, and :math:`\vec{v}` is the velocity difference
 between the two particles.
 
-The smoothing factor :math:`w` can be added or removed using the
-*smooth* keyword. It is constructed such that forces smoothly go
-to zero, avoiding discontinuities, as bonds approach the critical strain
+The smoothing factor :math:`w` can be added or removed by setting the
+*smooth* keyword to *yes* or *no*, respectively. It is constructed such
+that forces smoothly go to zero, avoiding discontinuities, as bonds
+approach the critical strain
 
 .. math::
 
@@ -105,21 +106,22 @@ the data file or restart files read by the :doc:`read_data
 * :math:`\epsilon_c`    (unit less)
 * :math:`\gamma`        (force/velocity units)
 
-However, the *normalize* option will normalize the elastic bond force by
-:math:`r_0` such that :math:`k` is unit less.
+If the *normalize* keyword is set to *yes*, the elastic bond force will be
+normalized by :math:`r_0` such that :math:`k` must be given in force units.
 
 By default, pair forces are not calculated between bonded particles.
-Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* option. These settings require specific
+Pair forces can alternatively be overlaid on top of bond forces by setting
+the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the `:doc: how to
-<Howto_BPM>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to
+<Howto_bpm>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break* option is used, then LAMMPS assumes bonds should not break
+If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
-However, if a bond does break, it will trigger an error.
+However, if a bond reaches a strain greater than :math:`\epsilon_c`,
+it will trigger an error.
 
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
@@ -189,16 +191,15 @@ This bond style is part of the BPM package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-By default if pair interactions are to be disabled, this bond style
-requires setting
+By default if pair interactions between bonded atoms are to be disabled,
+this bond style requires setting
 
 .. code-block:: LAMMPS
 
    special_bonds lj 0 1 1 coul 1 1 1
 
-and :doc:`newton <newton>` must be set to bond off.  If the
-*overlay/pair* option is used, this bond style alternatively requires
-setting
+and :doc:`newton <newton>` must be set to bond off.  If the *overlay/pair*
+keyword is set to *yes*, this bond style alternatively requires setting
 
 .. code-block:: LAMMPS
 

doc/src/compute_modify.rst

@@ -12,16 +12,14 @@ Syntax
 
 * compute-ID = ID of the compute to modify
 * one or more keyword/value pairs may be listed
-* keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic*
+* keyword = *extra/dof* or *dynamic/dof*
 
   .. parsed-literal::
 
        *extra/dof* value = N
          N = # of extra degrees of freedom to subtract
-       *extra* syntax is identical to *extra/dof*, will be disabled at some point
        *dynamic/dof* value = *yes* or *no*
          yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
-       *dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point
 
 Examples
 """"""""
@@ -37,19 +35,18 @@ Description
 Modify one or more parameters of a previously defined compute.  Not
 all compute styles support all parameters.
 
-The *extra/dof* or *extra* keyword refers to how many degrees of
-freedom are subtracted (typically from :math:`3N`) as a normalizing
-factor in a temperature computation.  Only computes that compute a
-temperature use this option.  The default is 2 or 3 for :doc:`2d or 3d
-systems <dimension>` which is a correction factor for an ensemble of
-velocities with zero total linear momentum. For compute temp/partial,
-if one or more velocity components are excluded, the value used for
-*extra* is scaled accordingly. You can use a negative number for the
-*extra* parameter if you need to add degrees-of-freedom.  See the
-:doc:`compute temp/asphere <compute_temp_asphere>` command for an
-example.
+The *extra/dof* keyword refers to how many degrees of freedom are
+subtracted (typically from :math:`3N`) as a normalizing factor in a
+temperature computation.  Only computes that compute a temperature use
+this option.  The default is 2 or 3 for :doc:`2d or 3d systems
+<dimension>` which is a correction factor for an ensemble of velocities
+with zero total linear momentum. For compute temp/partial, if one or
+more velocity components are excluded, the value used for *extra/dof* is
+scaled accordingly. You can use a negative number for the *extra/dof*
+parameter if you need to add degrees-of-freedom.  See the :doc:`compute
+temp/asphere <compute_temp_asphere>` command for an example.
 
-The *dynamic/dof* or *dynamic* keyword determines whether the number
+The *dynamic/dof* keyword determines whether the number
 of atoms :math:`N` in the compute group and their associated degrees
 of freedom (DOF) are re-computed each time a temperature is computed.
 Only compute styles that calculate a temperature use this option.  By
@@ -61,12 +58,6 @@ are adding atoms or molecules to the system (see the :doc:`fix pour
 <fix_evaporate>`), then this option should be used to ensure the
 temperature is correctly normalized.
 
-.. note::
-
-   The *extra* and *dynamic* keywords should not be used as they
-   are deprecated (March 2017) and will eventually be disabled.  Instead,
-   use the equivalent *extra/dof* and *dynamic/dof* keywords.
-
 Restrictions
 """"""""""""
  none
@@ -79,5 +70,5 @@ Related commands
 Default
 """""""
 
-The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
-dynamic/dof = *no*.
+The option defaults are extra/dof = 2 or 3 for 2d or 3d systems,
+respectively, and dynamic/dof = *no*.

doc/src/compute_property_grid.rst

@@ -6,7 +6,7 @@ compute property/grid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID property/grid Nx Ny Nz input1 input2 ...
 

doc/src/compute_rdf.rst

@@ -202,7 +202,7 @@ change from zero to one at the location of the spike in :math:`g(r)`.
    parallel efficiency and scaling. For systems, where only the type
    of atoms changes (e.g., when using :doc:`fix atom/swap <fix_atom_swap>`),
    you need to explicitly request the dynamic normalization updates
-   via :doc:`compute_modify dynamic yes <compute_modify>`
+   via :doc:`compute_modify dynamic/dof yes <compute_modify>`
 
 Related commands
 """"""""""""""""

doc/src/compute_reduce_chunk.rst

@@ -6,7 +6,7 @@ compute reduce/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID reduce/chunk chunkID mode input1 input2 ...
 

doc/src/compute_saed.rst

@@ -6,7 +6,7 @@ compute saed command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
 

doc/src/compute_slice.rst

@@ -6,7 +6,7 @@ compute slice command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID slice Nstart Nstop Nskip input1 input2 ...
 

doc/src/compute_smd_contact_radius.rst

@@ -6,7 +6,7 @@ compute smd/contact/radius command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/contact/radius
 

doc/src/compute_smd_damage.rst

@@ -6,7 +6,7 @@ compute smd/damage command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/damage
 

doc/src/compute_smd_hourglass_error.rst

@@ -6,7 +6,7 @@ compute smd/hourglass/error command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/hourglass/error
 

doc/src/compute_smd_internal_energy.rst

@@ -6,7 +6,7 @@ compute smd/internal/energy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/internal/energy
 

doc/src/compute_smd_plastic_strain.rst

@@ -6,7 +6,7 @@ compute smd/plastic/strain command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/plastic/strain
 

doc/src/compute_smd_plastic_strain_rate.rst

@@ -6,7 +6,7 @@ compute smd/plastic/strain/rate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/plastic/strain/rate
 

doc/src/compute_smd_rho.rst

@@ -6,7 +6,7 @@ compute smd/rho command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/rho
 

doc/src/compute_smd_tlsph_defgrad.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/defgrad command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/defgrad
 

doc/src/compute_smd_tlsph_dt.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/dt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/dt
 

doc/src/compute_smd_tlsph_num_neighs.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/num/neighs command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/num/neighs
 

doc/src/compute_smd_tlsph_shape.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/shape command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/shape
 

doc/src/compute_smd_tlsph_strain.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/strain command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/strain
 

doc/src/compute_smd_tlsph_strain_rate.rst

@@ -6,7 +6,7 @@ compute smd/tlsph/strain/rate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/strain/rate